WorldWideScience

Sample records for lines identifies molecular

  1. Comprehensive expression profiling of tumor cell lines identifies molecular signatures of melanoma progression.

    Directory of Open Access Journals (Sweden)

    Byungwoo Ryu

    2007-07-01

    Full Text Available Gene expression profiling has revolutionized our ability to molecularly classify primary human tumors and significantly enhanced the development of novel tumor markers and therapies; however, progress in the diagnosis and treatment of melanoma over the past 3 decades has been limited, and there is currently no approved therapy that significantly extends lifespan in patients with advanced disease. Profiling studies of melanoma to date have been inconsistent due to the heterogeneous nature of this malignancy and the limited availability of informative tissue specimens from early stages of disease.In order to gain an improved understanding of the molecular basis of melanoma progression, we have compared gene expression profiles from a series of melanoma cell lines representing discrete stages of malignant progression that recapitulate critical characteristics of the primary lesions from which they were derived. Here we describe the unsupervised hierarchical clustering of profiling data from melanoma cell lines and melanocytes. This clustering identifies two distinctive molecular subclasses of melanoma segregating aggressive metastatic tumor cell lines from less-aggressive primary tumor cell lines. Further analysis of expression signatures associated with melanoma progression using functional annotations categorized these transcripts into three classes of genes: 1 Upregulation of activators of cell cycle progression, DNA replication and repair (CDCA2, NCAPH, NCAPG, NCAPG2, PBK, NUSAP1, BIRC5, ESCO2, HELLS, MELK, GINS1, GINS4, RAD54L, TYMS, and DHFR, 2 Loss of genes associated with cellular adhesion and melanocyte differentiation (CDH3, CDH1, c-KIT, PAX3, CITED1/MSG-1, TYR, MELANA, MC1R, and OCA2, 3 Upregulation of genes associated with resistance to apoptosis (BIRC5/survivin. While these broad classes of transcripts have previously been implicated in the progression of melanoma and other malignancies, the specific genes identified within each class

  2. Molecular Cytogenetic Characterization Identified the Murine B-Cell Lymphoma Cell Line A-20 as a Model for Sporadic Burkitt's Lymphoma.

    Science.gov (United States)

    Guja, Karolina; Liehr, Thomas; Rincic, Martina; Kosyakova, Nadezda; Hussein Azawi, Shaymaa S

    2017-11-01

    Here, we report the first molecular cytogenetic characterization of the BALB/cAnN mouse derived B-cell non-Hodgkin lymphoma (B-cell NHL) cell lines A-20. Even though previously used as a model for testing of, for example, dexametason, up to present, no data in the genetic properties of A-20 were available. The present study closed this gap and provides evidence that A-20 is a model for B-cell NHL subgroup sporadic Burkitt's lymphoma. C-myc oncogene is involved in a translocation and copy number alterations as gain of murine 14q material could be observed. Interestingly, the cell line showed the karyotype 39,X,-X or -Y,t(2;15)(qE5;qD2),del(6)(qB3qC3),del(9)(qA3qA4),dup(14)(qE1qE4) in ~95% of the cells, being exceptionally stable for cell lines being established 38 years ago. Still, ~5% of the cells showed polyploidization followed by chromothripsis. It remains to be determined if this can be observed also in other cell lines, just has not been reported yet, and/or if it is a unique feature of A-20. Overall, finally here, the necessary genetic data to identify A-20 as a model for human sporadic Burkitt's lymphoma are provided.

  3. NEWLY IDENTIFIED EXTENDED GREEN OBJECTS (EGOs) FROM THE SPITZER GLIMPSE II SURVEY. II. MOLECULAR CLOUD ENVIRONMENTS

    Energy Technology Data Exchange (ETDEWEB)

    Chen Xi; Gan Conggui; Shen Zhiqiang [Key Laboratory for Research in Galaxies and Cosmology, Shanghai Astronomical Observatory, Chinese Academy of Sciences, Shanghai 200030 (China); Ellingsen, Simon P.; Titmarsh, Anita [School of Mathematics and Physics, University of Tasmania, Hobart, Tasmania (Australia); He Jinhua, E-mail: chenxi@shao.ac.cn [Key Laboratory for the Structure and Evolution of Celestial Objects, Yunnan Astronomical Observatory/National Astronomical Observatory, Chinese Academy of Sciences, P.O. Box 110, Kunming 650011, Yunnan Province (China)

    2013-06-01

    We have undertaken a survey of molecular lines in the 3 mm band toward 57 young stellar objects using the Australia Telescope National Facility Mopra 22 m radio telescope. The target sources were young stellar objects with active outflows (extended green objects (EGOs)) newly identified from the GLIMPSE II survey. We observe a high detection rate (50%) of broad line wing emission in the HNC and CS thermal lines, which combined with the high detection rate of class I methanol masers toward these sources (reported in Paper I) further demonstrates that the GLIMPSE II EGOs are associated with outflows. The physical and kinematic characteristics derived from the 3 mm molecular lines for these newly identified EGOs are consistent with these sources being massive young stellar objects with ongoing outflow activity and rapid accretion. These findings support our previous investigations of the mid-infrared properties of these sources and their association with other star formation tracers (e.g., infrared dark clouds, methanol masers and millimeter dust sources) presented in Paper I. The high detection rate (64%) of the hot core tracer CH{sub 3}CN reveals that the majority of these new EGOs have evolved to the hot molecular core stage. Comparison of the observed molecular column densities with predictions from hot core chemistry models reveals that the newly identified EGOs from the GLIMPSE II survey are members of the youngest hot core population, with an evolutionary time scale of the order of 10{sup 3} yr.

  4. Radiative transfer in molecular lines

    Science.gov (United States)

    Asensio Ramos, A.; Trujillo Bueno, J.; Cernicharo, J.

    2001-07-01

    The highly convergent iterative methods developed by Trujillo Bueno and Fabiani Bendicho (1995) for radiative transfer (RT) applications are generalized to spherical symmetry with velocity fields. These RT methods are based on Jacobi, Gauss-Seidel (GS), and SOR iteration and they form the basis of a new NLTE multilevel transfer code for atomic and molecular lines. The benchmark tests carried out so far are presented and discussed. The main aim is to develop a number of powerful RT tools for the theoretical interpretation of molecular spectra.

  5. Molecular predictors of 3D morphogenesis by breast cancer cell lines in 3D culture.

    Directory of Open Access Journals (Sweden)

    Ju Han

    2010-02-01

    Full Text Available Correlative analysis of molecular markers with phenotypic signatures is the simplest model for hypothesis generation. In this paper, a panel of 24 breast cell lines was grown in 3D culture, their morphology was imaged through phase contrast microscopy, and computational methods were developed to segment and represent each colony at multiple dimensions. Subsequently, subpopulations from these morphological responses were identified through consensus clustering to reveal three clusters of round, grape-like, and stellate phenotypes. In some cases, cell lines with particular pathobiological phenotypes clustered together (e.g., ERBB2 amplified cell lines sharing the same morphometric properties as the grape-like phenotype. Next, associations with molecular features were realized through (i differential analysis within each morphological cluster, and (ii regression analysis across the entire panel of cell lines. In both cases, the dominant genes that are predictive of the morphological signatures were identified. Specifically, PPARgamma has been associated with the invasive stellate morphological phenotype, which corresponds to triple-negative pathobiology. PPARgamma has been validated through two supporting biological assays.

  6. Molecular Predictors of 3D Morphogenesis by Breast Cancer Cell Lines in 3D Culture

    Energy Technology Data Exchange (ETDEWEB)

    Han, Ju; Chang, Hang; Giricz, Orsi; Lee, Genee; Baehner, Frederick; Gray, Joe; Bissell, Mina; Kenny, Paraic; Parvin, Bahram

    2010-02-01

    Correlative analysis of molecular markers with phenotypic signatures is the simplest model for hypothesis generation. In this paper, a panel of 24 breast cell lines was grown in 3D culture, their morphology was imaged through phase contrast microscopy, and computational methods were developed to segment and represent each colony at multiple dimensions. Subsequently, subpopulations from these morphological responses were identified through consensus clustering to reveal three clusters of round, grape-like, and stellate phenotypes. In some cases, cell lines with particular pathobiological phenotypes clustered together (e.g., ERBB2 amplified cell lines sharing the same morphometric properties as the grape-like phenotype). Next, associations with molecular features were realized through (i) differential analysis within each morphological cluster, and (ii) regression analysis across the entire panel of cell lines. In both cases, the dominant genes that are predictive of the morphological signatures were identified. Specifically, PPAR? has been associated with the invasive stellate morphological phenotype, which corresponds to triple-negative pathobiology. PPAR? has been validated through two supporting biological assays.

  7. Cancer in silico drug discovery: a systems biology tool for identifying candidate drugs to target specific molecular tumor subtypes.

    Science.gov (United States)

    San Lucas, F Anthony; Fowler, Jerry; Chang, Kyle; Kopetz, Scott; Vilar, Eduardo; Scheet, Paul

    2014-12-01

    Large-scale cancer datasets such as The Cancer Genome Atlas (TCGA) allow researchers to profile tumors based on a wide range of clinical and molecular characteristics. Subsequently, TCGA-derived gene expression profiles can be analyzed with the Connectivity Map (CMap) to find candidate drugs to target tumors with specific clinical phenotypes or molecular characteristics. This represents a powerful computational approach for candidate drug identification, but due to the complexity of TCGA and technology differences between CMap and TCGA experiments, such analyses are challenging to conduct and reproduce. We present Cancer in silico Drug Discovery (CiDD; scheet.org/software), a computational drug discovery platform that addresses these challenges. CiDD integrates data from TCGA, CMap, and Cancer Cell Line Encyclopedia (CCLE) to perform computational drug discovery experiments, generating hypotheses for the following three general problems: (i) determining whether specific clinical phenotypes or molecular characteristics are associated with unique gene expression signatures; (ii) finding candidate drugs to repress these expression signatures; and (iii) identifying cell lines that resemble the tumors being studied for subsequent in vitro experiments. The primary input to CiDD is a clinical or molecular characteristic. The output is a biologically annotated list of candidate drugs and a list of cell lines for in vitro experimentation. We applied CiDD to identify candidate drugs to treat colorectal cancers harboring mutations in BRAF. CiDD identified EGFR and proteasome inhibitors, while proposing five cell lines for in vitro testing. CiDD facilitates phenotype-driven, systematic drug discovery based on clinical and molecular data from TCGA. ©2014 American Association for Cancer Research.

  8. Molecular and Recombination Lines in the Central Region of Sagittarius B2

    Science.gov (United States)

    Curtis, J.; Langston, G.

    2005-12-01

    We present observations of recombination and molecular lines towards Sgr B2 in the frequency range 12.4 to 15.0 GHz. In this frequency range, Hα , β , and γ lines, Heα recombination lines and emission from the SO molecule are detected. Molecular absorption lines from OH, H2CO, and CH3CO are detected at velocity 62±3 km/s. Measurements of the line widths and intensities are presented for the central region of Sgr B2. We detect two previously un-reported molecular absorption lines at 12388.0 and 14625.8 MHz (v=0. in LSR Frame). For selected recombination and molecular lines, we present images of a 10x10 arc-minute region centered on Sgr B2(M). We discuss the sources of three H2CO absorption features detected at 62±3, 6±5, and 100±10 km/s. This was done as a summer REU project in 2005 at the National Radio Astronomy Observatory's Green Bank site, and was funded by the National Science Foundation's REU program.

  9. Cell Line Data Base: structure and recent improvements towards molecular authentication of human cell lines.

    Science.gov (United States)

    Romano, Paolo; Manniello, Assunta; Aresu, Ottavia; Armento, Massimiliano; Cesaro, Michela; Parodi, Barbara

    2009-01-01

    The Cell Line Data Base (CLDB) is a well-known reference information source on human and animal cell lines including information on more than 6000 cell lines. Main biological features are coded according to controlled vocabularies derived from international lists and taxonomies. HyperCLDB (http://bioinformatics.istge.it/hypercldb/) is a hypertext version of CLDB that improves data accessibility by also allowing information retrieval through web spiders. Access to HyperCLDB is provided through indexes of biological characteristics and navigation in the hypertext is granted by many internal links. HyperCLDB also includes links to external resources. Recently, an interest was raised for a reference nomenclature for cell lines and CLDB was seen as an authoritative system. Furthermore, to overcome the cell line misidentification problem, molecular authentication methods, such as fingerprinting, single-locus short tandem repeat (STR) profile and single nucleotide polymorphisms validation, were proposed. Since this data is distributed, a reference portal on authentication of human cell lines is needed. We present here the architecture and contents of CLDB, its recent enhancements and perspectives. We also present a new related database, the Cell Line Integrated Molecular Authentication (CLIMA) database (http://bioinformatics.istge.it/clima/), that allows to link authentication data to actual cell lines.

  10. A New Radio Spectral Line Survey of Planetary Nebulae: Exploring Radiatively Driven Heating and Chemistry of Molecular Gas

    Science.gov (United States)

    Bublitz, Jesse

    Planetary nebulae contain shells of cold gas and dust whose heating and chemistry is likely driven by UV and X-ray emission from their central stars and from wind-collision-generated shocks. We present the results of a survey of molecular line emissions in the 88 - 235 GHz range from nine nearby (Radioastronomie Millimetrique. Rotational transitions of nine molecules, including the well-studied CO isotopologues and chemically important trace species, were observed and the results compared with and augmented by previous studies of molecular gas in PNe. Lines of the molecules HCO+, HNC, HCN, and CN, which were detected in most objects, represent new detections for five planetary nebulae in our study. Flux ratios were analyzed to identify correlations between the central star and/or nebular ultraviolet/X-ray luminosities and the molecular chemistries of the nebulae. Analysis reveals the apparent dependence of the HNC/HCN line ratio on PN central star UV luminosity. There exists no such clear correlation between PN X-rays and various diagnostics of PN molecular chemistry. The correlation between HNC/HCN ratio and central star UV luminosity hints at the potential of molecular emission line studies of PNe for improving our understanding of the role that high-energy radiation plays in the heating and chemistry of photodissociation regions.

  11. ExoCross: Spectra from molecular line lists

    Science.gov (United States)

    Yurchenko, Sergei N.; Al-Refaie, Ahmed; Tennyson, Jonathan

    2018-03-01

    ExoCross generates spectra and thermodynamic properties from molecular line lists in ExoMol, HITRAN, or several other formats. The code is parallelized and also shows a high degree of vectorization; it works with line profiles such as Doppler, Lorentzian and Voigt and supports several broadening schemes. ExoCross is also capable of working with the recently proposed method of super-lines. It supports calculations of lifetimes, cooling functions, specific heats and other properties. ExoCross converts between different formats, such as HITRAN, ExoMol and Phoenix, and simulates non-LTE spectra using a simple two-temperature approach. Different electronic, vibronic or vibrational bands can be simulated separately using an efficient filtering scheme based on the quantum numbers.

  12. Optical polarimetry and molecular line studies of L1157 dark molecular cloud

    Science.gov (United States)

    Sharma, Ekta; Soam, Archana; Gopinathan, Maheswar

    2018-04-01

    Filaments are omnipresent in molecular clouds which are believed to fragment into cores. The detailed process of the evolution from filaments to cores depends critically on the physical conditions in the star forming region. This study aims at characterising gas motions using velocity structure and finding the dynamical importance of magnetic fields in the filament morphology. The plane-of-the-sky component of the magnetic field has been measured using optical polarization of the background stars. The orientation is found to be almost perpendicular to the filament implying its dynamical importance in the evolution of the cloud. Optical polarimetric results match very well with the sub millimetre polarization angles obtained in the inner core regions. The magnetic fields are found to have an orientation of 130° east with respect to north. The angular offset between the outflow axis and the magnetic field direction is found to be 25°. Values for parameters like the excitation temperature, optical depth and column densities have been derived using molecular lines. Optically thick lines show non-gaussian features. The non-thermal widths tell about the presence of turbulent motions whereas the C180 lines follow Gaussian features almost at all the locations observed in the filament.

  13. Moving contact lines: linking molecular dynamics and continuum-scale modelling.

    Science.gov (United States)

    Smith, Edward R; Theodorakis, Panagiotis E; Craster, Richard V; Matar, Omar K

    2018-05-04

    Despite decades of research, the modelling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily-life applications. On the one hand, molecular dynamics (MD) simulation has the ability to provide unique insight into the microscopic details that determine the dynamic behavior of the contact line, which is not possible with either continuum-scale simulations or experiments. On the other hand, continuum-based models provide the link to the macroscopic description of the system. In this Feature Article, we explore the complex range of physical factors, including the presence of surfactants, which govern the contact line motion through MD simulations. We also discuss links between continuum- and molecular-scale modelling, and highlight the opportunities for future developments in this area.

  14. Recent interstellar molecular line work

    International Nuclear Information System (INIS)

    Winnewisser, G.

    1975-01-01

    A summary of recent interstellar molecular line work is presented. Transitions of the following molecules have been detected in Sgr B2: Vinylcyanide, H 2 C 2 HCN, formic acid, HCOOH, dimethyl ether (CH 3 ) 2 O and isotopically labelled cyanoacetylene- 13 C,HC 13 CCN and HCC 13 CN. The data on cyanoacetylene give an upper limit to the abundance ratio 12 C/ 13 C of 36 +- 5. A short discussion of the interstellar chemistry leads to the conclusion that hydrocarbons such as acetylene, HCCH, ethylen, H 2 CCH 2 and ethane H 3 CCH 3 should be present in interstellar clouds. 13 refs

  15. Molecular hydrogen line ratios in four regions of shock-excited gas

    International Nuclear Information System (INIS)

    Burton, M.G.

    1989-01-01

    Five emission lines of molecular hydrogen, with wavelengths in the ranges of 2.10-2.25 and 3.80-3.85 μm, have been observed in four objects of different type in which the line emission is believed to be excited by shocks. (author)

  16. Optical line shape of molecular rings: Influence of correlated nondiagonal disorder

    International Nuclear Information System (INIS)

    Barvik, I.; Warns, Ch.; Reineker, P.

    2006-01-01

    We investigate the optical properties of molecular rings which are generally influenced by many kinds of static disorder. Recently, Papiz suggested that quasistatic disorder, anticorrelated between neighboring transfer integrals, plays an important role. We simulate such a disorder by slow colored dichotomic Markov processes with long-time constants for the decay of their correlation functions. The colored dichotomic Markov processes leading to transfer integral fluctuations can be uncorrelated, anticorrelated or partially correlated between nearest neighboring transfer integrals in the ring. The optical line shape of the molecular ring is modeled and investigated in dependence on the parameters of the stochastic processes. Conclusions as regards the influence of the correlation on the splitting of the optical line shape, the shift of the optical absorption maximum and the width of the optical line are drawn

  17. Critical comparison of the on-line and off-line molecularly imprinted solid-phase extraction of patulin coupled with liquid chromatography.

    Science.gov (United States)

    Lhotská, Ivona; Holznerová, Anežka; Solich, Petr; Šatínský, Dalibor

    2017-12-01

    Reaching trace amounts of mycotoxin contamination requires sensitive and selective analytical tools for their determination. Improving the selectivity of sample pretreatment steps covering new and modern extraction techniques is one way to achieve it. Molecularly imprinted polymers as selective sorbent for extraction undoubtedly meet these criteria. The presented work is focused on the hyphenation of on-line molecularly imprinted solid-phase extraction with a chromatography system using a column-switching approach. Making a critical comparison with a simultaneously developed off-line extraction procedure, evaluation of pros and cons of each method, and determining the reliability of both methods on a real sample analysis were carried out. Both high-performance liquid chromatography methods, using off-line extraction on molecularly imprinted polymer and an on-line column-switching approach, were validated, and the validation results were compared against each other. Although automation leads to significant time savings, fewer human errors, and required no handling of toxic solvents, it reached worse detection limits (15 versus 6 μg/L), worse recovery values (68.3-123.5 versus 81.2-109.9%), and worse efficiency throughout the entire clean-up process in comparison with the off-line extraction method. The difficulties encountered, the compromises made during the optimization of on-line coupling and their critical evaluation are presented in detail. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Molecular characterization of breast cancer cell lines through multiple omic approaches.

    Science.gov (United States)

    Smith, Shari E; Mellor, Paul; Ward, Alison K; Kendall, Stephanie; McDonald, Megan; Vizeacoumar, Frederick S; Vizeacoumar, Franco J; Napper, Scott; Anderson, Deborah H

    2017-06-05

    Breast cancer cell lines are frequently used as model systems to study the cellular properties and biology of breast cancer. Our objective was to characterize a large, commonly employed panel of breast cancer cell lines obtained from the American Type Culture Collection (ATCC 30-4500 K) to enable researchers to make more informed decisions in selecting cell lines for specific studies. Information about these cell lines was obtained from a wide variety of sources. In addition, new information about cellular pathways that are activated within each cell line was generated. We determined key protein expression data using immunoblot analyses. In addition, two analyses on serum-starved cells were carried out to identify cellular proteins and pathways that are activated in these cells. These analyses were performed using a commercial PathScan array and a novel and more extensive phosphopeptide-based kinome analysis that queries 1290 phosphorylation events in major signaling pathways. Data about this panel of breast cancer cell lines was also accessed from several online sources, compiled and summarized for the following areas: molecular classification, mRNA expression, mutational status of key proteins and other possible cancer-associated mutations, and the tumorigenic and metastatic capacity in mouse xenograft models of breast cancer. The cell lines that were characterized included 10 estrogen receptor (ER)-positive, 12 human epidermal growth factor receptor 2 (HER2)-amplified and 18 triple negative breast cancer cell lines, in addition to 4 non-tumorigenic breast cell lines. Within each subtype, there was significant genetic heterogeneity that could impact both the selection of model cell lines and the interpretation of the results obtained. To capture the net activation of key signaling pathways as a result of these mutational combinations, profiled pathway activation status was examined. This provided further clarity for which cell lines were particularly deregulated

  19. NARROW Na AND K ABSORPTION LINES TOWARD T TAURI STARS: TRACING THE ATOMIC ENVELOPE OF MOLECULAR CLOUDS

    Energy Technology Data Exchange (ETDEWEB)

    Pascucci, I.; Simon, M. N. [Lunar and Planetary Laboratory, The University of Arizona, Tucson, AZ 85721 (United States); Edwards, S. [Five College Astronomy Department, Smith College, Northampton, MA 01063 (United States); Heyer, M. [Department of Astronomy, University of Massachusetts, Amherst, MA 01003-9305 (United States); Rigliaco, E. [Institute for Astronomy, ETH Zurich, Wolfgang-Pauli-Strasse 27, CH-8093 Zurich (Switzerland); Hillenbrand, L. [Department of Astronomy, California Institute of Technology, Pasadena, CA 91125 (United States); Gorti, U.; Hollenbach, D., E-mail: pascucci@lpl.arizona.edu [SETI Institute, Mountain View, CA 94043 (United States)

    2015-11-20

    We present a detailed analysis of narrow Na i and K i absorption resonance lines toward nearly 40 T Tauri stars in Taurus with the goal of clarifying their origin. The Na i λ5889.95 line is detected toward all but one source, while the weaker K i λ7698.96 line is detected in about two-thirds of the sample. The similarity in their peak centroids and the significant positive correlation between their equivalent widths demonstrate that these transitions trace the same atomic gas. The absorption lines are present toward both disk and diskless young stellar objects, which excludes cold gas within the circumstellar disk as the absorbing material. A comparison of Na i and CO detections and peak centroids demonstrates that the atomic gas and molecular gas are not co-located, the atomic gas being more extended than the molecular gas. The width of the atomic lines corroborates this finding and points to atomic gas about an order of magnitude warmer than the molecular gas. The distribution of Na i radial velocities shows a clear spatial gradient along the length of the Taurus molecular cloud filaments. This suggests that absorption is associated with the Taurus molecular cloud. Assuming that the gradient is due to cloud rotation, the rotation of the atomic gas is consistent with differential galactic rotation, whereas the rotation of the molecular gas, although with the same rotation axis, is retrograde. Our analysis shows that narrow Na i and K i absorption resonance lines are useful tracers of the atomic envelope of molecular clouds. In line with recent findings from giant molecular clouds, our results demonstrate that the velocity fields of the atomic and molecular gas are misaligned. The angular momentum of a molecular cloud is not simply inherited from the rotating Galactic disk from which it formed but may be redistributed by cloud–cloud interactions.

  20. NARROW Na AND K ABSORPTION LINES TOWARD T TAURI STARS: TRACING THE ATOMIC ENVELOPE OF MOLECULAR CLOUDS

    International Nuclear Information System (INIS)

    Pascucci, I.; Simon, M. N.; Edwards, S.; Heyer, M.; Rigliaco, E.; Hillenbrand, L.; Gorti, U.; Hollenbach, D.

    2015-01-01

    We present a detailed analysis of narrow Na i and K i absorption resonance lines toward nearly 40 T Tauri stars in Taurus with the goal of clarifying their origin. The Na i λ5889.95 line is detected toward all but one source, while the weaker K i λ7698.96 line is detected in about two-thirds of the sample. The similarity in their peak centroids and the significant positive correlation between their equivalent widths demonstrate that these transitions trace the same atomic gas. The absorption lines are present toward both disk and diskless young stellar objects, which excludes cold gas within the circumstellar disk as the absorbing material. A comparison of Na i and CO detections and peak centroids demonstrates that the atomic gas and molecular gas are not co-located, the atomic gas being more extended than the molecular gas. The width of the atomic lines corroborates this finding and points to atomic gas about an order of magnitude warmer than the molecular gas. The distribution of Na i radial velocities shows a clear spatial gradient along the length of the Taurus molecular cloud filaments. This suggests that absorption is associated with the Taurus molecular cloud. Assuming that the gradient is due to cloud rotation, the rotation of the atomic gas is consistent with differential galactic rotation, whereas the rotation of the molecular gas, although with the same rotation axis, is retrograde. Our analysis shows that narrow Na i and K i absorption resonance lines are useful tracers of the atomic envelope of molecular clouds. In line with recent findings from giant molecular clouds, our results demonstrate that the velocity fields of the atomic and molecular gas are misaligned. The angular momentum of a molecular cloud is not simply inherited from the rotating Galactic disk from which it formed but may be redistributed by cloud–cloud interactions

  1. CO line ratios in molecular clouds: the impact of environment

    Science.gov (United States)

    Peñaloza, Camilo H.; Clark, Paul C.; Glover, Simon C. O.; Klessen, Ralf S.

    2018-04-01

    Line emission is strongly dependent on the local environmental conditions in which the emitting tracers reside. In this work, we focus on modelling the CO emission from simulated giant molecular clouds (GMCs), and study the variations in the resulting line ratios arising from the emission from the J = 1-0, J = 2-1, and J = 3-2 transitions. We perform a set of smoothed particle hydrodynamics simulations with time-dependent chemistry, in which environmental conditions - including total cloud mass, density, size, velocity dispersion, metallicity, interstellar radiation field (ISRF), and the cosmic ray ionization rate (CRIR) - were systematically varied. The simulations were then post-processed using radiative transfer to produce synthetic emission maps in the three transitions quoted above. We find that the cloud-averaged values of the line ratios can vary by up to ±0.3 dex, triggered by changes in the environmental conditions. Changes in the ISRF and/or in the CRIR have the largest impact on line ratios since they directly affect the abundance, temperature, and distribution of CO-rich gas within the clouds. We show that the standard methods used to convert CO emission to H2 column density can underestimate the total H2 molecular gas in GMCs by factors of 2 or 3, depending on the environmental conditions in the clouds.

  2. Metastatic non-small-cell lung cancer: consensus on pathology and molecular tests, first-line, second-line, and third-line therapy: 1st ESMO Consensus Conference in Lung Cancer; Lugano 2010

    DEFF Research Database (Denmark)

    Felip, E; Gridelli, C; Baas, P

    2011-01-01

    the conference, the expert panel prepared clinically relevant questions concerning five areas: early and locally advanced non-small-cell lung cancer (NSCLC), first-line metastatic NSCLC, second-/third-line NSCLC, NSCLC pathology and molecular testing, and small-cell lung cancer to be addressed through discussion......The 1st ESMO Consensus Conference on lung cancer was held in Lugano, Switzerland on 21 and 22 May 2010 with the participation of a multidisciplinary panel of leading professionals in pathology and molecular diagnostics, medical oncology, surgical oncology and radiation oncology. Before...... at the Consensus Conference. All relevant scientific literature for each question was reviewed in advance. During the Consensus Conference, the panel developed recommendations for each specific question. The consensus agreement on three of these areas: NSCLC pathology and molecular testing, the treatment of first-line...

  3. ExoMol molecular line lists - XXVII: spectra of C2H4

    Science.gov (United States)

    Mant, Barry P.; Yachmenev, Andrey; Yurchenko, Jonathan Tennyson Sergei N.

    2018-05-01

    A new line list for ethylene, 12C21H4 is presented. The line list is based on high level ab initiopotential energy and dipole moment surfaces. The potential energy surface is refined by fitting to experimental energies. The line list covers the range up to 7000 cm-1(1.43 μm) with all ro-vibrational transitions (50 billion) with the lower state below 5000 cm-1included and thus should be applicable for temperatures up to 700 K. A technique for computing molecular opacities from vibrational band intensities is proposed and used to provide temperature dependent cross sections of ethylene for shorter wavelength and higher temperatures. When combined with realistic band profiles (such as the proposed three-band model), the vibrational intensity technique offers a cheap but reasonably accurate alternative to the full ro-vibrational calculations at high temperatures and should be reliable for representing molecular opacities. The C2H4 line list, which is called MaYTY, is rmade available in electronic form from the CDS (http://cdsarc.u-strasbg.fr) and ExoMol (www.exomol.com) databases.

  4. Depression of molecular emission in the line of sight of Sgr A West

    International Nuclear Information System (INIS)

    Fukui, Y.; Ogawa, H.; Deguchi, S.; Suzuki, H.

    1982-01-01

    The galatic center region has been mapped in the 4-mm emission lines of HCCCN (J = 8-7) and H 2 CO (JK-K+ = 1 01 -0 00 ) with a 1.5 arc min beam. The molecular lines are found to show depression in intensity in the line of sight of Sgr A West. Comparison with other molecular data indicates that NH 3 also shows a significant depression while HCN and HCO + show little sign of similar depression. Based on some density estimates we suggest that the depression means abnormally reduced abundance in HCCCN, NH 3 , and H 2 CO in the line of sight of Sgr A West. The difference in the degree of depression could be interpreted in terms of a time-dependent ion-molecule reaction scheme because HCO + and HCN are formed much more rapidly than the other molecules in the scheme

  5. Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling

    DEFF Research Database (Denmark)

    Ghaffari, Pouyan; Mardinoglu, Adil; Asplund, Anna

    2015-01-01

    Human cancer cell lines are used as important model systems to study molecular mechanisms associated with tumor growth, hereunder how genomic and biological heterogeneity found in primary tumors affect cellular phenotypes. We reconstructed Genome scale metabolic models (GEMs) for eleven cell lines...... based on RNA-Seq data and validated the functionality of these models with data from metabolite profiling. We used cell line-specific GEMs to analyze the differences in the metabolism of cancer cell lines, and to explore the heterogeneous expression of the metabolic subsystems. Furthermore, we predicted...... for inhibition of cell growth may provide leads for the development of efficient cancer treatment strategies....

  6. Achieving deeper molecular response is associated with a better clinical outcome in chronic myeloid leukemia patients on imatinib front-line therapy

    Science.gov (United States)

    Etienne, Gabriel; Dulucq, Stéphanie; Nicolini, Franck-Emmanuel; Morisset, Stéphane; Fort, Marie-Pierre; Schmitt, Anna; Etienne, Madeleine; Hayette, Sandrine; Lippert, Eric; Bureau, Caroline; Tigaud, Isabelle; Adiko, Didier; Marit, Gérald; Reiffers, Josy; Mahon, François-Xavier

    2014-01-01

    Sustained imatinib treatment in chronic myeloid leukemia patients can result in complete molecular response allowing discontinuation without relapse. We set out to evaluate the frequency of complete molecular response in imatinib de novo chronic phase chronic myeloid leukemia patients, to identify base-line and under-treatment predictive factors of complete molecular response in patients achieving complete cytogenetic response, and to assess if complete molecular response is associated with a better outcome. A random selection of patients on front-line imatinib therapy (n=266) were considered for inclusion. Complete molecular response was confirmed and defined as MR 4.5 with undetectable BCR-ABL transcript levels. Median follow up was 4.43 years (range 0.79–10.8 years). Sixty-five patients (24%) achieved complete molecular response within a median time of 32.7 months. Absence of spleen enlargement at diagnosis, achieving complete cytogenetic response before 12 months of therapy, and major molecular response during the year following complete cytogenetic response was predictive of achieving further complete molecular response. Patients who achieved complete molecular response had better event-free and failure-free survivals than those with complete cytogenetic response irrespective of major molecular response status (95.2% vs. 64.7% vs. 27.7%, P=0.00124; 98.4% vs. 82.3% vs. 56%, P=0.0335), respectively. Overall survival was identical in the 3 groups. In addition to complete cytogenetic response and major molecular response, further deeper molecular response is associated with better event-free and failure-free survivals, and complete molecular response confers the best outcome. PMID:24362549

  7. Observations of far-infrared molecular emission lines from the Orion molecular cloud

    International Nuclear Information System (INIS)

    Viscuso, P.J.

    1986-01-01

    The Orion Nebula has been the subject of intensive study for over one hundred years. Far-infrared (FIR) molecular line observations of CO in the shock region surrounding the infrared source IRc2 have suggested that the molecular hydrogen density in the shocked and post-shock gas is roughly 3 x 10 6 cm -3 . The temperature of this gas is on the order of 750-2000K. IRc2, like other nearby infrared sources within the Nebula, is thought to be a site of recent star formation. This object is apparently at the center of a massive bipolar molecular outflow of gas, which is producing a shock front where it meets the ambient molecular cloud surrounding IRc2. Study of such regions is important for the understanding of the chemical and physical processes that are involved in the formation of stars from molecular clouds. Recently, several far-infrared transitions among the low-lying levels of OH have been observed toward IRc2. OH is thought to be abundant, and it plays an important role in the chemical evolution of the shock and post-shock regions. The OH emission serves as a sensitive probe of the temperature and density for the shock-processed gas. A rigorous treatment of the radiative transfer of these measured transitions is performed using the escape probability formalism. From this analysis, the author determines the temperature of the OH-emitting region to be on the order of 40K. This suggests that the gas is part of the post-shock gas that has cooled sufficiently, most likely by way of radiative cooling by CO

  8. A New Radio Spectral Line Survey of Planetary Nebulae: Exploring Radiatively-driven Heating and Chemistry of Molecular Gas

    Science.gov (United States)

    Bublitz, Jesse; Kastner, Joel H.; Santander-García, Miguel; Montez, Rodolfo; Alcolea, Javier; Balick, Bruce; Bujarrabal, Valentín

    2018-01-01

    We report the results of a survey of mm-wave molecular line emission from nine nearby (Radioastronomie Millimétrique (IRAM) 30 m telescope. Our sample comprises molecule-rich PNe spanning a wide range of central star UV luminosities as well as central star and nebular X-ray emission properties. Nine molecular line frequencies were chosen to investigate the molecular chemistry of these nebulae. New detections of one or more of five molecules -- the molecular mass tracer 13CO and the chemically important trace species HCO+, CN, HCN, and HNC -- were made in at least one PN. We present analysis of emission line flux ratios that are potential diagnostics of the influence that ultraviolet and X-ray radiation have on the chemistry of residual molecular gas in PNe.

  9. Molecular subtypes of osteosarcoma identified by reducing tumor heterogeneity through an interspecies comparative approach

    Science.gov (United States)

    Scott, Milcah C.; Sarver, Aaron L.; Gavin, Katherine J.; Thayanithy, Venugopal; Getzy, David M.; Newman, Robert A.; Cutter, Gary R.; Lindblad-Toh, Kerstin; Kisseberth, William C.; Hunter, Lawrence E.; Subramanian, Subbaya; Breen, Matthew; Modiano, Jaime F.

    2011-01-01

    The heterogeneous and chaotic nature of osteosarcoma has confounded accurate molecular classification, prognosis, and prediction for this tumor. The occurrence of spontaneous osteosarcoma is largely confined to humans and dogs. While the clinical features are remarkably similar in both species, the organization of dogs into defined breeds provides a more homogeneous genetic background that may increase the likelihood to uncover molecular subtypes for this complex disease. We thus hypothesized that molecular profiles derived from canine osteosarcoma would aid in molecular subclassification of this disease when applied to humans. To test the hypothesis, we performed genome wide gene expression profiling in a cohort of dogs with osteosarcoma, primarily from high-risk breeds. To further reduce inter-sample heterogeneity, we assessed tumor-intrinsic properties through use of an extensive panel of osteosarcoma-derived cell lines. We observed strong differential gene expression that segregated samples into two groups with differential survival probabilities. Groupings were characterized by the inversely correlated expression of genes associated with G2/M transition and DNA damage checkpoint and microenvironment-interaction categories. This signature was preserved in data from whole tumor samples of three independent dog osteosarcoma cohorts, with stratification into the two expected groups. Significantly, this restricted signature partially overlapped a previously defined, predictive signature for soft tissue sarcomas, and it unmasked orthologous molecular subtypes and their corresponding natural histories in five independent data sets from human patients with osteosarcoma. Our results indicate that the narrower genetic diversity of dogs can be utilized to group complex human osteosarcoma into biologically and clinically relevant molecular subtypes. This in turn may enhance prognosis and prediction, and identify relevant therapeutic targets. PMID:21621658

  10. Pollen developmental defects in ZD-CMS rice line explored by cytological, molecular and proteomic approaches.

    Science.gov (United States)

    Yan, Junjie; Tian, Han; Wang, Shuzhen; Shao, Jinzhen; Zheng, Yinzhen; Zhang, Hongyuan; Guo, Lin; Ding, Yi

    2014-08-28

    Cytoplasmic male sterility (CMS) is a widely observed phenomenon, which is especially useful in hybrid seed production. Meixiang A (MxA) is a new rice CMS line derived from a pollen-free sterile line named Yunnan ZidaoA (ZD-CMS). In this study, a homologous WA352 gene with variation in two nucleotides was identified in MxA. Cytological analysis revealed that MxA was aborted in the early uninucleate stage. The protein expression profiles of MxA and its maintainer line MeixiangB (MxB) were systematically compared using iTRAQ-based quantitative proteomics technology using young florets at the early uninucleate stage. A total of 688 proteins were quantified in both rice lines, and 45 of these proteins were found to be differentially expressed. Bioinformatics analysis indicated a large number of the proteins involved in carbohydrate metabolism or the stress response were downregulated in MxA, suggesting that these metabolic processes had been hindered during pollen development in MxA. The ROS (reactive oxygen species) level was increased in the mitochondrion of MxA, and further ultrastructural analysis showed the mitochondria with disrupted cristae in the rice CMS line MxA. These findings substantially contribute to our knowledge of pollen developmental defects in ZD-CMS rice line. MeixiangA (MxA) is a new type of rice CMS line, which is derived from pollen-free sterile line Yunnan ZidaoA. In this study, the cytological, molecular and proteomic approaches were used to study the characteristics of this new CMS line. Cytological study indicates the CMS line is aborted at the early uninucleate stage. A potential sterile gene ZD352 is identified in MxA, the protein product of which is mainly accumulated at the MMC/Meiotic stage. iTRAQ based proteomic analysis is performed to study the relevant proteins involved in the CMS occurance, 45 proteins are found to be significant differentially expressed and these proteins are involved in many cellular processes such as

  11. Controlling the transmission line shape of molecular t-stubs and potential thermoelectric applications

    DEFF Research Database (Denmark)

    Stadler, Robert; Markussen, Troels

    2011-01-01

    Asymmetric line shapes can occur in the transmission function describing electron transport in the vicinity of a minimum caused by quantum interference effects. Such asymmetry can be used to increase the thermoelectric efficiency of molecular junctions. So far, however, asymmetric line shapes hav...... calculations for a variety of t-stub molecules and also address their suitability for thermoelectric applications....

  12. Molecular cytogenetic identification of a novel dwarf wheat line with ...

    Indian Academy of Sciences (India)

    2012-01-08

    Jan 8, 2012 ... of a pAs1 hybridization band on 2DL chromosome of 31505-1. Two SSR ... [Chen G, Zheng Q, Bao Y, Liu S, Wang H and Li X 2012 Molecular cytogenetic identification of a novel dwarf wheat line with ..... translocations (Fedak and Han 2005; Li et al. ... growth (Cambridge, UK: Cambridge University Press).

  13. Molecular basis for vulnerability to mitochondrial and oxidative stress in a neuroendocrine CRI-G1 cell line.

    Directory of Open Access Journals (Sweden)

    Natasha Chandiramani

    2011-01-01

    Full Text Available Many age-associated disorders (including diabetes, cancer, and neurodegenerative diseases are linked to mitochondrial dysfunction, which leads to impaired cellular bioenergetics and increased oxidative stress. However, it is not known what genetic and molecular pathways underlie differential vulnerability to mitochondrial dysfunction observed among different cell types.Starting with an insulinoma cell line as a model for a neuronal/endocrine cell type, we isolated a novel subclonal line (named CRI-G1-RS that was more susceptible to cell death induced by mitochondrial respiratory chain inhibitors than the parental CRI-G1 line (renamed CRI-G1-RR for clarity. Compared to parental RR cells, RS cells were also more vulnerable to direct oxidative stress, but equally vulnerable to mitochondrial uncoupling and less vulnerable to protein kinase inhibition-induced apoptosis. Thus, differential vulnerability to mitochondrial toxins between these two cell types likely reflects differences in their ability to handle metabolically generated reactive oxygen species rather than differences in ATP production/utilization or in downstream apoptotic machinery. Genome-wide gene expression analysis and follow-up biochemical studies revealed that, in this experimental system, increased vulnerability to mitochondrial and oxidative stress was associated with (1 inhibition of ARE/Nrf2/Keap1 antioxidant pathway; (2 decreased expression of antioxidant and phase I/II conjugation enzymes, most of which are Nrf2 transcriptional targets; (3 increased expression of molecular chaperones, many of which are also considered Nrf2 transcriptional targets; (4 increased expression of β cell-specific genes and transcription factors that specify/maintain β cell fate; and (5 reconstitution of glucose-stimulated insulin secretion.The molecular profile presented here will enable identification of individual genes or gene clusters that shape vulnerability to mitochondrial dysfunction and

  14. SPECTRAL LINE SURVEY TOWARD MOLECULAR CLOUDS IN THE LARGE MAGELLANIC CLOUD

    Energy Technology Data Exchange (ETDEWEB)

    Nishimura, Yuri; Watanabe, Yoshimasa; Yamamoto, Satoshi [Department of Physics, the University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033 (Japan); Shimonishi, Takashi [Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Aramakiazaaoba 6-3, Aoba-ku, Sendai, Miyagi, 980-8578 (Japan); Sakai, Nami [RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Aikawa, Yuri [Center for Computational Sciences, The University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki 305-8577 (Japan); Kawamura, Akiko [National Astronomical Observatory of Japan, Osawa, Mitaka, Tokyo, 181-8588 (Japan)

    2016-02-20

    Spectral line survey observations of seven molecular clouds in the Large Magellanic Cloud (LMC) have been conducted in the 3 mm band with the Mopra 22 m telescope to reveal chemical compositions in low metallicity conditions. Spectral lines of fundamental species such as CS, SO, CCH, HCN, HCO{sup +}, and HNC are detected in addition to those of CO and {sup 13}CO, while CH{sub 3}OH is not detected in any source and N{sub 2}H{sup +} is marginally detected in two sources. The molecular-cloud scale (10 pc scale) chemical composition is found to be similar among the seven sources regardless of different star formation activities, and hence, it represents the chemical composition characteristic of the LMC without influences by star formation activities. In comparison with chemical compositions of Galactic sources, the characteristic features are (1) deficient N-bearing molecules, (2) abundant CCH, and (3) deficient CH{sub 3}OH. Feature (1) is due to a lower elemental abundance of nitrogen in the LMC, whereas features (2) and (3) seem to originate from extended photodissociation regions and warmer temperature in cloud peripheries due to a lower abundance of dust grains in the low metallicity condition. In spite of general resemblance of chemical abundances among the seven sources, the CS/HCO{sup +} and SO/HCO{sup +} ratios are found to be slightly higher in a quiescent molecular cloud. An origin of this trend is discussed in relation to possible depletion of sulfur along the molecular cloud formation.

  15. Wall-collision line broadening of molecular oxygen within nanoporous materials

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Can T.; Lewander, Maerta; Andersson-Engels, Stefan; Svensson, Tomas; Svanberg, Sune [Department of Physics, Lund University, P. O. Box 118, SE-221 00 Lund (Sweden); Adolfsson, Erik [Ceramic Materials, SWEREA IVF, Box 104, SE-431 22 Moelndal (Sweden)

    2011-10-15

    Wall-collision broadening of near-infrared absorption lines of molecular oxygen confined in nanoporous zirconia is studied by employing high-resolution diode-laser spectroscopy. The broadening is studied for pores of different sizes under a range of pressures, providing new insights on how wall collisions and intermolecular collisions influence the total spectroscopic line profile. The pressure series show that wall-collision broadening is relatively more prominent under reduced pressures, enabling sensitive means to probe pore sizes of porous materials. In addition, we show that the total wall-collision-broadened profile strongly deviates from a Voigt profile and that wall-collision broadening exhibits an additive-like behavior to the pressure and Doppler broadening.

  16. Low-Frequency Carbon Recombination Lines in the Orion Molecular Cloud Complex

    Science.gov (United States)

    Tremblay, Chenoa D.; Jordan, Christopher H.; Cunningham, Maria; Jones, Paul A.; Hurley-Walker, Natasha

    2018-05-01

    We detail tentative detections of low-frequency carbon radio recombination lines from within the Orion molecular cloud complex observed at 99-129 MHz. These tentative detections include one alpha transition and one beta transition over three locations and are located within the diffuse regions of dust observed in the infrared at 100 μm, the Hα emission detected in the optical, and the synchrotron radiation observed in the radio. With these observations, we are able to study the radiation mechanism transition from collisionally pumped to radiatively pumped within the H ii regions within the Orion molecular cloud complex.

  17. A new mathematical formulation of the line-by-line method in case of weak line overlapping

    Science.gov (United States)

    Ishov, Alexander G.; Krymova, Natalie V.

    1994-01-01

    A rigorous mathematical proof is presented for multiline representation on the equivalent width of a molecular band which consists in the general case of n overlapping spectral lines. The multiline representation includes a principal term and terms of minor significance. The principal term is the equivalent width of the molecular band consisting of the same n nonoverlapping spectral lines. The terms of minor significance take into consideration the overlapping of two, three and more spectral lines. They are small in case of the weak overlapping of spectral lines in the molecular band. The multiline representation can be easily generalized for optically inhomogeneous gas media and holds true for combinations of molecular bands. If the band lines overlap weakly the standard formulation of line-by-line method becomes too labor-consuming. In this case the multiline representation permits line-by-line calculations to be performed more effectively. Other useful properties of the multiline representation are pointed out.

  18. Molecular line parameters for the atmospheric trace molecule spectroscopy experiment

    Science.gov (United States)

    Brown, L. R.; Farmer, C. B.; Toth, R. A.; Rinsland, Curtis P.

    1987-01-01

    During its first mission in 1985 onboard Spacelab 3, the ATMOS (atmospheric trace molecule spectroscopy) instrument, a high speed Fourier transform spectrometer, produced a large number of high resolution infrared solar absorption spectra recorded in the occultation mode. The analysis and interpretation of these data in terms of composition, chemistry, and dynamics of the earth's upper atmosphere required good knowledge of the molecular line parameters for those species giving rise to the absorptions in the atmospheric spectra. This paper describes the spectroscopic line parameter database compiled for the ATMOS experiment and referenced in other papers describing ATMOS results. With over 400,000 entries, the linelist catalogs parameters of 46 minor and trace species in the 1-10,000/cm region.

  19. Prediction of temperature-insensitive molecular absorption lines in laser-assisted combustion diagnostics

    International Nuclear Information System (INIS)

    Walewski, Joachim W.; Elmqvist, Anders

    2005-01-01

    In laser-assisted combustion diagnostics it is a recurring task to predict molecular transitions whose signal strength depends only weakly on variations in temperature. The signal strength is proportional to the Boltzmann fraction of the level probed and the amplitude of the absorption line profile. In the past investigations have been presented in which this task was attack by detailed numerical calculations of the temperature dependence of pertinent physical properties of the molecule. Another widely applied approach relies on an analytical formula for the Boltzmann fraction of hetero-nuclear diatomic molecules and the neglect of line shape effects. The analytical approach experiences a continuing popularity in laser-assisted combustion diagnostics, which is why we compared both approaches with each other. The objective of this comparison was to assess the accuracy of the analytical approach and to reveal its potential pitfalls. Our comparison revealed that the analytical approach suffers from mediocre accuracy, which makes it unfit for practical applications. One cause is the neglect of higher lying vibrational levels, which show a non-negligible population for typical flame temperatures. Another reason is the neglect of fine structure splitting in molecules with non-zero orbit angular momentum in the ground state. Another reason for the observed inaccuracy is the neglect of line shape effects quenching, which were found to have a significant effect on the temperature sensitivity of a line. Because of its insufficient accuracy due to both oversimplified models of the molecular energy levels and the neglect of line shape effects and quenching we discourage from applying the analytical approach and recommend the use of detailed numerical approaches that are free of the above limitations

  20. Millimeter-wave molecular line observations of the Tornado nebula

    International Nuclear Information System (INIS)

    Sakai, D.; Oka, T.; Tanaka, K.; Matsumura, S.; Miura, K.; Takekawa, S.

    2014-01-01

    We report the results of millimeter-wave molecular line observations of the Tornado Nebula (G357.7-0.1), which is a bright radio source behind the Galactic center region. A 15' × 15' area was mapped in the J = 1-0 lines of CO, 13 CO, and HCO + with the Nobeyama Radio Observatory 45 m telescope. The Very Large Array archival data of OH at 1720 MHz were also reanalyzed. We found two molecular clouds with separate velocities, V LSR = –14 km s –1 and +5 km s –1 . These clouds show rough spatial anti-correlation. Both clouds are associated with OH 1720 MHz emissions in the area overlapping with the Tornado Nebula. The spatial and velocity coincidence indicates violent interaction between the clouds and the Tornado Nebula. Modestly excited gas prefers the position of the Tornado 'head' in the –14 km s –1 cloud, also suggesting the interaction. Virial analysis shows that the +5 km s –1 cloud is more tightly bound by self-gravity than the –14 km s –1 cloud. We propose a formation scenario for the Tornado Nebula; the +5 km s –1 cloud collided into the –14 km s –1 cloud, generating a high-density layer behind the shock front, which activates a putative compact object by Bondi-Hoyle-Lyttleton accretion to eject a pair of bipolar jets.

  1. A Systems Biology Framework Identifies Molecular Underpinnings of Coronary Heart Disease

    Science.gov (United States)

    Huan, Tianxiao; Zhang, Bin; Wang, Zhi; Joehanes, Roby; Zhu, Jun; Johnson, Andrew D.; Ying, Saixia; Munson, Peter J.; Raghavachari, Nalini; Wang, Richard; Liu, Poching; Courchesne, Paul; Hwang, Shih-Jen; Assimes, Themistocles L.; McPherson, Ruth; Samani, Nilesh J.; Schunkert, Heribert; Meng, Qingying; Suver, Christine; O'Donnell, Christopher J.; Derry, Jonathan; Yang, Xia; Levy, Daniel

    2013-01-01

    Objective Genetic approaches have identified numerous loci associated with coronary heart disease (CHD). The molecular mechanisms underlying CHD gene-disease associations, however, remain unclear. We hypothesized that genetic variants with both strong and subtle effects drive gene subnetworks that in turn affect CHD. Approach and Results We surveyed CHD-associated molecular interactions by constructing coexpression networks using whole blood gene expression profiles from 188 CHD cases and 188 age- and sex-matched controls. 24 coexpression modules were identified including one case-specific and one control-specific differential module (DM). The DMs were enriched for genes involved in B-cell activation, immune response, and ion transport. By integrating the DMs with altered gene expression associated SNPs (eSNPs) and with results of GWAS of CHD and its risk factors, the control-specific DM was implicated as CHD-causal based on its significant enrichment for both CHD and lipid eSNPs. This causal DM was further integrated with tissue-specific Bayesian networks and protein-protein interaction networks to identify regulatory key driver (KD) genes. Multi-tissue KDs (SPIB and TNFRSF13C) and tissue-specific KDs (e.g. EBF1) were identified. Conclusions Our network-driven integrative analysis not only identified CHD-related genes, but also defined network structure that sheds light on the molecular interactions of genes associated with CHD risk. PMID:23539213

  2. High-resolution molecular line observations of active galaxies

    Science.gov (United States)

    García-Burillo, S.; Combes, F.; Usero, A.; Graciá-Carpio, J.

    2008-10-01

    The study of the content, distribution and kinematics of interstellar gas is a key to understand the origin and maintenance of both starburst and nuclear (AGN) activity in galaxies. The processes involved in AGN fueling encompass a wide range of scales, both spatial and temporal, which have to be studied. Probing the gas flow from the outer disk down to the central engine of an AGN host, requires the use of specific tracers of the interstellar medium adapted to follow the change of phase of the gas as a function of radius. Current mm-interferometers can provide a sharp view of the distribution and kinematics of molecular gas in the circumnuclear disks of galaxies through extensive CO line mapping. As such, CO maps are an essential tool to study AGN feeding mechanisms in the local universe. This is the scientific driver of the NUclei of GAlaxies (NUGA) survey, whose latest results are here reviewed. On the other hand, the use of specific molecular tracers of the dense gas phase can probe the feedback influence of activity on the chemistry and energy balance/redistribution in the interstellar medium of nearby galaxies. Millimeter interferometers are able to unveil the strong chemical differentiation present in the molecular gas disks of nearby starbursts and AGNs. Nearby active galaxies can be used as local templates to address the study of more distant galaxies where both star formation and AGN activity are deeply embedded.

  3. HIFISTARS Herschel/HIFI observations of VY Canis Majoris. Molecular-line inventory of the envelope around the largest known star

    Science.gov (United States)

    Alcolea, J.; Bujarrabal, V.; Planesas, P.; Teyssier, D.; Cernicharo, J.; De Beck, E.; Decin, L.; Dominik, C.; Justtanont, K.; de Koter, A.; Marston, A. P.; Melnick, G.; Menten, K. M.; Neufeld, D. A.; Olofsson, H.; Schmidt, M.; Schöier, F. L.; Szczerba, R.; Waters, L. B. F. M.

    2013-11-01

    Aims: The study of the molecular gas in the circumstellar envelopes of evolved stars is normally undertaken by observing lines of CO (and other species) in the millimetre-wave domain. In general, the excitation requirements of the observed lines are low at these wavelengths, and therefore these observations predominantly probe the cold outer envelope while studying the warm inner regions of the envelopes normally requires sub-millimetre (sub-mm) and far-infrared (FIR) observational data. Methods: To gain insight into the physical conditions and kinematics of the warm (100-1000 K) gas around the red hyper-giant VY CMa, we performed sensitive high spectral resolution observations of molecular lines in the sub-mm/FIR using the HIFI instrument of the Herschel Space Observatory. We observed CO, H2O, and other molecular species, sampling excitation energies from a few tens to a few thousand K. These observations are part of the Herschel guaranteed time key program HIFISTARS. Results: We detected the J = 6-5, J = 10-9, and J = 16-15 lines of 12CO and 13CO at ~100, 300, and 750 K above the ground state (and the 13CO J = 9-8 line). These lines are crucial for improving the modelling of the internal layers of the envelope around VY CMa. We also detected 27 lines of H2O and its isotopomers, and 96 lines of species such as NH3, SiO, SO, SO2 HCN, OH and others, some of them originating from vibrationally excited levels. Three lines were not unambiguously assigned. Conclusions: Our observations confirm that VY CMa's envelope must consist of two or more detached components. The molecular excitation in the outer layers is significantly lower than in the inner ones, resulting in strong self-absorbed profiles in molecular lines that are optically thick in this outer envelope, for instance, low-lying lines of H2O. Except for the most abundant species, CO and H2O, most of the molecular emission detected at these sub-mm/FIR wavelengths arise from the central parts of the envelope. The

  4. Millimeter-wave molecular line observations of the Tornado nebula

    Energy Technology Data Exchange (ETDEWEB)

    Sakai, D. [Department of Astronomy, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Oka, T.; Tanaka, K.; Matsumura, S.; Miura, K.; Takekawa, S., E-mail: sakai.daisuke@nao.ac.jp [Department of Physics, Institute of Science and Technology, Keio University, 3-14-1 Hiyoshi, Yokohama, Kanagawa 223-8522 (Japan)

    2014-08-10

    We report the results of millimeter-wave molecular line observations of the Tornado Nebula (G357.7-0.1), which is a bright radio source behind the Galactic center region. A 15' × 15' area was mapped in the J = 1-0 lines of CO, {sup 13}CO, and HCO{sup +} with the Nobeyama Radio Observatory 45 m telescope. The Very Large Array archival data of OH at 1720 MHz were also reanalyzed. We found two molecular clouds with separate velocities, V{sub LSR} = –14 km s{sup –1} and +5 km s{sup –1}. These clouds show rough spatial anti-correlation. Both clouds are associated with OH 1720 MHz emissions in the area overlapping with the Tornado Nebula. The spatial and velocity coincidence indicates violent interaction between the clouds and the Tornado Nebula. Modestly excited gas prefers the position of the Tornado 'head' in the –14 km s{sup –1} cloud, also suggesting the interaction. Virial analysis shows that the +5 km s{sup –1} cloud is more tightly bound by self-gravity than the –14 km s{sup –1} cloud. We propose a formation scenario for the Tornado Nebula; the +5 km s{sup –1} cloud collided into the –14 km s{sup –1} cloud, generating a high-density layer behind the shock front, which activates a putative compact object by Bondi-Hoyle-Lyttleton accretion to eject a pair of bipolar jets.

  5. MHOs toward HMOs: A Search for Molecular Hydrogen Emission-Line Objects toward High-mass Outflows

    Energy Technology Data Exchange (ETDEWEB)

    Wolf-Chase, Grace [Astronomy Department Adler Planetarium 1300 S. Lake Shore Drive Chicago, IL 60605 (United States); Arvidsson, Kim [Trull School of Sciences and Mathematics Schreiner University 2100 Memorial Blvd. Kerrville, TX 78028 (United States); Smutko, Michael, E-mail: gwolfchase@adlerplanetarium.org [Center for Interdisciplinary Exploration and Research in Astrophysics (CIERA), and Dept. of Physics and Astronomy, Northwestern University, 2131 Tech Drive, Evanston, IL 60208 (United States)

    2017-07-20

    We present the results of a narrow-band near-infrared imaging survey for Molecular Hydrogen emission-line Objects (MHOs) toward 26 regions containing high-mass protostellar candidates and massive molecular outflows. We have detected a total of 236 MHOs, 156 of which are new detections, in 22 out of the 26 regions. We use H{sub 2} 2.12 μ m/H{sub 2} 2.25 μ m flux ratios, together with morphology, to separate the signatures of fluorescence associated with photo-dissociation regions (PDRs) from shocks associated with outflows in order to identify the MHOs. PDRs have typical low flux ratios of ∼1.5–3, while the vast majority of MHOs display flux ratios typical of C-type shocks (∼6–20). A few MHOs exhibit flux ratios consistent with expected values for J-type shocks (∼3–4), but these are located in regions that may be contaminated with fluorescent emission. Some previously reported MHOs have low flux ratios, and are likely parts of PDRs rather than shocks indicative of outflows. We identify a total of 36 outflows across the 22 target regions where MHOs were detected. In over half these regions, MHO arrangements and fluorescent structures trace features present in CO outflow maps, suggesting that the CO emission traces a combination of dynamical effects, which may include gas entrained in expanding PDRs as well as bipolar outflows. Where possible, we link MHO complexes to distinct outflows and identify candidate driving sources.

  6. The Far Infrared Lines of OH as Molecular Cloud Diagnostics

    Science.gov (United States)

    Smith, Howard A.

    2004-01-01

    Future IR missions should give some priority to high resolution spectroscopic observations of the set of far-IR transitions of OH. There are 15 far-IR lines arising between the lowest eight rotational levels of OH, and ISO detected nine of them. Furthermore, ISO found the OH lines, sometimes in emission and sometimes in absorption, in a wide variety of galactic and extragalactic objects ranging from AGB stars to molecular clouds to active galactic nuclei and ultra-luminous IR galaxies. The ISO/LWS Fabry-Perot resolved the 119 m doublet line in a few of the strong sources. This set of OH lines provides a uniquely important diagnostic for many reasons: the lines span a wide wavelength range (28.9 m to 163.2 m); the transitions have fast radiative rates; the abundance of the species is relatively high; the IR continuum plays an important role as a pump; the contribution from shocks is relatively minor; and, not least, the powerful centimeter-wave radiation from OH allows comparison with radio and VLBI datasets. The problem is that the large number of sensitive free parameters, and the large optical depths of the strongest lines, make modeling the full set a difficult job. The SWAS montecarlo radiative transfer code has been used to analyze the ISO/LWS spectra of a number of objects with good success, including in both the lines and the FIR continuum; the DUSTY radiative transfer code was used to insure a self-consistent continuum. Other far IR lines including those from H2O, CO, and [OI] are also in the code. The OH lines all show features which future FIR spectrometers should be able to resolve, and which will enable further refinements in the details of each cloud's structure. Some examples are given, including the case of S140, for which independent SWAS data found evidence for bulk flows.

  7. Molecular-cloud-scale Chemical Composition. II. Mapping Spectral Line Survey toward W3(OH) in the 3 mm Band

    Energy Technology Data Exchange (ETDEWEB)

    Nishimura, Yuri [Institute of Astronomy, The University of Tokyo, 2-21-1, Osawa, Mitaka, Tokyo 181-0015 (Japan); Watanabe, Yoshimasa; Yamamoto, Satoshi [Department of Physics, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Harada, Nanase [Academia Sinica Institute of Astronomy and Astrophysics, No.1, Sec. 4, Roosevelt Road, 10617 Taipei, Taiwan, R.O.C. (China); Shimonishi, Takashi [Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Aramakiazaaoba 6-3, Aoba-ku, Sendai, Miyagi 980-8578 (Japan); Sakai, Nami [RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Aikawa, Yuri [Department of Astronomy, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Kawamura, Akiko [Chile Observatory, National Astronomical Observatory of Japan, 2-21-1, Osawa, Mitaka, Tokyo 181-8588 (Japan)

    2017-10-10

    To study a molecular-cloud-scale chemical composition, we conducted a mapping spectral line survey toward the Galactic molecular cloud W3(OH), which is one of the most active star-forming regions in the Perseus arm. We conducted our survey through the use of the Nobeyama Radio Observatory 45 m telescope, and observed the area of 16′ × 16′, which corresponds to 9.0 pc × 9.0 pc. The observed frequency ranges are 87–91, 96–103, and 108–112 GHz. We prepared the spectrum averaged over the observed area, in which eight molecular species (CCH, HCN, HCO{sup +}, HNC, CS, SO, C{sup 18}O, and {sup 13}CO) are identified. On the other hand, the spectrum of the W3(OH) hot core observed at a 0.17 pc resolution shows the lines of various molecules such as OCS, H{sub 2}CS CH{sub 3}CCH, and CH{sub 3}CN in addition to the above species. In the spatially averaged spectrum, emission of the species concentrated just around the star-forming core, such as CH{sub 3}OH and HC{sub 3}N, is fainter than in the hot core spectrum, whereas emission of the species widely extended over the cloud such as CCH is relatively brighter. We classified the observed area into five subregions according to the integrated intensity of {sup 13}CO, and evaluated the contribution to the averaged spectrum from each subregion. The CCH, HCN, HCO{sup +}, and CS lines can be seen even in the spectrum of the subregion with the lowest {sup 13}CO integrated intensity range (<10 K km s{sup −1}). Thus, the contributions of the spatially extended emission is confirmed to be dominant in the spatially averaged spectrum.

  8. Clustering the Orion B giant molecular cloud based on its molecular emission.

    Science.gov (United States)

    Bron, Emeric; Daudon, Chloé; Pety, Jérôme; Levrier, François; Gerin, Maryvonne; Gratier, Pierre; Orkisz, Jan H; Guzman, Viviana; Bardeau, Sébastien; Goicoechea, Javier R; Liszt, Harvey; Öberg, Karin; Peretto, Nicolas; Sievers, Albrecht; Tremblin, Pascal

    2018-02-01

    identified, likely related to the higher critical density of the CN and HCO + (1 - 0) lines. These distinctions are only possible because the high-density regions are spatially resolved. Molecules are versatile tracers of GMCs because their line intensities bear the signature of the physics and chemistry at play in the gas. The association of simultaneous multi-line, wide-field mapping and powerful machine learning methods such as the Meanshift clustering algorithm reveals how to decode the complex information available in these molecular tracers.

  9. Thermal histories of chondrules in solar nebula shocks, including the effect of molecular line cooling

    Science.gov (United States)

    Morris, Melissa A.

    Chondrules are millimeter-sized, silicate (mostly ferromagnesian) igneous spheres found within chondritic meteorites. They are some of the oldest materials in our Solar System, having formed within a few million years of its birth. Chondrules were melted at high temperature (over 1800 K), while they were free-floating objects in the early solar nebula. Their petrology and chemistry constrain their formation, especially their thermal histories. Chondrules provide some of the most powerful constraints on conditions in the solar nebula. Models in which chondrule precursors melted by passage through solar nebula shocks are very promising, and meet most constraints on chondrule formation in broad brush. However, these models have been lacking in some of the relevant physics. Previous shock models have used incorrect approximations to the input radiation boundary condition, and the opacity of solids has been treated simply. Most important, a proper treatment of cooling due to molecular line emission has not been included. In this thesis, the shock model is significantly improved in order to determine if it remains consistent with observational constraints. The appropriate boundary condition for the input radiation and the proper method for calculation of the opacity of solids are determined, and a complete treatment of molecular line cooling due to water is included. Previous estimates of the effect of line cooling predicted chondrule cooling rates in excess of 10,000 K per hour. However, once molecular line cooling due to water was incorporated into the full shock model, it was found that line cooling has a minimal effect on the thermal histories of gas and chondrules. This behavior is attributed mostly to the thermal buffering of the gas due to hydrogen dissociation and recombination, which tends to keep the gas temperature at approximately 2000 K until the column densities of water become optically thick to line emission. Chondrule cooling rates in the range of 10

  10. The spatial distribution and velocity field of the molecular hydrogen line emission from the centre of the Galaxy

    International Nuclear Information System (INIS)

    Gatley, I.; Krisciunas, K.; Jones, T.J.; Hyland, A.R.; Geballe, T.R.; Rijksuniversiteit Groningen

    1986-01-01

    In an earlier paper the existence of a ring of molecular hydrogen-line emission surrounding the nucleus of the Galaxy was demonstrated. Here are presented the first detailed maps of the surface brightness and the velocity field, made in the upsilon=1-0 S(1) line of molecular hydrogen with a spatial resolution of 18 arcsec and a velocity resolution of 130 km s -1 . It is found that the molecular ring is tilted approximately 20 0 out of the plane of the Galaxy, has a broken and clumpy appearance, rotates at 100 km s -1 in the sense of galactic rotation, and exhibits radial motion at a velocity of 50 km s -1 . (author)

  11. Modeling and simulations for molecular scale hydrodynamics of the moving contact line in immiscible two-phase flows

    KAUST Repository

    Qian, Tiezheng

    2009-10-29

    This paper starts with an introduction to the Onsager principle of minimum energy dissipation which governs the optimal paths of deviation and restoration to equilibrium. Then there is a review of the variational approach to moving contact line hydrodynamics. To demonstrate the validity of our continuum hydrodynamic model, numerical results from model calculations and molecular dynamics simulations are presented for immiscible Couette and Poiseuille flows past homogeneous solid surfaces, with remarkable overall agreement. Our continuum model is also used to study the contact line motion on surfaces patterned with stripes of different contact angles (i.e. surfaces of varying wettability). Continuum calculations predict the stick-slip motion for contact lines moving along these patterned surfaces, in quantitative agreement with molecular dynamics simulation results. This periodic motion is tunable through pattern period (geometry) and contrast in wetting property (chemistry). The consequence of stick-slip contact line motion on energy dissipation is discussed. © 2009 IOP Publishing Ltd.

  12. Widespread molecular patterns associated with drug sensitivity in breast cancer cell lines, with implications for human tumors.

    Directory of Open Access Journals (Sweden)

    Chad J Creighton

    Full Text Available BACKGROUND: Recent landmark studies have profiled cancer cell lines for molecular features, along with measuring the corresponding growth inhibitory effects for specific drug compounds. These data present a tool for determining which subsets of human cancer might be more responsive to particular drugs. To this end, the NCI-DREAM-sponsored DREAM7: Drug Sensitivity Prediction Challenge (sub-challenge 1 set out to predict the sensitivities of 18 breast cancer cell lines to 31 previously untested compounds, on the basis of molecular profiling data and a training subset of cell lines. METHODS AND RESULTS: With 47 teams submitting blinded predictions, team Creighton scored third in terms of overall accuracy. Team Creighton's method was simple and straightforward, incorporated multiple expression data types (RNA-seq, gene array, RPPA, and incorporated all profiled features (not only the "best" predictive ones. As an extension of the approach, cell line data, from public datasets of expression profiling coupled with drug sensitivities (Barretina, Garnett, Heiser were used to "predict" the drug sensitivities in human breast tumors (using data from The Cancer Genome Atlas. Drug sensitivity correlations within human breast tumors showed differences by expression-based subtype, with many associations in line with the expected (e.g. Lapatinib sensitivity in HER2-enriched cancers and others inviting further study (e.g. relative resistance to PI3K inhibitors in basal-like cancers. CONCLUSIONS: Molecular patterns associated with drug sensitivity are widespread, with potentially hundreds of genes that could be incorporated into making predictions, as well as offering biological clues as to the mechanisms involved. Applying the cell line patterns to human tumor data may help generate hypotheses on what tumor subsets might be more responsive to therapies, where multiple cell line datasets representing various drugs may be used, in order to assess consistency of

  13. Pressure-induced organic topological nodal-line semimetal in the three-dimensional molecular crystal Pd (dddt) 2

    Science.gov (United States)

    Liu, Zhao; Wang, Haidi; Wang, Z. F.; Yang, Jinlong; Liu, Feng

    2018-04-01

    The nodal-line semimetal represents a class of topological materials characterized with highest band degeneracy. It is usually found in inorganic materials of high crystal symmetry or a minimum symmetry of inversion aided with accidental band degeneracy [Phys. Rev. Lett. 118, 176402 (2017), 10.1103/PhysRevLett.118.176402]. Based on first-principles band structure, Wannier charge center, and topological surface state calculations, here we predict a pressure-induced topological nodal-line semimetal in the absence of spin-orbit coupling (SOC) in the synthesized single-component 3D molecular crystal Pd (dddt) 2 . We show a Γ -centered single nodal line undulating within a narrow energy window across the Fermi level. This intriguing nodal line is generated by pressure-induced accidental band degeneracy, without protection from any crystal symmetry. When SOC is included, the fourfold degenerated nodal line is gapped and Pd (dddt) 2 becomes a strong 3D topological metal with an Z2 index of (1;000). However, the tiny SOC gap makes it still possible to detect the nodal-line properties experimentally. Our findings afford an attractive route for designing and realizing topological states in 3D molecular crystals, as they are weakly bonded through van der Waals forces with a low crystal symmetry so that their electronic structures can be easily tuned by pressure.

  14. Multi-scale modelling of supercapacitors: From molecular simulations to a transmission line model

    Science.gov (United States)

    Pean, C.; Rotenberg, B.; Simon, P.; Salanne, M.

    2016-09-01

    We perform molecular dynamics simulations of a typical nanoporous-carbon based supercapacitor. The organic electrolyte consists in 1-ethyl-3-methylimidazolium and hexafluorophosphate ions dissolved in acetonitrile. We simulate systems at equilibrium, for various applied voltages. This allows us to determine the relevant thermodynamic (capacitance) and transport (in-pore resistivities) properties. These quantities are then injected in a transmission line model for testing its ability to predict the charging properties of the device. The results from this macroscopic model are in good agreement with non-equilibrium molecular dynamics simulations, which validates its use for interpreting electrochemical impedance experiments.

  15. LID: Computer code for identifying atomic and ionic lines below 3500 Angstroms

    International Nuclear Information System (INIS)

    Peek, J.M.; Dukart, R.J.

    1987-08-01

    An interactive computer code has been written to search a data base containing information useful for identifying lines in experimentally-observed spectra or for designing experiments. The data base was the basis for the Kelly and Palumbo critical review of well-resolved lines below 2000 Angstroms, includes lines below 3500 Angstroms for atoms and ions of hydrogen through krypton, and was obtained from R.L. Kelly. This code allows the user to search the data base for a user-specified wavelength region, with this search either limited to atoms or ions of the user's choice for all atoms and ions contained in the data base. The line information found in the search is stored in a local file for later reference. A plotting capability is provided to graphically display the lines resulting from the search. Several options are available to control the nature of these graphs. It is also possible to bring in data from another source, such as an experimental spectra, for display along with the lines from the data-base search. Options for manipulating the experimental spectra's background intensity and wavelength scale are also available to the user. The intensities for the lines from each ion found in the data-base search can be scaled by a multiplicative constant to better simulate the observed spectrum

  16. DISCOVERY OF BROAD MOLECULAR LINES AND OF SHOCKED MOLECULAR HYDROGEN FROM THE SUPERNOVA REMNANT G357.7+0.3: HHSMT, APEX, SPITZER , AND SOFIA OBSERVATIONS

    Energy Technology Data Exchange (ETDEWEB)

    Rho, J. [SETI Institute, 189 N. Bernardo Ave., Mountain View, CA 94043 (United States); Hewitt, J. W. [CRESST/University of Maryland, Baltimore County, Baltimore, MD 21250 and NASA Goddard Space Flight Center, Greenbelt, MD 20771 (United States); Bieging, J. [Steward Observatory, The University of Arizona, Tucson AZ 85721 (United States); Reach, W. T. [Universities Space Research Association, SOFIA Science Center, NASA Ames Research Center, MS 232, Moffett Field, CA 94034 (United States); Andersen, M. [Gemini Observatory, Casilla 603, La Serena (Chile); Güsten, R., E-mail: jrho@seti.org, E-mail: john.w.hewitt@unf.edu, E-mail: jbieging@as.arizona.edu, E-mail: wreach@sofia.usra.edu, E-mail: manderse@gemini.edu, E-mail: guesten@mpifr-bonn.mpg.de [Max Planck Institut für Radioastronomie, Auf dem Hugel 69, D-53121 Bonn (Germany)

    2017-01-01

    We report a discovery of shocked gas from the supernova remnant (SNR) G357.7+0.3. Our millimeter and submillimeter observations reveal broad molecular lines of CO(2-1), CO(3-2), CO(4-3), {sup 13}CO (2-1), and {sup 13}CO (3-2), HCO{sup +}, and HCN using the Heinrich Hertz Submillimeter Telescope, the Arizona 12 m Telescope, APEX, and the MOPRA Telescope. The widths of the broad lines are 15–30 km s{sup −1}, and the detection of such broad lines is unambiguous, dynamic evidence showing that the SNR G357.7+0.3 is interacting with molecular clouds. The broad lines appear in extended regions (>4.′5 × 5′). We also present the detection of shocked H{sub 2} emission in the mid-infrared but lacking ionic lines using Spitzer /IRS observations to map a few-arcminute area. The H{sub 2} excitation diagram shows a best fit with a two-temperature local thermal equilibrium model with the temperatures of ∼200 and 660 K. We observed [C ii] at 158 μ m and high- J CO(11-10) with the German Receiver for Astronomy at Terahertz Frequencies (GREAT) on the Stratospheric Observatory for Infrared Astronomy. The GREAT spectrum of [C ii], a 3 σ detection, shows a broad line profile with a width of 15.7 km{sup −1} that is similar to those of broad CO molecular lines. The line width of [C ii] implies that ionic lines can come from a low-velocity C-shock. Comparison of H{sub 2} emission with shock models shows that a combination of two C-shock models is favored over a combination of C- and J-shocks or a single shock. We estimate the CO density, column density, and temperature using a RADEX model. The best-fit model with n (H{sub 2}) = 1.7 × 10{sup 4} cm{sup −3}, N(CO) = 5.6 × 10{sup 16} cm{sup −2}, and T  = 75 K can reproduce the observed millimeter CO brightnesses.

  17. On-line structural response analysis: using the extended Kalman estimator/identifier

    International Nuclear Information System (INIS)

    Candy, J.V.

    1979-01-01

    This report disucsses the development of on-line state and parameter estimators used to analyze the structural response of buildings. The estimator/identifier is an extended Kalman filter (EKF), which has been applied with great success in other technological areas. It is shown that the EKF can perform quite well on simulated noisy structural response data

  18. The Design of a Molecular Assembly Line Based on Biological Molecules

    Science.gov (United States)

    2003-06-01

    parenthesis in figure 1.8 is a bi-stable toggle switch. Introduction: Molecular assembly lines O=P-O- O O HOH H0P-0- O -O- 4 Polymerase HO H--- O HHO ...sample. Therefore, the samples are self-consistent. From here on, the calculated temperature based on FAM emission MNSowmm" RF Biology: Results and...irradiation for one hour. Figure 2.11 shows the fluorescence spectra of FAM emission (4 scans averaged over 200 seconds) in a 300MHz field. The increased

  19. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles

    Directory of Open Access Journals (Sweden)

    Farshad Farshidfar

    2017-03-01

    Full Text Available Cholangiocarcinoma (CCA is an aggressive malignancy of the bile ducts, with poor prognosis and limited treatment options. Here, we describe the integrated analysis of somatic mutations, RNA expression, copy number, and DNA methylation by The Cancer Genome Atlas of a set of predominantly intrahepatic CCA cases and propose a molecular classification scheme. We identified an IDH mutant-enriched subtype with distinct molecular features including low expression of chromatin modifiers, elevated expression of mitochondrial genes, and increased mitochondrial DNA copy number. Leveraging the multi-platform data, we observed that ARID1A exhibited DNA hypermethylation and decreased expression in the IDH mutant subtype. More broadly, we found that IDH mutations are associated with an expanded histological spectrum of liver tumors with molecular features that stratify with CCA. Our studies reveal insights into the molecular pathogenesis and heterogeneity of cholangiocarcinoma and provide classification information of potential therapeutic significance.

  20. THE EVOLUTION OF MOLECULAR LINE PROFILES INDUCED BY THE PROPAGATION OF C-SHOCK WAVES

    International Nuclear Information System (INIS)

    Jimenez-Serra, I.; Caselli, P.; Martin-Pintado, J.; RodrIguez-Franco, A.; Viti, S.

    2009-01-01

    We present the first results of the expected variations of the molecular line emission arising from material recently affected by C-shocks (shock precursors). Our parametric model of the structure of C-shocks has been coupled with a radiative transfer code to calculate the molecular excitation and line profiles of shock tracers such as SiO, and of ion and neutral molecules such as H 13 CO + and HN 13 C, as the shock propagates through the unperturbed medium. Our results show that the SiO emission arising from the early stage of the magnetic precursor typically has very narrow line profiles slightly shifted in velocity with respect to the ambient cloud. This narrow emission is generated in the region where the bulk of the ion fluid has already slipped to larger velocities in the precursor as observed toward the young L1448-mm outflow. This strongly suggests that the detection of narrow SiO emission, and of an ion enhancement in young shocks, is produced by the magnetic precursor of C-shocks. In addition, our model shows that the different velocity components observed toward this outflow can be explained by the coexistence of different shocks at different evolutionary stages, within the same beam of the single-dish observations.

  1. Improving Blast Resistance of a Thermo-Sensitive Genic Male Sterile Rice Line GD-8S by Molecular Marker-Assisted Selection

    Directory of Open Access Journals (Sweden)

    Wu-ge LIU

    2008-09-01

    Full Text Available The broad-spectrum blast resistance gene Pi-1, from donor line BL122, was introduced into a thermo-sensitive genic male sterile rice line GD-8S, which possessed good grain quality but high susceptibility to rice blast, by using backcross breeding and molecular marker-assisted selection. Five elite improved male sterile lines, RGD8S-1, RGD8S-2, RGD8S-3, RGD8S-4 and RGD8S-5, were selected based on the results of molecular marker analysis, spikelet sterility, recovery rate of genetic background and agronomic traits. Thirty-three representative blast isolates collected from Guangdong Province, China were used to inoculate the improved lines and the original line GD-8S artificially. The resistance frequencies of the improved lines ranged from 76.47% to 100%, much higher than that of the original line GD-8S (9.09%. On the agronomic characters, there were no significant differences between the improved lines and GD-8S except for flag leaf length and panicle number per plant. The improved lines could be used for breeding hybrid rice with high blast resistance.

  2. DISCOVERY OF TIME VARIATION OF THE INTENSITY OF MOLECULAR LINES IN IRC+10216 IN THE SUBMILLIMETER AND FAR-INFRARED DOMAINS

    Energy Technology Data Exchange (ETDEWEB)

    Cernicharo, J.; Quintana-Lacaci, G.; Agúndez, M.; Velilla-Prieto, L. [Group of Molecular Astrophysics, ICMM, CSIC, C/Sor Juana Inés de La Cruz N3, E-28049 Madrid (Spain); Teyssier, D.; García-Lario, P. [ESA, ESAC, P.O. Box 78, Villanueva de la Cañada, E-28691 Madrid (Spain); Daniel, F. [Univ. Grenoble Alpes, IPAG, F-38000 Grenoble (France); Decin, L. [Instituut voor Sterrenkunde, Katholieke Universiteit Leuven, Celestijnenlaan 200D, B-3001 Leuven (Belgium); Guélin, M. [Institut de Radioastronomie Millimétrique, 300 rue de la Piscine, F-38406 St-Martin d' Hères (France); Encrenaz, P. [LERMA, Observatoire de Paris, 61 Av. de l' Observatoire, F-75014 Paris (France); De Beck, E. [Department of Earth and Space Sciences, Chalmers University of Technology, Onsala Space Observatory, SE 439 92 Onsala (Sweden); Barlow, M. J. [Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT (United Kingdom); Groenewegen, M. A. T. [Koninklijke Sterrenwacht van België, Ringlaan 3, B-1180 Brussels (Belgium); Neufeld, D. [Department of Physics and Astronomy, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218 (United States); Pearson, J. [Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109 (United States)

    2014-11-20

    We report on the discovery of strong intensity variations in the high rotational lines of abundant molecular species toward the archetypical circumstellar envelope of IRC+10216. The observations have been carried out with the Heterodyne Instrument for the Far-Infrared (HIFI) instrument on board Herschel and with the IRAM30 m telescope. They cover several observing periods spreading over three years. The line intensity variations for molecules produced in the external layers of the envelope most likely result from time variations in the infrared pumping rates. We analyze the main implications this discovery has on the interpretation of molecular line emission in the envelopes of Mira-type stars. Radiative transfer calculations must take into account both the time variability of infrared pumping and the possible variation of the dust and gas temperatures with stellar phase in order to reproduce the observation of molecular lines at different epochs. The effect of gas temperature variations with stellar phase could be particularly important for lines produced in the innermost regions of the envelope. Each layer of the circumstellar envelope sees the stellar light radiation with a different lag time (phase). Our results show that this effect must be included in the models. The submillimeter and far infrared lines of asymptotic giant branch stars can no longer be considered as safe intensity calibrators.

  3. Molecular Line Studies of Ballistic Stellar Interlopers Burrowing through Dense Interstellar Clouds

    Science.gov (United States)

    Rosen, Anna; Sahai, R.; Claussen, M.; Morris, M.

    2010-01-01

    When an intermediate-mass star speeds through a dense interstellar cloud at a high velocity, it can produce a cometary or bow shock structure due to the cloud being impacted by the intense stellar wind. This class of objects, recently discovered in an HST imaging survey, has been dubbed "ballistic stellar interlopers" (Sahai et al. 2009). Using the ARO's 12m and SMT 10m millimeter-wave dishes, we have obtained molecular line emission data towards 10 stellar interloper sources, in order to identify and characterize the dense clouds with which the interlopers are interacting. We have made small "on-the-fly" maps in the 12CO (J=2-1) and 13CO (J=2-1) lines for each cloud, and obtained spectra of high-density tracers such as N2H+ (J=3-2), HCO+ (J=3-2), CN(N=2-1), and SO(J=5-4), which probe a range of physical conditions in the interstellar clouds being impacted by the interlopers. The data have been reduced and analyzed, and preliminary estimates of the cloud temperatures (9-22 K) and 13CO optical depths (0.18-0.37) have been made. The maps, which show the emission as a function of radial velocity and spatial offset from the location of the interlopers, have helped us distinguish between the clouds interacting with the interlopers, and those which are unrelated but happen to lie along the line of sight. These data will now enable us to carry out high-resolution mm-wave interferometric observations of the interlopers in the future. This research was performed at JPL under the Minority Education Initiatives program. RS and MM were funded by a Long Term Space Astrophysics award from NASA for this work. The National Radio Astronomy Observatory is a facility of the National Science Foundation operated under cooperative agreement by Associated Universities, Inc. Special thanks goes to John Bieging and Bill Peters of the Arizona Radio Observatory.

  4. Clustering the Orion B giant molecular cloud based on its molecular emission

    Science.gov (United States)

    Bron, Emeric; Daudon, Chloé; Pety, Jérôme; Levrier, François; Gerin, Maryvonne; Gratier, Pierre; Orkisz, Jan H.; Guzman, Viviana; Bardeau, Sébastien; Goicoechea, Javier R.; Liszt, Harvey; Öberg, Karin; Peretto, Nicolas; Sievers, Albrecht; Tremblin, Pascal

    2018-02-01

    identified, likely related to the higher critical density of the CN and HCO+ (1-0) lines. These distinctions are only possible because the high-density regions are spatially resolved. Conclusions: Molecules are versatile tracers of GMCs because their line intensities bear the signature of the physics and chemistry at play in the gas. The association of simultaneous multi-line, wide-field mapping and powerful machine learning methods such as the Meanshift clustering algorithm reveals how to decode the complex information available in these molecular tracers. Data products associated with this paper are available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/610/A12 and at http://www.iram.fr/ pety/ORION-B

  5. Molecular cytogenetic characterization of a new wheat Secale ...

    Indian Academy of Sciences (India)

    A stable, highly fertile wheat Secale africanum substitution line LF24, derived from the F7 generation of a cross between Mianyang11 (MY11) and Triticum durum, S. africanum amphiploid (YF) was identified through molecular cytogenetic analysis. Application of C-banding, in situ hybridization and molecular markers ...

  6. HIFISTARS Herschel/HIFI observations of VY Canis Majoris. Molecular-line inventory of the envelope around the largest known star

    NARCIS (Netherlands)

    Alcolea, J.; Bujarrabal, V.; Planesas, P.; Teyssier, D.; Cernicharo, J.; De Beck, E.; Decin, L.; Dominik, C.; Justtanont, K.; de Koter, A.; Marston, A.P.; Melnick, G.; Menten, K.M.; Neufeld, D.A.; Olofsson, H.; Schmidt, M.; Schöier, F.L.; Szczerba, R.; Waters, L.B.F.M.

    2013-01-01

    Aims. The study of the molecular gas in the circumstellar envelopes of evolved stars is normally undertaken by observing lines of CO (and other species) in the millimetre-wave domain. In general, the excitation requirements of the observed lines are low at these wavelengths, and therefore these

  7. Sustained productivity in recombinant Chinese Hamster Ovary (CHO) cell lines: proteome analysis of the molecular basis for a process-related phenotype

    LENUS (Irish Health Repository)

    Meleady, Paula

    2011-07-24

    Abstract Background The ability of mammalian cell lines to sustain cell specific productivity (Qp) over the full duration of bioprocess culture is a highly desirable phenotype, but the molecular basis for sustainable productivity has not been previously investigated in detail. In order to identify proteins that may be associated with a sustained productivity phenotype, we have conducted a proteomic profiling analysis of two matched pairs of monoclonal antibody-producing Chinese hamster ovary (CHO) cell lines that differ in their ability to sustain productivity over a 10 day fed-batch culture. Results Proteomic profiling of inherent differences between the two sets of comparators using 2D-DIGE (Difference Gel Electrophoresis) and LC-MS\\/MS resulted in the identification of 89 distinct differentially expressed proteins. Overlap comparisons between the two sets of cell line pairs identified 12 proteins (AKRIB8, ANXA1, ANXA4, EIF3I, G6PD, HSPA8, HSP90B1, HSPD1, NUDC, PGAM1, RUVBL1 and CNN3) that were differentially expressed in the same direction. Conclusion These proteins may have an important role in sustaining high productivity of recombinant protein over the duration of a fed-batch bioprocess culture. It is possible that many of these proteins could be useful for future approaches to successfully manipulate or engineer CHO cells in order to sustain productivity of recombinant protein.

  8. Comparing hair-morphology and molecular methods to identify fecal samples from Neotropical felids.

    Directory of Open Access Journals (Sweden)

    Carlos C Alberts

    Full Text Available To avoid certain problems encountered with more-traditional and invasive methods in behavioral-ecology studies of mammalian predators, such as felids, molecular approaches have been employed to identify feces found in the field. However, this method requires a complete molecular biology laboratory, and usually also requires very fresh fecal samples to avoid DNA degradation. Both conditions are normally absent in the field. To address these difficulties, identification based on morphological characters (length, color, banding, scales and medullar patterns of hairs found in feces could be employed as an alternative. In this study we constructed a morphological identification key for guard hairs of eight Neotropical felids (jaguar, oncilla, Geoffroy's cat, margay, ocelot, Pampas cat, puma and jaguarundi and compared its efficiency to that of a molecular identification method, using the ATP6 region as a marker. For this molecular approach, we simulated some field conditions by postponing sample-conservation procedures. A blind test of the identification key obtained a nearly 70% overall success rate, which we considered equivalent to or better than the results of some molecular methods (probably due to DNA degradation found in other studies. The jaguar, puma and jaguarundi could be unequivocally discriminated from any other Neotropical felid. On a scale ranging from inadequate to excellent, the key proved poor only for the margay, with only 30% of its hairs successfully identified using this key; and have intermediate success rates for the remaining species, the oncilla, Geoffroy's cat, ocelot and Pampas cat, were intermediate. Complementary information about the known distributions of felid populations may be necessary to substantially improve the results obtained with the key. Our own molecular results were even better, since all blind-tested samples were correctly identified. Part of these identifications were made from samples kept in suboptimal

  9. [Analysis of software for identifying spectral line of laser-induced breakdown spectroscopy based on LabVIEW].

    Science.gov (United States)

    Hu, Zhi-yu; Zhang, Lei; Ma, Wei-guang; Yan, Xiao-juan; Li, Zhi-xin; Zhang, Yong-zhi; Wang, Le; Dong, Lei; Yin, Wang-bao; Jia, Suo-tang

    2012-03-01

    Self-designed identifying software for LIBS spectral line was introduced. Being integrated with LabVIEW, the soft ware can smooth spectral lines and pick peaks. The second difference and threshold methods were employed. Characteristic spectrum of several elements matches the NIST database, and realizes automatic spectral line identification and qualitative analysis of the basic composition of sample. This software can analyze spectrum handily and rapidly. It will be a useful tool for LIBS.

  10. Rotational emission-line spectrum of Orion A between 247 and 263 GHZ

    International Nuclear Information System (INIS)

    Blake, G.A.; Sutton, E.C.; Masson, C.R.; Phillips, T.G.

    1986-01-01

    Results are presented from a molecular line survey of the core of the Orion molecular cloud between 247 and 263 GHz. The spectrum contains a total of 243 resolvable lines from 23 different chemical species. When combined with the earlier survey of Orion from 215 to 247 GHz by Sutton et al (1985), the complete data set includes over 780 emission features from 29 distinct molecules. Of the 23 molecules detected in this survey, only NO, CCH, and HCO + were identified not in the lower frequency data

  11. A Sclerostin super-producer cell line derived from the human cell line SaOS-2: a new tool for the study of the molecular mechanisms driving Sclerostin expression.

    Science.gov (United States)

    Pérez-Campo, Flor M; Sañudo, Carolina; Delgado-Calle, Jesús; Arozamena, Jana; Zarrabeitia, María T; Riancho, José A

    2014-08-01

    Sclerostin, the product of the SOST gene, is a key regulator of bone homeostasis. Sclerostin interferes with the Wnt signalling pathway and, therefore, has a negative effect on bone formation. Although the importance of sclerostin in bone homeostasis is well established, many aspects of its biology are still unknown. Due to its restricted pattern of expression, in vitro studies of SOST gene regulation are technically challenging. Furthermore, a more profound investigation of the molecular mechanism controlling sclerostin expression has been hampered by the lack of a good human in vitro model. Here, we describe two cell lines derived from the human osteosarcoma cell line SaOS-2 that produce elevated levels of sclerostin. Analysis of the super-producer cell lines showed that sclerostin levels were still reduced in response to parathyroid hormone treatment or in response to mechanical loading, indicating that these regulatory mechanisms were not affected in the presented cell lines. In addition, we did not find differences between the promoter or ECR5 sequences of our clones and the SaOS-2 parental line. However, the methylation of the proximal CpG island located at the SOST promoter was lower in the super-producer clones, in agreement with a higher level of SOST transcription. Although the underlying biological causes of the elevated levels of sclerostin production in this cell line are not yet clear, we believe that it could be an extremely useful tool to study the molecular mechanisms driving sclerostin expression in humans.

  12. Development of a new marker system for identifying the complex members of the low-molecular-weight glutenin subunit gene family in bread wheat (Triticum aestivum L.).

    Science.gov (United States)

    Zhang, Xiaofei; Liu, Dongcheng; Yang, Wenlong; Liu, Kunfan; Sun, Jiazhu; Guo, Xiaoli; Li, Yiwen; Wang, Daowen; Ling, Hongqing; Zhang, Aimin

    2011-05-01

    Low-molecular-weight glutenin subunits (LMW-GSs) play an important role in determining the bread-making quality of bread wheat. However, LMW-GSs display high polymorphic protein complexes encoded by multiple genes, and elucidating the complex LMW-GS gene family in bread wheat remains challenging. In the present study, using conventional polymerase chain reaction (PCR) with conserved primers and high-resolution capillary electrophoresis, we developed a new molecular marker system for identifying LMW-GS gene family members. Based on sequence alignment of 13 LMW-GS genes previously identified in the Chinese bread wheat variety Xiaoyan 54 and other genes available in GenBank, PCR primers were developed and assigned to conserved sequences spanning the length polymorphism regions of LMW-GS genes. After PCR amplification, 17 DNA fragments in Xiaoyan 54 were detected using capillary electrophoresis. In total, 13 fragments were identical to previously identified LMW-GS genes, and the other 4 were derived from unique LMW-GS genes by sequencing. This marker system was also used to identify LMW-GS genes in Chinese Spring and its group 1 nulli-tetrasomic lines. Among the 17 detected DNA fragments, 4 were located on chromosome 1A, 5 on 1B, and 8 on 1D. The results suggest that this marker system is useful for large-scale identification of LMW-GS genes in bread wheat varieties, and for the selection of desirable LMW-GS genes to improve the bread-making quality in wheat molecular breeding programmes.

  13. A signature of the intermittency of interstellar turbulence - The wings of molecular line profiles

    International Nuclear Information System (INIS)

    Falgarone, E.; Phillips, T.G.

    1990-01-01

    Ensembles of line profiles of molecular clouds are presented, and it is shown that most of the profiles can be fitted by a strong and narrow Gaussian plus a weak and broad Gaussian. The remarkably self-similar scaling of the wing widths to that of the cores is shown and the available information on the density and velocity structure of the fast gas is discussed. It is shown that the line wings can be used as tracers of the probability distribution of the projected velocity field within the cloud volume sampled by the profile. The statistical properties of this distribution are compared with that of the velocity in atmospheric turbulence and recent duct flow measurements. 62 refs

  14. Integrative genome-wide expression profiling identifies three distinct molecular subgroups of renal cell carcinoma with different patient outcome

    Directory of Open Access Journals (Sweden)

    Beleut Manfred

    2012-07-01

    Full Text Available Abstract Background Renal cell carcinoma (RCC is characterized by a number of diverse molecular aberrations that differ among individuals. Recent approaches to molecularly classify RCC were based on clinical, pathological as well as on single molecular parameters. As a consequence, gene expression patterns reflecting the sum of genetic aberrations in individual tumors may not have been recognized. In an attempt to uncover such molecular features in RCC, we used a novel, unbiased and integrative approach. Methods We integrated gene expression data from 97 primary RCC of different pathologic parameters, 15 RCC metastases as well as 34 cancer cell lines for two-way nonsupervised hierarchical clustering using gene groups suggested by the PANTHER Classification System. We depicted the genomic landscape of the resulted tumor groups by means of Single Nuclear Polymorphism (SNP technology. Finally, the achieved results were immunohistochemically analyzed using a tissue microarray (TMA composed of 254 RCC. Results We found robust, genome wide expression signatures, which split RCC into three distinct molecular subgroups. These groups remained stable even if randomly selected gene sets were clustered. Notably, the pattern obtained from RCC cell lines was clearly distinguishable from that of primary tumors. SNP array analysis demonstrated differing frequencies of chromosomal copy number alterations among RCC subgroups. TMA analysis with group-specific markers showed a prognostic significance of the different groups. Conclusion We propose the existence of characteristic and histologically independent genome-wide expression outputs in RCC with potential biological and clinical relevance.

  15. A systems biology strategy to identify molecular mechanisms of action and protein indicators of traumatic brain injury.

    Science.gov (United States)

    Yu, Chenggang; Boutté, Angela; Yu, Xueping; Dutta, Bhaskar; Feala, Jacob D; Schmid, Kara; Dave, Jitendra; Tawa, Gregory J; Wallqvist, Anders; Reifman, Jaques

    2015-02-01

    The multifactorial nature of traumatic brain injury (TBI), especially the complex secondary tissue injury involving intertwined networks of molecular pathways that mediate cellular behavior, has confounded attempts to elucidate the pathology underlying the progression of TBI. Here, systems biology strategies are exploited to identify novel molecular mechanisms and protein indicators of brain injury. To this end, we performed a meta-analysis of four distinct high-throughput gene expression studies involving different animal models of TBI. By using canonical pathways and a large human protein-interaction network as a scaffold, we separately overlaid the gene expression data from each study to identify molecular signatures that were conserved across the different studies. At 24 hr after injury, the significantly activated molecular signatures were nonspecific to TBI, whereas the significantly suppressed molecular signatures were specific to the nervous system. In particular, we identified a suppressed subnetwork consisting of 58 highly interacting, coregulated proteins associated with synaptic function. We selected three proteins from this subnetwork, postsynaptic density protein 95, nitric oxide synthase 1, and disrupted in schizophrenia 1, and hypothesized that their abundance would be significantly reduced after TBI. In a penetrating ballistic-like brain injury rat model of severe TBI, Western blot analysis confirmed our hypothesis. In addition, our analysis recovered 12 previously identified protein biomarkers of TBI. The results suggest that systems biology may provide an efficient, high-yield approach to generate testable hypotheses that can be experimentally validated to identify novel mechanisms of action and molecular indicators of TBI. © 2014 The Authors. Journal of Neuroscience Research Published by Wiley Periodicals, Inc.

  16. VizieR Online Data Catalog: Sgr B2 los molecular absorption line spectra (Corby+, 2018)

    Science.gov (United States)

    Corby, J. F.; McGuire, B. A.; Herbst, E.; Remijan, A. J.

    2017-11-01

    Spectra covering transitions of c-C3H2, c-H1 SO, CCS, H2CS, HCS+, OH, SiO, 29SiO, H2CO, H2(13C)O, l-C3H, and l-C3H+ with line-of-sight absorption observed in the 1-50 GHz data from the PRebiotic Interstellar MOlecular Survey (PRIMOS) taken with the Robert C. Byrd Green Bank Telescope (GBT). Data were observed between 2001 and 2014, with the majority of the data obtained in 2007 in GBT Key Science project ID GBT07A-051. Spectra have been baseline-subtracted using best fit polynomials as described in the paper, and normalized by the continuum, so that the y-axis represents (T/TC-1). Data are provided in the FITS format; each FITS file contains all lines of a single molecule that are observed to have foreground absorption. Please refer to Table 1 of the paper to obtain molecular transition rest frequencies, energies, GBT beam sizes, and transition quantum numbers. (2 data files).

  17. Genomic analyses identify molecular subtypes of pancreatic cancer.

    Science.gov (United States)

    Bailey, Peter; Chang, David K; Nones, Katia; Johns, Amber L; Patch, Ann-Marie; Gingras, Marie-Claude; Miller, David K; Christ, Angelika N; Bruxner, Tim J C; Quinn, Michael C; Nourse, Craig; Murtaugh, L Charles; Harliwong, Ivon; Idrisoglu, Senel; Manning, Suzanne; Nourbakhsh, Ehsan; Wani, Shivangi; Fink, Lynn; Holmes, Oliver; Chin, Venessa; Anderson, Matthew J; Kazakoff, Stephen; Leonard, Conrad; Newell, Felicity; Waddell, Nick; Wood, Scott; Xu, Qinying; Wilson, Peter J; Cloonan, Nicole; Kassahn, Karin S; Taylor, Darrin; Quek, Kelly; Robertson, Alan; Pantano, Lorena; Mincarelli, Laura; Sanchez, Luis N; Evers, Lisa; Wu, Jianmin; Pinese, Mark; Cowley, Mark J; Jones, Marc D; Colvin, Emily K; Nagrial, Adnan M; Humphrey, Emily S; Chantrill, Lorraine A; Mawson, Amanda; Humphris, Jeremy; Chou, Angela; Pajic, Marina; Scarlett, Christopher J; Pinho, Andreia V; Giry-Laterriere, Marc; Rooman, Ilse; Samra, Jaswinder S; Kench, James G; Lovell, Jessica A; Merrett, Neil D; Toon, Christopher W; Epari, Krishna; Nguyen, Nam Q; Barbour, Andrew; Zeps, Nikolajs; Moran-Jones, Kim; Jamieson, Nigel B; Graham, Janet S; Duthie, Fraser; Oien, Karin; Hair, Jane; Grützmann, Robert; Maitra, Anirban; Iacobuzio-Donahue, Christine A; Wolfgang, Christopher L; Morgan, Richard A; Lawlor, Rita T; Corbo, Vincenzo; Bassi, Claudio; Rusev, Borislav; Capelli, Paola; Salvia, Roberto; Tortora, Giampaolo; Mukhopadhyay, Debabrata; Petersen, Gloria M; Munzy, Donna M; Fisher, William E; Karim, Saadia A; Eshleman, James R; Hruban, Ralph H; Pilarsky, Christian; Morton, Jennifer P; Sansom, Owen J; Scarpa, Aldo; Musgrove, Elizabeth A; Bailey, Ulla-Maja Hagbo; Hofmann, Oliver; Sutherland, Robert L; Wheeler, David A; Gill, Anthony J; Gibbs, Richard A; Pearson, John V; Waddell, Nicola; Biankin, Andrew V; Grimmond, Sean M

    2016-03-03

    Integrated genomic analysis of 456 pancreatic ductal adenocarcinomas identified 32 recurrently mutated genes that aggregate into 10 pathways: KRAS, TGF-β, WNT, NOTCH, ROBO/SLIT signalling, G1/S transition, SWI-SNF, chromatin modification, DNA repair and RNA processing. Expression analysis defined 4 subtypes: (1) squamous; (2) pancreatic progenitor; (3) immunogenic; and (4) aberrantly differentiated endocrine exocrine (ADEX) that correlate with histopathological characteristics. Squamous tumours are enriched for TP53 and KDM6A mutations, upregulation of the TP63∆N transcriptional network, hypermethylation of pancreatic endodermal cell-fate determining genes and have a poor prognosis. Pancreatic progenitor tumours preferentially express genes involved in early pancreatic development (FOXA2/3, PDX1 and MNX1). ADEX tumours displayed upregulation of genes that regulate networks involved in KRAS activation, exocrine (NR5A2 and RBPJL), and endocrine differentiation (NEUROD1 and NKX2-2). Immunogenic tumours contained upregulated immune networks including pathways involved in acquired immune suppression. These data infer differences in the molecular evolution of pancreatic cancer subtypes and identify opportunities for therapeutic development.

  18. Molecular analysis of primary gastric cancer, corresponding xenografts, and 2 novel gastric carcinoma cell lines reveals novel alterations in gastric carcinogenesis

    NARCIS (Netherlands)

    Milne, Anya N. A.; Sitarz, Robert; Carvalho, Ralph; Polak, Mirjam M.; Ligtenberg, Madolijn; Pauwels, Patrick; Offerhaus, G. Johan A.; Weterman, Marian A. J.

    2007-01-01

    We report the molecular characterization of 8 primary gastric carcinomas, corresponding xenografts, and 2 novel gastric carcinoma cell lines. We compared the tumors and cell lines, with respect to histology, immunohistochemistry, copy number, and hypermethylation of up to 38 genes using

  19. Using Genetic Buffering Relationships Identified in Fission Yeast To Elucidate the Molecular Pathology of Tuberous Sclerosis

    Science.gov (United States)

    2016-07-01

    tsc1 and tsc2 loss of function mutations in Schizosaccharomyces pombe. Northeast Regional Yeast Meeting, June 16-17, University at Buffalo, The State...AWARD NUMBER: W81XWH-14-1-0169 TITLE: Using Genetic Buffering Relationships Identified in Fission Yeast To Elucidate the Molecular Pathology of...SUBTITLE Using Genetic Buffering Relationships Identified in Fission 5a. CONTRACT NUMBER W81XWH-14-1-0169 Yeast to Elucidate the Molecular Pathology

  20. Genome-wide methylation analysis identifies genes silenced in non-seminoma cell lines.

    Science.gov (United States)

    Noor, Dzul Azri Mohamed; Jeyapalan, Jennie N; Alhazmi, Safiah; Carr, Matthew; Squibb, Benjamin; Wallace, Claire; Tan, Christopher; Cusack, Martin; Hughes, Jaime; Reader, Tom; Shipley, Janet; Sheer, Denise; Scotting, Paul J

    2016-01-01

    Silencing of genes by DNA methylation is a common phenomenon in many types of cancer. However, the genome-wide effect of DNA methylation on gene expression has been analysed in relatively few cancers. Germ cell tumours (GCTs) are a complex group of malignancies. They are unique in developing from a pluripotent progenitor cell. Previous analyses have suggested that non-seminomas exhibit much higher levels of DNA methylation than seminomas. The genomic targets that are methylated, the extent to which this results in gene silencing and the identity of the silenced genes most likely to play a role in the tumours' biology have not yet been established. In this study, genome-wide methylation and expression analysis of GCT cell lines was combined with gene expression data from primary tumours to address this question. Genome methylation was analysed using the Illumina infinium HumanMethylome450 bead chip system and gene expression was analysed using Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays. Regulation by methylation was confirmed by demethylation using 5-aza-2-deoxycytidine and reverse transcription-quantitative PCR. Large differences in the level of methylation of the CpG islands of individual genes between tumour cell lines correlated well with differential gene expression. Treatment of non-seminoma cells with 5-aza-2-deoxycytidine verified that methylation of all genes tested played a role in their silencing in yolk sac tumour cells and many of these genes were also differentially expressed in primary tumours. Genes silenced by methylation in the various GCT cell lines were identified. Several pluripotency-associated genes were identified as a major functional group of silenced genes.

  1. Murine transgenic embryonic stem cell lines for the investigation of sinoatrial node-related molecular pathways

    Directory of Open Access Journals (Sweden)

    Stefanie Schmitteckert

    2017-12-01

    Full Text Available The elucidation of molecular mechanisms that restrict the potential of pluripotent stem cells and promote cardiac lineage differentiation is of crucial relevance, since embryonic stem cells (ESCs hold great potential for cell based heart therapies. The homeodomain transcription factor Shox2 is essential for the development and proper function of the native cardiac pacemaker, the sinoatrial node. This prompted us to develop a cardiac differentiation model using ESC lines isolated from blastocysts of Shox2-deficient mice. The established cell model provides a fundamental basis for the investigation of molecular pathways under physiological and pathophysiological conditions for evaluating novel therapeutic approaches.

  2. Molecular cytogenetic characterization of a human thyroid cancercell line

    Energy Technology Data Exchange (ETDEWEB)

    Weier, Heinz-Ulrich G.; Tuton, Tiffany B.; Ito, Yuko; Chu, LisaW.; Lu, Chung-Mei; Baumgartner, Adolf; Zitzelsberger, Horst F.; Weier,Jingly F.

    2006-01-04

    The incidence of papillary thyroid carcinoma (PTC) increases significantly after exposure of the head and neck region to ionizing radiation, yet we know neither the steps involved in malignant transformation of thyroid epithelium nor the specific carcinogenic mode of action of radiation. Such increased tumor frequency became most evident in children after the 1986 nuclear accident in Chernobyl, Ukraine. In the twelve years following the accident, the average incidence of childhood PTCs (chPTC) increased over one hundred-fold compared to the rate of about 1 tumor incidence per 10{sup 6} children per year prior to 1986. To study the etiology of radiation-induced thyroid cancer, we formed an international consortium to investigate chromosomal changes and altered gene expression in cases of post-Chernobyl chPTC. Our approach is based on karyotyping of primary cultures established from chPTC specimens, establishment of cell lines and studies of genotype-phenotype relationships through high resolution chromosome analysis, DNA/cDNA micro-array studies, and mouse xenografts that test for tumorigenicity. Here, we report the application of fluorescence in situ hybridization (FISH)-based techniques for the molecular cytogenetic characterization of a highly tumorigenic chPTC cell line, S48TK, and its subclones. Using chromosome 9 rearrangements as an example, we describe a new approach termed ''BAC-FISH'' to rapidly delineate chromosomal breakpoints, an important step towards a better understanding of the formation of translocations and their functional consequences.

  3. MOLECULAR LINE OBSERVATIONS OF THE CARBON-RICH CIRCUMSTELLAR ENVELOPE CIT 6 AT 7 mm WAVELENGTHS

    Energy Technology Data Exchange (ETDEWEB)

    Chau, Wayne; Zhang Yong; Nakashima, Jun-ichi; Kwok, Sun [Department of Physics, University of Hong Kong (Hong Kong); Deguchi, Shuji [Nobeyama Radio Observatory, National Astronomical Observatory, Minamimaki, Minamisaku, Nagano 384-1305 (Japan)

    2012-11-20

    We present a {lambda}7 mm spectral line survey of the carbon-rich circumstellar envelope (CSE) CIT 6 using the 45 m telescope at the Nobeyama Radio Observatory. A total of 25 spectral features belonging to five molecular species (HC{sub 3}N, HC{sub 5}N, HC{sub 7}N, SiO, and CS) are detected, enabling us to investigate the chemistry of cyanopolyyne chains. The line strengths are compared with those of the proto-typical carbon-rich CSE IRC+10216. The results show that the cyanopolyyne molecules are enhanced in CIT 6, suggesting that it is more evolved than IRC+10216. In order to investigate the structure of CIT 6, we have constructed a three-dimensional spatiokinematic model. By comparing the observed line profiles with the models, we conclude that this envelope is asymmetric and is composed of several incomplete shells.

  4. On the effects of rotation on interstellar molecular line profiles

    International Nuclear Information System (INIS)

    Adelson, L.M.; Chunming Leung

    1988-01-01

    Theoretical models are constructed to study the effects of systematic gas rotation on the emergent profiles of interstellar molecular lines, in particular the effects of optical depth and different velocity laws. Both rotational and radial motions (expansion or contraction) may produce similar asymmetric profiles, but the behaviour of the velocity centroid of the emergent profile over the whole cloud (iso-centroid maps) can be used to distinguish between these motions. Iso-centroid maps can also be used to determine the location and orientation of the rotation axis and of the equatorial axis. For clouds undergoing both radial and rotational motion, the component of the centroid due to the rotational motion can be separated from that due to the radial motion. Information on the form of the rotational velocity law can also be derived. (author)

  5. Cortical GABA markers identify a molecular subtype of psychotic and bipolar disorders.

    Science.gov (United States)

    Volk, D W; Sampson, A R; Zhang, Y; Edelson, J R; Lewis, D A

    2016-09-01

    Deficits in gamma aminobutyric acid (GABA) neuron-related markers, including the GABA-synthesizing enzyme GAD67, the calcium-binding protein parvalbumin, the neuropeptide somatostatin, and the transcription factor Lhx6, are most pronounced in a subset of schizophrenia subjects identified as having a 'low GABA marker' (LGM) molecular phenotype. Furthermore, schizophrenia shares degrees of genetic liability, clinical features and cortical circuitry abnormalities with schizoaffective disorder and bipolar disorder. Therefore, we determined the extent to which a similar LGM molecular phenotype may also exist in subjects with these disorders. Transcript levels for GAD67, parvalbumin, somatostatin, and Lhx6 were quantified using quantitative PCR in prefrontal cortex area 9 of 184 subjects with a diagnosis of schizophrenia (n = 39), schizoaffective disorder (n = 23) or bipolar disorder (n = 35), or with a confirmed absence of any psychiatric diagnoses (n = 87). A blinded clustering approach was employed to determine the presence of a LGM molecular phenotype across all subjects. Approximately 49% of the subjects with schizophrenia, 48% of the subjects with schizoaffective disorder, and 29% of the subjects with bipolar disorder, but only 5% of unaffected subjects, clustered in the cortical LGM molecular phenotype. These findings support the characterization of psychotic and bipolar disorders by cortical molecular phenotype which may help elucidate more pathophysiologically informed and personalized medications.

  6. Submillimeter and far-infrared line observations of M17 SW - A clumpy molecular cloud penetrated by ultraviolet radiation

    Science.gov (United States)

    Stutzki, J.; Genzel, R.; Harris, A. I.; Stacey, G. J.; Jaffe, D. T.

    1988-01-01

    Millimeter, submillimeter, and far-IR spectroscopic observations of the M17 SW star formation region are reported. Strong forbidden C II 158 micron and CO J = 7 - 6 line emission arises in an H II region/molecular cloud interface of several pc thickness. Weaker forbidden C II emission appears to be extended over 15 pc throughout the molecular cloud. CO J = 14 - 13 and forbidden O I 145 micron spectra indicate high temperatures and densities for both molecular and atomic gas in the interface. The results require the molecular cloud near the interface to be clumpy or filamentary. The extended forbidden C II emission throughout the molecular cloud has a level around 20 times higher than expected from a single molecular cloud interface exposed to an ultraviolet radiation field typical of the solar neighborhood. The high gas temperature of molecular material in the UV-illuminated interface region suggests that CO self-shielding and heating of CO by photoelectrons are important.

  7. Rings of Molecular Line Emission in the Disk Orbiting the Young, Close Binary V4046 Sgr

    Science.gov (United States)

    Dickson-Vandervelde, Dorothy; Kastner, Joel H.; Qi, C.; Forveille, Thierry; Hily-Blant, Pierre; Oberg, Karin; Wilner, David; Andrews, Sean; Gorti, Uma; Rapson, Valerie; Sacco, Germano; Principe, David

    2018-01-01

    We present analysis of a suite of subarcsecond ALMA Band 6 (1.1 - 1.4 mm) molecular line images of the circumbinary, protoplanetary disk orbiting V4046 Sgr. The ~20 Myr-old V4046 Sgr system, which lies a mere ~73 pc from Earth, consists of a close (separation ~10 Rsun) pair of roughly solar-mass stars that are orbited by a gas-rich crcumbinary disk extending to ~350 AU in radius. The ALMA images reveal that the molecules CO and HCN and their isotopologues display centrally peaked surface brightness morphologies, whereas the cyanide group molecules (HC3N, CH3CN), deuterated molecules (DCN, DCO+), hydrocarbons (as traced by C2H), and potential CO ice line tracers (N2H+, and H2CO) appear as a sequence of sharp and diffuse rings of increasing radii. The characteristic sizes of these molecular emission rings, which range from ~25 to >100 AU in radius, are evident in radial emission-line surface brightness profiles extracted from the deprojected disk images. We find that emission from 13CO emission transitions from optically thin to thick within ~50 AU, whereas C18O emission remains optically thin within this radius. We summarize the insight into the physical and chemical processes within this evolved protoplanetary disk that can be obtained from comparisons of the various emission-line morphologies with each other and with that of the continuum (large-grain) emission on size scales of tens of AU.This research is supported by NASA Exoplanets program grant NNX16AB43G to RIT

  8. Fast neutron radiation induced Glu-B1 deficient lines of an elite bread wheat variety

    Science.gov (United States)

    Five isogenic wheat lines deficient in high-molecular weight subunit (HMW-GS) proteins encoded by the B-genome were identified from a fast-neutron radiation-mutagenized population of Summit, an elite variety of bread wheat (Triticum aestivum L.). The mutant lines differ from the wild-type progenit...

  9. The constancy of the ratio of the molecular hydrogen lines at 3.8 μm in Orion

    International Nuclear Information System (INIS)

    Brand, P.W.J.L.; Toner, M.P.; Williams, P.M.; Burton, M.G.

    1989-01-01

    The 1-0 O(7) and O-O S(13) lines of H 2 , at 3.807 and 3.846 μm, have been mapped over the region of the Orion molecular outflow. The intensity ratio of these lines is found to be independent of position in the outflow. From this it is inferred that the structure of the shocks and their cooling flows in Orion may be more akin to hydrodynamic shocks than the low-temperature C-shocks that are currently favoured. (author)

  10. On-line method to identify control rod drops in Pressurized Water Reactors

    International Nuclear Information System (INIS)

    Souza, T.J.; Martinez, A.S.; Medeiros, J.A.C.C.; Palma, D.A.P.; Gonçalves, A.C.

    2014-01-01

    Highlights: • On-line method to identify control rod drops in PWR reactors. • Identification method based on the readings of the ex-core detector. • Recognition of the patterns in the ex-core detector responses. - Abstract: A control rod drop event in PWR reactors leads to an unsafe operating condition. It is important to quickly identify the rod to minimise undesirable effects in such a scenario. The goal of this work is to develop an online method to identify control rod drops in PWR reactors. The method entails the construction of a tool based on ex-core detector responses. It proposes to recognize patterns in the neutron ex-core detectors responses and thus to make an online identification of a control rod drop in the core during the reactor operation. The results of the study, as well as the behaviour of the detector responses demonstrated the feasibility of this method

  11. Molecular Line Survey of CRL618 and Complete Modeling

    Science.gov (United States)

    Pardo, J. R.; Cernicharo, J.; Goicoechea, J. R.; Phillips, T. G.

    We present a complete survey and model of the emission from the C-rich protoplanetary nebula CRL 618 at the frequencies accessible with the IRAM-30m telescope (80.25-115.75 GHz, 131.25-179.25 GHz, and 204.25-275.25 GHz) and some results of still on-going observations at the Caltech Submillimeter Observatory (280-360 GHz). Although the number of lines detected is large (several hundreds), the number of chemical species from which they arise is rather small. In fact, lines from cyanopolyynes HC3N and HC5N dominate by far the long-wave spectrum of CRL618, with detection of numerous vibrationally excited states and isotopic substituted species. Most of detected species exhibit P-Cygni profiles at the lowest frequencies (3 mm window), and they evolve to pure emission as frequency increases. This fact can only be explained by the behavior of the continuum emission arising from the inner ultracompact HII region and surrounding dust. The data set itself has been used to characterize the continuum emission by averaging all the continuum measurements during the time span of the survey (~8 years). The physical parameters of the different gas regions have been established by studying the large number of detected cyanopolyynes lines. Using these constraints, the abundances of many other species relative to HC3N could also be determined and a general model, that reproduce the whole data set at a very detailed level of agreement, could be built. 1. Introduction The motivation to perform the complete millimeter line survey presented here with the IRAM-30m telescope has been to gather the most complete information on the molecular content in one particular stage (protoplanetary nebula, PPNe) of stellar evolution from the Asymptotic Giant Branch (AGB) to Planetary Nebulae (PN), of which CRL618 is the best example. Its chemical richness and its complex morphology are now very well known. Detailed chemical models for this object have been developed (Cernicharo 2004) indicating the

  12. Molecular conservation of estrogen-response associated with cell cycle regulation, hormonal carcinogenesis and cancer in zebrafish and human cancer cell lines

    Directory of Open Access Journals (Sweden)

    Govindarajan Kunde R

    2011-05-01

    Full Text Available Abstract Background The zebrafish is recognized as a versatile cancer and drug screening model. However, it is not known whether the estrogen-responsive genes and signaling pathways that are involved in estrogen-dependent carcinogenesis and human cancer are operating in zebrafish. In order to determine the potential of zebrafish model for estrogen-related cancer research, we investigated the molecular conservation of estrogen responses operating in both zebrafish and human cancer cell lines. Methods Microarray experiment was performed on zebrafish exposed to estrogen (17β-estradiol; a classified carcinogen and an anti-estrogen (ICI 182,780. Zebrafish estrogen-responsive genes sensitive to both estrogen and anti-estrogen were identified and validated using real-time PCR. Human homolog mapping and knowledge-based data mining were performed on zebrafish estrogen responsive genes followed by estrogen receptor binding site analysis and comparative transcriptome analysis with estrogen-responsive human cancer cell lines (MCF7, T47D and Ishikawa. Results Our transcriptome analysis captured multiple estrogen-responsive genes and signaling pathways that increased cell proliferation, promoted DNA damage and genome instability, and decreased tumor suppressing effects, suggesting a common mechanism for estrogen-induced carcinogenesis. Comparative analysis revealed a core set of conserved estrogen-responsive genes that demonstrate enrichment of estrogen receptor binding sites and cell cycle signaling pathways. Knowledge-based and network analysis led us to propose that the mechanism involving estrogen-activated estrogen receptor mediated down-regulation of human homolog HES1 followed by up-regulation cell cycle-related genes (human homologs E2F4, CDK2, CCNA, CCNB, CCNE, is highly conserved, and this mechanism may involve novel crosstalk with basal AHR. We also identified mitotic roles of polo-like kinase as a conserved signaling pathway with multiple entry

  13. 'Ogura'-based 'CMS' lines with different nuclear backgrounds of cabbage revealed substantial diversity at morphological and molecular levels.

    Science.gov (United States)

    Parkash, Chander; Kumar, Sandeep; Singh, Rajender; Kumar, Ajay; Kumar, Satish; Dey, Shyam Sundar; Bhatia, Reeta; Kumar, Raj

    2018-01-01

    A comprehensive study on characterization and genetic diversity analysis was carried out in 16 'Ogura'-based 'CMS' lines of cabbage using 14 agro-morphological traits and 29 SSR markers. Agro-morphological characterization depicted considerable variations for different horticultural traits studied. The genotype, ZHA-2, performed better for most of the economically important quantitative traits. Further, gross head weight (0.76), head length (0.60) and head width (0.83) revealed significant positive correlation with net head weight. Dendrogram based on 10 quantitative traits exhibited considerable diversity among different CMS lines and principle component analysis (PCA) indicated that net and gross head weight, and head length and width are the main components of divergence between 16 CMS lines of cabbage. In molecular study, a total of 58 alleles were amplified by 29 SSR primers, averaging to 2.0 alleles in each locus. High mean values of Shannon's Information index (0.62), expected (0.45) and observed (0.32) heterozygosity and polymorphic information content (0.35) depicted substantial polymorphism. Dendrogram based on Jaccard's similarity coefficient constructed two major groups and eight sub-groups, which revealed substantial diversity among different CMS lines. In overall, based on agro-morphological and molecular studies genotype RRMA, ZHA-2 and RCA were found most divergent. Hence, they have immense potential in future breeding programs for the high-yielding hybrid development in cabbage.

  14. A COUP-TFII Human Embryonic Stem Cell Reporter Line to Identify and Select Atrial Cardiomyocytes

    NARCIS (Netherlands)

    Schwach, Verena; Verkerk, Arie O.; Mol, Mervyn; Monshouwer-Kloots, Jantine J.; Devalla, Harsha D.; Orlova, Valeria V.; Anastassiadis, Konstantinos; Mummery, Christine L.; Davis, Richard P.; Passier, Robert

    2017-01-01

    Reporter cell lines have already proven valuable in identifying, tracking, and purifying cardiac subtypes and progenitors during differentiation of human pluripotent stem cells (hPSCs). We previously showed that chick ovalbumin upstream promoter transcription factor II (COUP-TFII) is highly enriched

  15. Cell lines authentication and mycoplasma detection as minimun quality control of cell lines in biobanking.

    Science.gov (United States)

    Corral-Vázquez, C; Aguilar-Quesada, R; Catalina, P; Lucena-Aguilar, G; Ligero, G; Miranda, B; Carrillo-Ávila, J A

    2017-06-01

    Establishment of continuous cell lines from human normal and tumor tissues is an extended and useful methodology for molecular characterization of cancer pathophysiology and drug development in research laboratories. The exchange of these cell lines between different labs is a common practice that can compromise assays reliability due to contamination with microorganism such as mycoplasma or cells from different flasks that compromise experiment reproducibility and reliability. Great proportions of cell lines are contaminated with mycoplasma and/or are replaced by cells derived for a different origin during processing or distribution process. The scientific community has underestimated this problem and thousand of research experiment has been done with cell lines that are incorrectly identified and wrong scientific conclusions have been published. Regular contamination and authentication tests are necessary in order to avoid negative consequences of widespread misidentified and contaminated cell lines. Cell banks generate, store and distribute cell lines for research, being mandatory a consistent and continuous quality program. Methods implementation for guaranteeing both, the absence of mycoplasma and authentication in the supplied cell lines, has been performed in the Andalusian Health System Biobank. Specifically, precise results were obtained using real time PCR detection for mycoplasma and 10 STRs identification by capillary electrophoresis for cell line authentication. Advantages and disadvantages of these protocols are discussed.

  16. Analysis of genetic diversity among rapeseed cultivars and breeding lines by srap and ssr molecular markers

    International Nuclear Information System (INIS)

    Channa, S.A.; Tian, H.

    2016-01-01

    The knowledge of genetic diversity is very important for developing new rapeseed (Brassica napus L.) cultivars. The genetic diversity among 77 rapeseed accessions, including 22 varieties and 55 advanced breeding lines were analyzed by 47 sequence-related amplified polymorphism (SRAP) and 56 simple sequence repeat (SSR) primers. A total of 270 SRAP and 194 SSR polymorphic fragments were detected with an average of 5.74 and 3.46 for SRAP and SSR primer, respectively. The cluster analysis grouped the 77 accessions into five major clusters. Cluster I contained spring and winter type varieties from Czech Republic and semi-winter varieties and their respective breeding lines from China. The 16 elite breeding lines discovered in Cluster II, III, IV and V indicated higher genetic distance than accessions in Cluster I. The principal component analysis and structure analysis exhibited similar results to the cluster analysis. Analysis of molecular variance revealed that genetic diversity of the selected breeding lines was comparable to the rapeseed varieties, and variation among varieties and lines was significant. The diverse and unique group of 16 elite breeding lines detected in this study can be utilized in the future breeding program as a source for development of commercial varieties with more desirable characters. (author)

  17. Muscle Insertion Line as a Simple Landmark To Identify the Transverse Sinus When Neuronavigation Is Unavailable.

    Science.gov (United States)

    Kivelev, Juri; Kivisaari, Riku; Niemelä, Mika; Hernesniemi, Juha

    2016-10-01

    Skull opening in occipital and suboccipital regions might be associated with risk of damage to the transverse venous sinus and the confluence of sinuses. We analyze the value of magnetic resonance (MR) imaging in localizing the venous sinuses in relation to the superior muscle insertion line (MIL) on the occipital bone. We retrospectively analyzed head MR images of 100 consecutive patients imaged for any reason from 1 January 2013. All MR images were interpreted by a radiologist (R.K.). The superior MIL was identified at the midline and on both midpupillar lines, which represent the most frequent sites of skin incision and craniotomy (median and lateral suboccipital craniotomy, respectively). Patients comprised 56 women (56%) and 44 men (44%). Their mean age was 54 (range 18-84) years. The muscles of the posterior skull were readily visible and clearly identified in both T1 and T2 images of all patients. Identification of the insertion zone and its relation to the venous structures was most readily made in the sagittal plane. We found that the upper muscle insertion line on occipital bone corresponds to the underlying venous sinus and can be used as a reliable anatomic landmark. We identified it in 100% of preoperative MR images of heads with an intact occiput. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. Molecular gas in the Herschel-selected strongly lensed submillimeter galaxies at z 2-4 as probed by multi-J CO lines

    Science.gov (United States)

    Yang, C.; Omont, A.; Beelen, A.; Gao, Y.; van der Werf, P.; Gavazzi, R.; Zhang, Z.-Y.; Ivison, R.; Lehnert, M.; Liu, D.; Oteo, I.; González-Alfonso, E.; Dannerbauer, H.; Cox, P.; Krips, M.; Neri, R.; Riechers, D.; Baker, A. J.; Michałowski, M. J.; Cooray, A.; Smail, I.

    2017-12-01

    We present the IRAM-30 m observations of multiple-J CO (Jup mostly from 3 up to 8) and [C I](3P2 → 3P1) ([C I](2-1) hereafter) line emission in a sample of redshift 2-4 submillimeter galaxies (SMGs). These SMGs are selected among the brightest-lensed galaxies discovered in the Herschel-Astrophysical Terahertz Large Area Survey (H-ATLAS). Forty-seven CO lines and 7 [C I](2-1) lines have been detected in 15 lensed SMGs. A non-negligible effect of differential lensing is found for the CO emission lines, which could have caused significant underestimations of the linewidths, and hence of the dynamical masses. The CO spectral line energy distributions (SLEDs), peaking around Jup 5-7, are found to be similar to those of the local starburst-dominated ultra-luminous infrared galaxies and of the previously studied SMGs. After correcting for lensing amplification, we derived the global properties of the bulk of molecular gas in the SMGs using non-LTE radiative transfer modelling, such as the molecular gas density nH2 102.5-104.1 cm-3 and the kinetic temperature Tk 20-750 K. The gas thermal pressure Pth ranging from 105 K cm-3 to 106 K cm-3 is found to be correlated with star formation efficiency. Further decomposing the CO SLEDs into two excitation components, we find a low-excitation component with nH2 102.8-104.6 cm-3 and Tk 20-30 K, which is less correlated with star formation, and a high-excitation one (nH2 102.7-104.2 cm-3, Tk 60-400 K) which is tightly related to the on-going star-forming activity. Additionally, tight linear correlations between the far-infrared and CO line luminosities have been confirmed for the Jup ≥ 5 CO lines of these SMGs, implying that these CO lines are good tracers of star formation. The [C I](2-1) lines follow the tight linear correlation between the luminosities of the [C I](2-1) and the CO(1-0) line found in local starbursts, indicating that [C I] lines could serve as good total molecular gas mass tracers for high-redshift SMGs as well

  19. Genetic rearrangements of six wheat-agropyron cristatum 6P addition lines revealed by molecular markers.

    Directory of Open Access Journals (Sweden)

    Haiming Han

    Full Text Available Agropyron cristatum (L. Gaertn. (2n = 4x = 28, PPPP not only is cultivated as pasture fodder but also could provide many desirable genes for wheat improvement. It is critical to obtain common wheat-A. cristatum alien disomic addition lines to locate the desired genes on the P genome chromosomes. Comparative analysis of the homoeologous relationships between the P genome chromosome and wheat genome chromosomes is a key step in transferring different desirable genes into common wheat and producing the desired alien translocation line while compensating for the loss of wheat chromatin. In this study, six common wheat-A. cristatum disomic addition lines were produced and analyzed by phenotypic examination, genomic in situ hybridization (GISH, SSR markers from the ABD genomes and STS markers from the P genome. Comparative maps, six in total, were generated and demonstrated that all six addition lines belonged to homoeologous group 6. However, chromosome 6P had undergone obvious rearrangements in different addition lines compared with the wheat chromosome, indicating that to obtain a genetic compensating alien translocation line, one should recombine alien chromosomal regions with homoeologous wheat chromosomes. Indeed, these addition lines were classified into four types based on the comparative mapping: 6PI, 6PII, 6PIII, and 6PIV. The different types of chromosome 6P possessed different desirable genes. For example, the 6PI type, containing three addition lines, carried genes conferring high numbers of kernels per spike and resistance to powdery mildew, important traits for wheat improvement. These results may prove valuable for promoting the development of conventional chromosome engineering techniques toward molecular chromosome engineering.

  20. Broad line and pulsed NMR study of molecular motion in furfuryl alcohol resins

    International Nuclear Information System (INIS)

    Glowinkowski, S.; Pajak, Z.

    1978-01-01

    Broad line and pulsed nuclear magnetic resonance studies are carried out on a number of furfuryl alcohol resins differentiated by viscosity. Proton NMR spectra and relaxation times T 1 and Tsub(1rho) are measured over a wide temperature range and the results are interpreted in terms of molecular motion. The marked decrease in second moment and existence of high temperature spin-lattice relaxation times minima are presumed to result from rotational motion of polymer chains. The relaxation processes at low temperature are believed to be due to rotational motion of methyl endgroup and paramagnetic centres. (author)

  1. Identifying the molecular functions of electron transport proteins using radial basis function networks and biochemical properties.

    Science.gov (United States)

    Le, Nguyen-Quoc-Khanh; Nguyen, Trinh-Trung-Duong; Ou, Yu-Yen

    2017-05-01

    The electron transport proteins have an important role in storing and transferring electrons in cellular respiration, which is the most proficient process through which cells gather energy from consumed food. According to the molecular functions, the electron transport chain components could be formed with five complexes with several different electron carriers and functions. Therefore, identifying the molecular functions in the electron transport chain is vital for helping biologists understand the electron transport chain process and energy production in cells. This work includes two phases for discriminating electron transport proteins from transport proteins and classifying categories of five complexes in electron transport proteins. In the first phase, the performances from PSSM with AAIndex feature set were successful in identifying electron transport proteins in transport proteins with achieved sensitivity of 73.2%, specificity of 94.1%, and accuracy of 91.3%, with MCC of 0.64 for independent data set. With the second phase, our method can approach a precise model for identifying of five complexes with different molecular functions in electron transport proteins. The PSSM with AAIndex properties in five complexes achieved MCC of 0.51, 0.47, 0.42, 0.74, and 1.00 for independent data set, respectively. We suggest that our study could be a power model for determining new proteins that belongs into which molecular function of electron transport proteins. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Molecular and morpho-anatomical characterization of some Egyptian durum wheat cultivars/lines

    International Nuclear Information System (INIS)

    Saleh, O.M.; Hamiedeldin, N.; Khafaga, A.

    2016-01-01

    Grains of eight durum wheat cultivars were tested for identification of genetic relationship among molecular, anatomical and morphological levels. On the molecular level, two techniques have been used; Randomly Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeats (ISSR). Amplification of RAPD primers showed different numbers of fragments ranged from six to thirteen fragments. Percentage of polymorphism ranged from 0% to 100%. The highest similarity value recorded was 91%, while the lowest similarity value was 69%. Amplification of ISSR primers showed different numbers of fragments ranged from six to twelve fragments. The highest similarity value recorded was 91%, while the lowest similarity value was 68%. The grain's coat morphology was reticulated in all taxa. There were variations with regard to the alignment and the shape of network and architecture of interspaces enclosed by raised line. Reticulate surface patterns appeared some variations ranged from weakly reticulate such as G 413 to strongly reticulate such as G 203. Stem cuticles of all cultivars were thick except cultivar; Benisweif 1. For leaf anatomy, all cultivars had epidermis composed of one layer of thick wall cells except cultivars; G 203 and Benisweif 1. (author)

  3. The ATCA CABB Line Survey on Centaurus A: Properties of the Molecular Gas from the Dust Lanes to the Central Engine

    Science.gov (United States)

    Ott, Juergen; Koribalski, Baerbel; Henkel, Christian; Edwards, Philip; Norris, Ray; Meier, David; Feain, Ilana; Curran, Steve; Martin-Pintado, Jesus; Beelen, Alexandre; Aalto, Susanne; Combes, Francoise; Israel, Frank; Muller, Sebastien; Espada, Daniel; Guelin, Michel; Black, John Harry; V-Trung, Dinh; Impellizzeri, Caterina M. V.; Persson, Carina

    2011-10-01

    Centaurus A with its host NGC5128 is the most nearby radio galaxy. Its molecular spectrum exhibits three prominent features: a) gas that is located in the outer disk and dust lanes, b) absorption lines that are supposedly close to the central AGN, and c) gas in emission from the nucleus. We propose to perform an extensive line survey toward CenA using the exciting new capabilities of CABB. The broad basebands and narrow zoom bands of CABB are ideal to capture the full breath of the CenA spectral features. Our multi-band line observations will allow us to derive the exact physical conditions of each component as well as the chemistry involved. We will therefore obtain a comprehensive view of the physics imprinted on the molecular spectrum of a radio galaxy and its host, reaching from the central supermassive black hole, through the accretion region and the inner disk to the outer dust lanes.

  4. Quasi-molecular processes in dense plasmas

    International Nuclear Information System (INIS)

    Younger, S.M.

    1991-01-01

    Quasi-molecular phenomena occur in dense plasmas when the interatomic spacing is comparable to the characteristic wavelength of the electrons. If the electronic states are bound, covalent orbitals arise with different excitation energies, radiative rates, and collisional rates than for isolated ions. For continuum electrons, charge localization near transient clusters of nuclei can influence many scattering and transport processes. We identify several novel consequences of quasi-molecular phenomena in plasmas and give a possible explanation of high energy features associated with helium-like emissions lines observed in recent inertial fusion experiments. 7 refs

  5. On the fragmentation of filaments in a molecular cloud simulation

    Science.gov (United States)

    Chira, R.-A.; Kainulainen, J.; Ibáñez-Mejía, J. C.; Henning, Th.; Mac Low, M.-M.

    2018-03-01

    Context. The fragmentation of filaments in molecular clouds has attracted a lot of attention recently as there seems to be a close relation between the evolution of filaments and star formation. The study of the fragmentation process has been motivated by simple analytical models. However, only a few comprehensive studies have analysed the evolution of filaments using numerical simulations where the filaments form self-consistently as part of large-scale molecular cloud evolution. Aim. We address the early evolution of parsec-scale filaments that form within individual clouds. In particular, we focus on three questions: How do the line masses of filaments evolve? How and when do the filaments fragment? How does the fragmentation relate to the line masses of the filaments? Methods: We examine three simulated molecular clouds formed in kiloparsec-scale numerical simulations performed with the FLASH adaptive mesh refinement magnetohydrodynamic code. The simulations model a self-gravitating, magnetised, stratified, supernova-driven interstellar medium, including photoelectric heating and radiative cooling. We follow the evolution of the clouds for 6 Myr from the time self-gravity starts to act. We identify filaments using the DisPerSe algorithm, and compare the results to other filament-finding algorithms. We determine the properties of the identified filaments and compare them with the predictions of analytic filament stability models. Results: The average line masses of the identified filaments, as well as the fraction of mass in filamentary structures, increases fairly continuously after the onset of self-gravity. The filaments show fragmentation starting relatively early: the first fragments appear when the line masses lie well below the critical line mass of Ostriker's isolated hydrostatic equilibrium solution ( 16 M⊙ pc-1), commonly used as a fragmentation criterion. The average line masses of filaments identified in three-dimensional volume density cubes

  6. Molecular Line Emission as a Tool for Galaxy Observations (LEGO). I. HCN as a tracer of moderate gas densities in molecular clouds and galaxies

    Science.gov (United States)

    Kauffmann, Jens; Goldsmith, Paul F.; Melnick, Gary; Tolls, Volker; Guzman, Andres; Menten, Karl M.

    2017-09-01

    Trends observed in galaxies, such as the Gao & Solomon relation, suggest a linear relationship between the star formation rate and the mass of dense gas available for star formation. Validation of such trends requires the establishment of reliable methods to trace the dense gas in galaxies. One frequent assumption is that the HCN (J = 1-0) transition is unambiguously associated with gas at H2 densities ≫ 104 cm-3. If so, the mass of gas at densities ≫ 104 cm-3 could be inferred from the luminosity of this emission line, LHCN (1-0). Here we use observations of the Orion A molecular cloud to show that the HCN (J = 1-0) line traces much lower densities 103 cm-3 in cold sections of this molecular cloud, corresponding to visual extinctions AV ≈ 6 mag. We also find that cold and dense gas in a cloud like Orion produces too little HCN emission to explain LHCN (1-0) in star forming galaxies, suggesting that galaxies might contain a hitherto unknown source of HCN emission. In our sample of molecules observed at frequencies near 100 GHz (also including 12CO, 13CO, C18O, CN, and CCH), N2H+ is the only species clearly associated with relatively dense gas.

  7. Genome-wide comparative transcriptome analysis of CMS-D2 and its maintainer and restorer lines in upland cotton.

    Science.gov (United States)

    Wu, Jianyong; Zhang, Meng; Zhang, Bingbing; Zhang, Xuexian; Guo, Liping; Qi, Tingxiang; Wang, Hailin; Zhang, Jinfa; Xing, Chaozhu

    2017-06-08

    Cytoplasmic male sterility (CMS) conferred by the cytoplasm from Gossypium harknessii (D2) is an important system for hybrid seed production in Upland cotton (G. hirsutum). The male sterility of CMS-D2 (i.e., A line) can be restored to fertility by a restorer (i.e., R line) carrying the restorer gene Rf1 transferred from the D2 nuclear genome. However, the molecular mechanisms of CMS-D2 and its restoration are poorly understood. In this study, a genome-wide comparative transcriptome analysis was performed to identify differentially expressed genes (DEGs) in flower buds among the isogenic fertile R line and sterile A line derived from a backcross population (BC 8 F 1 ) and the recurrent parent, i.e., the maintainer (B line). A total of 1464 DEGs were identified among the three isogenic lines, and the Rf1-carrying Chr_D05 and its homeologous Chr_A05 had more DEGs than other chromosomes. The results of GO and KEGG enrichment analysis showed differences in circadian rhythm between the fertile and sterile lines. Eleven DEGs were selected for validation using qRT-PCR, confirming the accuracy of the RNA-seq results. Through genome-wide comparative transcriptome analysis, the differential expression profiles of CMS-D2 and its maintainer and restorer lines in Upland cotton were identified. Our results provide an important foundation for further studies into the molecular mechanisms of the interactions between the restorer gene Rf1 and the CMS-D2 cytoplasm.

  8. Heterogeneity of mammary lesions represent molecular differences

    International Nuclear Information System (INIS)

    Namba, Ruria; Gregg, Jeffrey P; Maglione, Jeannie E; Davis, Ryan R; Baron, Colin A; Liu, Stephenie; Carmack, Condie E; Young, Lawrence JT; Borowsky, Alexander D; Cardiff, Robert D

    2006-01-01

    Human breast cancer is a heterogeneous disease, histopathologically, molecularly and phenotypically. The molecular basis of this heterogeneity is not well understood. We have used a mouse model of DCIS that consists of unique lines of mammary intraepithelial neoplasia (MIN) outgrowths, the premalignant lesion in the mouse that progress to invasive carcinoma, to understand the molecular changes that are characteristic to certain phenotypes. Each MIN-O line has distinguishable morphologies, metastatic potentials and estrogen dependencies. We utilized oligonucleotide expression arrays and high resolution array comparative genomic hybridization (aCGH) to investigate whole genome expression patterns and whole genome aberrations in both the MIN-O and tumor from four different MIN-O lines that each have different phenotypes. From the whole genome analysis at 35 kb resolution, we found that chromosome 1, 2, 10, and 11 were frequently associated with whole chromosome gains in the MIN-Os. In particular, two MIN-O lines had the majority of the chromosome gains. Although we did not find any whole chromosome loss, we identified 3 recurring chromosome losses (2F1-2, 3E4, 17E2) and two chromosome copy number gains on chromosome 11. These interstitial deletions and duplications were verified with a custom made array designed to interrogate the specific regions at approximately 550 bp resolution. We demonstrated that expression and genomic changes are present in the early premalignant lesions and that these molecular profiles can be correlated to phenotype (metastasis and estrogen responsiveness). We also identified expression changes associated with genomic instability. Progression to invasive carcinoma was associated with few additional changes in gene expression and genomic organization. Therefore, in the MIN-O mice, early premalignant lesions have the major molecular and genetic changes required and these changes have important phenotypic significance. In contrast, the changes

  9. Molecular Breeding of Rice Restorer Lines and Hybrids for Brown Planthopper (BPH) Resistance Using the Bph14 and Bph15 Genes.

    Science.gov (United States)

    Wang, Hongbo; Ye, Shengtuo; Mou, Tongmin

    2016-12-01

    The development of hybrid rice is a practical approach for increasing rice production. However, the brown planthopper (BPH), Nilaparvata lugens Stål, causes severe yield loss of rice (Oryza sativa L.) and can threaten food security. Therefore, breeding hybrid rice resistant to BPH is the most effective and economical strategy to maintain high and stable production. Fortunately, numerous BPH resistance genes have been identified, and abundant linkage markers are available for molecular marker-assisted selection (MAS) in breeding programs. Hence, we pyramided two BPH resistance genes, Bph14 and Bph15, into a susceptive CMS restorer line Huahui938 and its derived hybrids using MAS to improve the BPH resistance of hybrid rice. Three near-isogenic lines (NILs) with pyramided Bph14 and Bph15 were obtained by molecular marker-assisted backcross (MAB) and phenotypic selection. The genomic components of these NILs were detected using the whole-genome SNP (Single nucleotide polymorphism) array, RICE6K, suggesting that the recurrent parent genome (RPG) recovery of the NILs was 87.88, 87.70 and 86.62 %, respectively. BPH bioassays showed that the improved NILs and their derived hybrids carrying homozygous Bph14 and Bph15 were resistant to BPH. However, the hybrids with heterozygous Bph14 and Bph15 remained susceptible to BPH. The developed NILs showed no significant differences in major agronomic traits and rice qualities compared with the recurrent parent. Moreover, the improved hybrids derived from the NILs exhibited better agronomic performance and rice quality compared with the controls under natural field conditions. This study demonstrates that it is essential to stack Bph14 and Bph15 into both the maternal and paternal parents for developing BPH-resistant hybrid rice varieties. The SNP array with abundant DNA markers is an efficient tool for analyzing the RPG recovery of progenies and can be used to monitor the donor segments in NILs, thus being extremely important

  10. Molecular, Physicochemical and Rheological Characteristics of Introgressive Triticale/Triticum monococcum ssp. monococcum Lines with Wheat 1D/1A Chromosome Substitution

    Directory of Open Access Journals (Sweden)

    Lidia Błaszczyk

    2013-07-01

    Full Text Available Three sets of hexaploid introgressive triticale lines, with Triticum monococcum ssp. monococcum (cultivated einkorn wheat genes and a bread wheat chromosome 1D substituted for chromosome 1A, and one set of secondary triticale lines were evaluated for grain and flour physicochemical and dough rheological characteristics in two generations (F7 and F8. Genomic in situ hybridization (GISH and fluorescence in situ hybridization (FISH confirmed the 1D/1A chromosome substitution. The presence or absence of einkorn high-molecular-weight (HMW glutenin subunits and the wheat Glu-D1d locus encoding the 5 + 10 subunits was assessed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE, capillary zone electrophoresis, and allele-specific molecular markers. Significant differences were found among physicochemical properties (with the exception of the Hagberg falling number of all introgressive Triticale/T. monococcum lines and the secondary triticale lines. The wheat 1D/1A chromosome substitution also affected these properties. The results showed that in all introgressive triticale lines, the protein and gluten content, Zeleny sedimentation value, and water absorption capacity, were increased. The rheological parameters estimated using micro-farinograph, reomixer, and Kieffer dough extensibility systems also showed an appreciable increase in dough-mixing properties, maximum resistance to extension (Rmax, and dough extensibility. Introgressive Triticale/T. monococcum lines with 5 + 10 subunits have particularly favorable rheological parameters. The results obtained in this study suggest that the cultivated einkorn genome Am, in the context of hexaploid secondary triticale lines and with a wheat 1D/1A substitution, has the potential to improve gluten polymer interactions and be a valuable genetic resource for triticale quality improvement.

  11. MicroRNA Expression Profiling Identifies Molecular Diagnostic Signatures for Anaplastic Large Cell Lymphoma

    DEFF Research Database (Denmark)

    Liu, Cuiling; Iqbal, Javeed; Teruya-Feldstein, Julie

    2013-01-01

    distinct clustering of ALCL, PTCL-NOS, and the AITL subtype of PTCL. Cases of ALK(+) ALCL and ALK(-) ALCL were interspersed in unsupervised analysis, suggesting a close relationship at the molecular level. We identified an miRNA signature of 7 miRNAs (5 upregulated: miR-512-3p, miR-886-5p, miR-886-3p, mi...

  12. Molecular cytogenetic identification of a novel wheat-Agropyron elongatum chromosome translocation line with powdery mildew resistance.

    Science.gov (United States)

    Li, Xiaojun; Jiang, Xiaoling; Chen, Xiangdong; Song, Jie; Ren, Cuicui; Xiao, Yajuan; Gao, Xiaohui; Ru, Zhengang

    2017-01-01

    Agropyron elongatum (Host.) Neviski (synonym, Thinopyrum ponticum Podp., 2n = 70) has been used extensively as a valuable source for wheat breeding. Numerous chromosome fragments containing valuable genes have been successfully translocated into wheat from A. elongatum. However, reports on the transfer of powdery mildew resistance from A. elongatum to wheat are rare. In this study, a novel wheat-A. elongatum translocation line, 11-20-1, developed and selected from the progenies of a sequential cross between wheat varieties (Lankaoaizaoba, Keyu 818 and BainongAK 58) and A. elongatum, was evaluated for disease resistance and characterized using molecular cytogenetic methods. Cytological observations indicated that 11-20-1 had 42 chromosomes and formed 21 bivalents at meiotic metaphase I. Genomic in situ hybridization analysis using whole genomic DNA from A. elongatum as a probe showed that the short arms of a pair of wheat chromosomes were replaced by a pair of A. elongatum chromosome arms. Fluorescence in situ hybridization, using wheat D chromosome specific sequence pAs1 as a probe, suggested that the replaced chromosome arms of 11-20-1 were 5DS. This was further confirmed by wheat SSR markers specific for 5DS. EST-SSR and EST-STS multiple loci markers confirmed that the introduced A. elongatum chromosome arms belonged to homoeologous group 5. Therefore, it was deduced that 11-20-1 was a wheat-A. elongatum T5DL∙5AgS translocation line. Both resistance observation and molecular marker analyses using two specific markers (BE443538 and CD452608) of A. elongatum in a F2 population from a cross between line 11-20-1 and a susceptible cultivar Yannong 19 verified that the A. elongatum chromosomes were responsible for the powdery mildew resistance. This work suggests that 11-20-1 likely contains a novel resistance gene against powdery mildew. We expect this line to be useful for the genetic improvement of wheat.

  13. Early and long-standing rheumatoid arthritis: distinct molecular signatures identified by gene-expression profiling in synovia

    Science.gov (United States)

    Lequerré, Thierry; Bansard, Carine; Vittecoq, Olivier; Derambure, Céline; Hiron, Martine; Daveau, Maryvonne; Tron, François; Ayral, Xavier; Biga, Norman; Auquit-Auckbur, Isabelle; Chiocchia, Gilles; Le Loët, Xavier; Salier, Jean-Philippe

    2009-01-01

    Introduction Rheumatoid arthritis (RA) is a heterogeneous disease and its underlying molecular mechanisms are still poorly understood. Because previous microarray studies have only focused on long-standing (LS) RA compared to osteoarthritis, we aimed to compare the molecular profiles of early and LS RA versus control synovia. Methods Synovial biopsies were obtained by arthroscopy from 15 patients (4 early untreated RA, 4 treated LS RA and 7 controls, who had traumatic or mechanical lesions). Extracted mRNAs were used for large-scale gene-expression profiling. The different gene-expression combinations identified by comparison of profiles of early, LS RA and healthy synovia were linked to the biological processes involved in each situation. Results Three combinations of 719, 116 and 52 transcripts discriminated, respectively, early from LS RA, and early or LS RA from healthy synovia. We identified several gene clusters and distinct molecular signatures specifically expressed during early or LS RA, thereby suggesting the involvement of different pathophysiological mechanisms during the course of RA. Conclusions Early and LS RA have distinct molecular signatures with different biological processes participating at different times during the course of the disease. These results suggest that better knowledge of the main biological processes involved at a given RA stage might help to choose the most appropriate treatment. PMID:19563633

  14. Molecular dynamics study of the nanosized droplet spreading: The effect of the contact line forces on the kinetic energy dissipation

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Hong Min [Department of Mechanical Engineering, Yonsei University, Seoul 120-749 (Korea, Republic of); Kondaraju, Sasidhar [Department of Mechanical Science, Indian Institute of Technology Bhubaneswar, Bhubaneswar, Odisha 751013 (India); Lee, Jung Shin [Department of Mechanical Engineering, Yonsei University, Seoul 120-749 (Korea, Republic of); Suh, Youngho; Lee, Joonho H. [Samsung Electronics, Mechatronics R& D Center, Hwaseong-si, Gyeonggi-do 445-330 (Korea, Republic of); Lee, Joon Sang, E-mail: joonlee@yonsei.ac.kr [Department of Mechanical Engineering, Yonsei University, Seoul 120-749 (Korea, Republic of)

    2017-07-01

    Highlights: • Contact line forces, including friction and spreading forces are directly calculated. • Overall trends of variations in contact line forces during droplet spreading process show characteristics of contact line forces. • Detail relations of contact line forces and atomic kinetics in the contact line provide a clear evidence of the possible energy dissipation mechanism in droplet spreading process. - Abstract: Recent studies have revealed that contact line forces play an important role in the droplet spreading process. Despite their significance, the physics related to them has been studied only indirectly and the effect of contact line forces is still being disputed. We performed a molecular dynamics simulation and mimicked the droplet spreading process at the nanoscale. Based on the results of the simulation, the contact line forces were directly calculated. We found that the forces acting on the bulk and the contact line region showed different trends. Distinct positive and negative forces, contact line spreading, and friction forces were observed near the contact line. We also observed a strong dependency of the atomic kinetics in the contact line region on the variations in the contact line forces. The atoms of the liquid in the contact line region lost their kinetic energy due to the contact line friction force and became partially immobile on the solid surface. The results of the current study will be useful for understanding the role of the contact line forces on the kinetic energy dissipation in the contact line region.

  15. Molecular dynamics study of the nanosized droplet spreading: The effect of the contact line forces on the kinetic energy dissipation

    International Nuclear Information System (INIS)

    Yoon, Hong Min; Kondaraju, Sasidhar; Lee, Jung Shin; Suh, Youngho; Lee, Joonho H.; Lee, Joon Sang

    2017-01-01

    Highlights: • Contact line forces, including friction and spreading forces are directly calculated. • Overall trends of variations in contact line forces during droplet spreading process show characteristics of contact line forces. • Detail relations of contact line forces and atomic kinetics in the contact line provide a clear evidence of the possible energy dissipation mechanism in droplet spreading process. - Abstract: Recent studies have revealed that contact line forces play an important role in the droplet spreading process. Despite their significance, the physics related to them has been studied only indirectly and the effect of contact line forces is still being disputed. We performed a molecular dynamics simulation and mimicked the droplet spreading process at the nanoscale. Based on the results of the simulation, the contact line forces were directly calculated. We found that the forces acting on the bulk and the contact line region showed different trends. Distinct positive and negative forces, contact line spreading, and friction forces were observed near the contact line. We also observed a strong dependency of the atomic kinetics in the contact line region on the variations in the contact line forces. The atoms of the liquid in the contact line region lost their kinetic energy due to the contact line friction force and became partially immobile on the solid surface. The results of the current study will be useful for understanding the role of the contact line forces on the kinetic energy dissipation in the contact line region.

  16. Molecular characterization and functional analysis of pteridine reductase in wild-type and antimony-resistant Leishmania lines.

    Science.gov (United States)

    de Souza Moreira, Douglas; Ferreira, Rafael Fernandes; Murta, Silvane M F

    2016-01-01

    Pteridine reductase (PTR1) is an NADPH-dependent reductase that participates in the salvage of pteridines, which are essential to maintain growth of Leishmania. In this study, we performed the molecular characterization of ptr1 gene in wild-type (WTS) and SbIII-resistant (SbR) lines from Leishmania guyanensis (Lg), Leishmania amazonensis (La), Leishmania braziliensis (Lb) and Leishmania infantum (Li), evaluating the chromosomal location, mRNA levels of the ptr1 gene and PTR1 protein expression. PFGE results showed that the ptr1 gene is located in a 797 kb chromosomal band in all Leishmania lines analyzed. Interestingly, an additional chromosomal band of 1070 kb was observed only in LbSbR line. Northern blot results showed that the levels of ptr1 mRNA are increased in the LgSbR, LaSbR and LbSbR lines. Western blot assays using the polyclonal anti-LmPTR1 antibody demonstrated that PTR1 protein is more expressed in the LgSbR, LaSbR and LbSbR lines compared to their respective WTS counterparts. Nevertheless, no difference in the level of mRNA and protein was observed between the LiWTS and LiSbR lines. Functional analysis of PTR1 enzyme was performed to determine whether the overexpression of ptr1 gene in the WTS L. braziliensis and L. infantum lines would change the SbIII-resistance phenotype of transfected parasites. Western blot results showed that the expression level of PTR1 protein was increased in the transfected parasites compared to the non-transfected ones. IC50 analysis revealed that the overexpression of ptr1 gene in the WTS L. braziliensis line increased 2-fold the SbIII-resistance phenotype compared to the non-transfected counterpart. Furthermore, the overexpression of ptr1 gene in the WTS L. infantum line did not change the SbIII-resistance phenotype. These results suggest that the PTR1 enzyme may be implicated in the SbIII-resistance phenotype in L. braziliensis line. Copyright © 2015 Elsevier Inc. All rights reserved.

  17. New Method to Identify Field Joint Coating Failures Based on MFL In-Line Inspection Signals

    Directory of Open Access Journals (Sweden)

    Lianshuang Dai

    2018-02-01

    Full Text Available Above ground indirect detections and random excavations that have applied the past years for buried long distance oil and gas pipelines can only identify some damaged coating locations. Hence, large number of field joint coating (FJC failures happen unconsciously until they lead to failures of the pipelines. Based on the analysis of magnetic flux leakage (MFL in-line inspection (ILI signals, combined with the statistical results of 414 excavations from two different pipeline sections, a new method to identify the failed FJC is established. Though it can only identify FJC failures when there are signs of corrosion on pipe body, it is much more efficient and cost-saving. The concluded identification rule still needs more validations and improvements to be more applicable and accuracy.

  18. C3H2 observations as a diagnostic probe for molecular clouds

    Science.gov (United States)

    Avery, L. W.

    1986-01-01

    Recently the three-membered ring molecule, cyclopropenylidene, C3H2, has been identified in the laboratory and detected in molecular clouds by Thaddeus, Vrtilek and Gottlieb (1985). This molecule is wide-spread throughout the Galaxy and has been detected in 25 separate sources including cold dust clouds, circumstellar envelopes, HII regions, and the spiral arms observed against the Cas supernova remnant. In order to evaluate the potential of C3H2 as a diagnostic probe for molecular clouds, and to attempt to identify the most useful transitions, statistical equilibrium calculations were carried out for the lowest 24 levels of the ortho species and the lowest 10 levels of the para species. Many of the sources observed by Matthews and Irvine (1985) show evidence of being optically thick in the 1(10)-1(01) line. Consequently, the effects of radiative trapping should be incorporated into the equilibrium calculations. This was done using the Large Velocity Gradient approximation for a spherical cloud of uniform density. Some results of the calculations for T(K)=10K are given. Figures are presented which show contours of the logarithm of the ratio of peak line brightness temperatures for ortho-para pairs of lines at similar frequencies. It appears that the widespread nature of C3H2, the relatively large strength of its spectral lines, and their sensitivity to density and molecular abundance combine to make this a useful molecule for probing physical conditions in molecular clouds. The 1(10)-1(01) and 2(20)-2(11) K-band lines may be especially useful in this regard because of the ease with which they are observed and their unusual density-dependent emission/absorption properties.

  19. Molecular outflows in the L1641 region of Orion

    International Nuclear Information System (INIS)

    Morgan, J.A.

    1990-01-01

    Little is known about the interaction between molecular outflows associated with young stellar objects and the parent molecular cloud that produced them. This is because molecular outflows are a recently discovered phenomenon and, so, have not had their global properties studied in great detail and molecular clouds were not mapped to sufficiently high spatial resolution to resolve the interaction. The interaction between molecular outflows and the L1641 molecular cloud is addressed by both identifying and mapping all the molecular outflows as well as the detailed structure of the cloud. Candidate molecular outflows were found from single point 12-CO observations of young stellar objects identified from the IRAS survey data. The candidate sources were then mapped to confirm their molecular outflow nature. From these maps, molecular outflow characteristics such as their morphology, orientation, and energetics were determined. In addition, the Orion molecular cloud was mapped to compare directly with the molecular outflows. The molecular outflows identified were found to have rising infrared spectra, radio continuum emission that suggests a stellar wind or optically thick H II region, and molecular line strengths that indicate that they are embedded within a very dense environment. The lack of an optical counterpart for many molecular outflows suggests that they occur at the earliest stages of stellar evolution. The lack of an optical counterpart for many molecular outflows suggest that they occur at the earliest stages of stellar evolution. The orientations of the molecular outflows appear to lie in no preferred direction and they have shapes that indicate that the molecular cloud is responsible for determining their direction and collimation

  20. Identifying molecular subtypes in human colon cancer using gene expression and DNA methylation microarray data

    OpenAIRE

    REN, ZHONGLU; WANG, WENHUI; LI, JINMING

    2015-01-01

    Identifying colon cancer subtypes based on molecular signatures may allow for a more rational, patient-specific approach to therapy in the future. Classifications using gene expression data have been attempted before with little concordance between the different studies carried out. In this study we aimed to uncover subtypes of colon cancer that have distinct biological characteristics and identify a set of novel biomarkers which could best reflect the clinical and/or biological characteristi...

  1. Production and identification of wheat - Agropyron cristatum (1.4P) alien translocation lines.

    Science.gov (United States)

    Liu, Wei-Hua; Luan, Yang; Wang, Jing-Chang; Wang, Xiao-Guang; Su, Jun-Ji; Zhang, Jin-Peng; Yang, Xin-Ming; Gao, Ai-Nong; Li, Li-Hui

    2010-06-01

    The P genome of Agropyron Gaertn., a wild relative of wheat, contains an abundance of desirable genes that can be utilized as genetic resources to improve wheat. In this study, wheat - Aegilops cylindrica Host gametocidal chromosome 2C addition lines were crossed with wheat - Agropyron cristatum (L.) Gaertn. disomic addition line accession II-21 with alien recombinant chromosome (1.4)P. We successfully induced wheat - A. cristatum alien chromosomal translocations for the first time. The frequency of translocation in the progeny was 3.75%, which was detected by molecular markers and genomic in situ hybridization (GISH). The translocation chromosomes were identified by dual-color GISH /fluorescence in situ hybridization (FISH). The P genomic DNA was used as probe to detect the (1.4)P chromosome fragment, and pHvG39, pAs1, or pSc119.2 repeated sequences were used as probes to identify wheat translocated chromosomes. The results showed that six types of translocations were identified in the three wheat - A. cristatum alien translocation lines, including the whole arm or terminal portion of a (1.4)P chromosome. The (1.4)P chromosome fragments were translocated to wheat chromosomes 1B, 2B, 5B, and 3D. The breakpoints were located at the centromeres of 1B and 2B, the pericentric locations of 5BS, and the terminals of 5BL and 3DS. In addition, we obtained 12 addition-deletion lines that contained alien A. cristatum chromosome (1.4)P in wheat background. All of these wheat - A. cristatum alien translocation lines and addition-deletion lines would be valuable for identifying A. cristatum chromosome (1.4)P-related genes and providing genetic resources and new germplasm accessions for the genetic improvement of wheat. The specific molecular markers of A. cristatum (1.4)P chromosome have been developed and used to track the (1.4)P chromatin.

  2. Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers

    OpenAIRE

    Girardot, Charles; Scholtalbers, Jelle; Sauer, Sajoscha; Su, Shu-Yi; Furlong, Eileen E.M.

    2016-01-01

    Background The yield obtained from next generation sequencers has increased almost exponentially in recent years, making sample multiplexing common practice. While barcodes (known sequences of fixed length) primarily encode the sample identity of sequenced DNA fragments, barcodes made of random sequences (Unique Molecular Identifier or UMIs) are often used to distinguish between PCR duplicates and transcript abundance in, for example, single-cell RNA sequencing (scRNA-seq). In paired-end sequ...

  3. RNA sequencing of Populus x canadensis roots identifies key molecular mechanisms underlying physiological adaption to excess zinc.

    Directory of Open Access Journals (Sweden)

    Andrea Ariani

    Full Text Available Populus x canadensis clone I-214 exhibits a general indicator phenotype in response to excess Zn, and a higher metal uptake in roots than in shoots with a reduced translocation to aerial parts under hydroponic conditions. This physiological adaptation seems mainly regulated by roots, although the molecular mechanisms that underlie these processes are still poorly understood. Here, differential expression analysis using RNA-sequencing technology was used to identify the molecular mechanisms involved in the response to excess Zn in root. In order to maximize specificity of detection of differentially expressed (DE genes, we consider the intersection of genes identified by three distinct statistical approaches (61 up- and 19 down-regulated and validate them by RT-qPCR, yielding an agreement of 93% between the two experimental techniques. Gene Ontology (GO terms related to oxidation-reduction processes, transport and cellular iron ion homeostasis were enriched among DE genes, highlighting the importance of metal homeostasis in adaptation to excess Zn by P. x canadensis clone I-214. We identified the up-regulation of two Populus metal transporters (ZIP2 and NRAMP1 probably involved in metal uptake, and the down-regulation of a NAS4 gene involved in metal translocation. We identified also four Fe-homeostasis transcription factors (two bHLH38 genes, FIT and BTS that were differentially expressed, probably for reducing Zn-induced Fe-deficiency. In particular, we suggest that the down-regulation of FIT transcription factor could be a mechanism to cope with Zn-induced Fe-deficiency in Populus. These results provide insight into the molecular mechanisms involved in adaption to excess Zn in Populus spp., but could also constitute a starting point for the identification and characterization of molecular markers or biotechnological targets for possible improvement of phytoremediation performances of poplar trees.

  4. Authentication of M14 melanoma cell line proves misidentification of MDA‐MB‐435 breast cancer cell line

    Science.gov (United States)

    Korch, Christopher; Hall, Erin M.; Dirks, Wilhelm G.; Ewing, Margaret; Faries, Mark; Varella‐Garcia, Marileila; Robinson, Steven; Storts, Douglas; Turner, Jacqueline A.; Wang, Ying; Burnett, Edward C.; Healy, Lyn; Kniss, Douglas; Neve, Richard M.; Nims, Raymond W.; Reid, Yvonne A.; Robinson, William A.

    2017-01-01

    A variety of analytical approaches have indicated that melanoma cell line UCLA‐SO‐M14 (M14) and breast carcinoma cell line MDA‐MB‐435 originate from a common donor. This indicates that at some point in the past, one of these cell lines became misidentified, meaning that it ceased to correspond to the reported donor and instead became falsely identified (through cross‐contamination or other means) as a cell line from a different donor. Initial studies concluded that MDA‐MB‐435 was the misidentified cell line and M14 was the authentic cell line, although contradictory evidence has been published, resulting in further confusion. To address this question, we obtained early samples of the melanoma cell line (M14), a lymphoblastoid cell line from the same donor (ML14), and donor serum preserved at the originator's institution. M14 samples were cryopreserved in December 1975, before MDA‐MB‐435 cells were established in culture. Through a series of molecular characterizations, including short tandem repeat (STR) profiling and cytogenetic analysis, we demonstrated that later samples of M14 and MDA‐MB‐435 correspond to samples of M14 frozen in 1975, to the lymphoblastoid cell line ML14, and to the melanoma donor's STR profile, sex and blood type. This work demonstrates conclusively that M14 is the authentic cell line and MDA‐MB‐435 is misidentified. With clear provenance information and authentication testing of early samples, it is possible to resolve debates regarding the origins of problematic cell lines that are widely used in cancer research. PMID:28940260

  5. Identifying Stages in a Learning Hierarchy for Use in Formative Assessment--The Example of Line Graphs

    Science.gov (United States)

    Stacey, Kaye; Price, Beth; Steinle, Vicki

    2012-01-01

    This paper discusses issues arising in the design of questions to use in an on-line computer-based formative assessment system, focussing on how best to identify the stages of a learning hierarchy for reporting to teachers. Data from several hundred students is used to illustrate how design decisions have been made for a test on interpreting line…

  6. Sponge cell culture? A molecular identification method for sponge cells

    NARCIS (Netherlands)

    Sipkema, D.; Heilig, G.H.J.; Akkermans, A.D.L.; Osinga, R.; Tramper, J.; Wijffels, R.H.

    2003-01-01

    Dissociated sponge cells are easily confused with unicellular organisms. This has been an obstacle in the development of sponge-cell lines. We developed a molecular detection method to identify cells of the sponge Dysidea avara in dissociated cell cultures. The 18S ribosomal RNA gene from a Dysidea

  7. Systematic identification of combinatorial drivers and targets in cancer cell lines.

    Directory of Open Access Journals (Sweden)

    Adel Tabchy

    Full Text Available There is an urgent need to elicit and validate highly efficacious targets for combinatorial intervention from large scale ongoing molecular characterization efforts of tumors. We established an in silico bioinformatic platform in concert with a high throughput screening platform evaluating 37 novel targeted agents in 669 extensively characterized cancer cell lines reflecting the genomic and tissue-type diversity of human cancers, to systematically identify combinatorial biomarkers of response and co-actionable targets in cancer. Genomic biomarkers discovered in a 141 cell line training set were validated in an independent 359 cell line test set. We identified co-occurring and mutually exclusive genomic events that represent potential drivers and combinatorial targets in cancer. We demonstrate multiple cooperating genomic events that predict sensitivity to drug intervention independent of tumor lineage. The coupling of scalable in silico and biologic high throughput cancer cell line platforms for the identification of co-events in cancer delivers rational combinatorial targets for synthetic lethal approaches with a high potential to pre-empt the emergence of resistance.

  8. Systematic identification of combinatorial drivers and targets in cancer cell lines.

    Science.gov (United States)

    Tabchy, Adel; Eltonsy, Nevine; Housman, David E; Mills, Gordon B

    2013-01-01

    There is an urgent need to elicit and validate highly efficacious targets for combinatorial intervention from large scale ongoing molecular characterization efforts of tumors. We established an in silico bioinformatic platform in concert with a high throughput screening platform evaluating 37 novel targeted agents in 669 extensively characterized cancer cell lines reflecting the genomic and tissue-type diversity of human cancers, to systematically identify combinatorial biomarkers of response and co-actionable targets in cancer. Genomic biomarkers discovered in a 141 cell line training set were validated in an independent 359 cell line test set. We identified co-occurring and mutually exclusive genomic events that represent potential drivers and combinatorial targets in cancer. We demonstrate multiple cooperating genomic events that predict sensitivity to drug intervention independent of tumor lineage. The coupling of scalable in silico and biologic high throughput cancer cell line platforms for the identification of co-events in cancer delivers rational combinatorial targets for synthetic lethal approaches with a high potential to pre-empt the emergence of resistance.

  9. Cytogenetic and molecular markers for detecting Aegilops uniaristata chromosomes in a wheat background.

    Science.gov (United States)

    Gong, Wenping; Li, Guangrong; Zhou, Jianping; Li, Genying; Liu, Cheng; Huang, Chengyan; Zhao, Zhendong; Yang, Zujun

    2014-09-01

    Aegilops uniaristata has many agronomically useful traits that can be used for wheat breeding. So far, a Triticum turgidum - Ae. uniaristata amphiploid and one set of Chinese Spring (CS) - Ae. uniaristata addition lines have been produced. To guide Ae. uniaristata chromatin transformation from these lines into cultivated wheat through chromosome engineering, reliable cytogenetic and molecular markers specific for Ae. uniaristata chromosomes need to be developed. Standard C-banding shows that C-bands mainly exist in the centromeric regions of Ae. uniaristata but rarely at the distal ends. Fluorescence in situ hybridization (FISH) using (GAA)8 as a probe showed that the hybridization signal of chromosomes 1N-7N are different, thus (GAA)8 can be used to identify all Ae. uniaristata chromosomes in wheat background simultaneously. Moreover, a total of 42 molecular markers specific for Ae. uniaristata chromosomes were developed by screening expressed sequence tag - sequence tagged site (EST-STS), expressed sequence tag - simple sequence repeat (EST-SSR), and PCR-based landmark unique gene (PLUG) primers. The markers were subsequently localized using the CS - Ae. uniaristata addition lines and different wheat cultivars as controls. The cytogenetic and molecular markers developed herein will be helpful for screening and identifying wheat - Ae. uniaristata progeny.

  10. Genetic and molecular characterization of photoperiod and thermo-sensitive male sterility in rice.

    Science.gov (United States)

    Fan, Yourong; Zhang, Qifa

    2018-03-01

    A review on photoperiod and temperature-sensitive genic male sterility in rice. Male sterility in plants, facilitating the development of hybrid crops, has made great contribution to crop productivity worldwide. Environment-sensitive genic male sterility (EGMS), including photoperiod-sensitive genic male sterility (PGMS) and temperature-sensitive genic male sterility (TGMS), has provided a special class of germplasms for the breeding of "two-line" hybrids in several crops. In rice, the finding of the PGMS NK58S mutant in 1973 started the journey of research and breeding of two-line hybrids. Genetic and molecular characterization of these germplasms demonstrated diverse genes and molecular mechanisms of male sterility regulation. Two loci identified from NK58S, PMS1 and PMS3, both encode long noncoding RNAs. A major TGMS locus, TMS5, found in the TGMS line Annong S-1, encodes an RNase Z. A reverse PGMS mutant carbon starved anther encodes an R2R3 MYB transcription factor. Breeding efforts in the last three decades have resulted in hundreds of EGMS lines and two-line hybrids released to rice production, which have greatly elevated the yield potential and grain quality of rice varieties. The enhanced molecular understanding will offer new strategies for the development of EGMS lines thus further improving two-line hybrid breeding of rice as well as other crops.

  11. Identification of genes associated with cisplatin resistance in human oral squamous cell carcinoma cell line

    OpenAIRE

    Zhang Ping; Zhang Zhiyuan; Zhou Xiaojian; Qiu Weiliu; Chen Fangan; Chen Wantao

    2006-01-01

    Abstract Background Cisplatin is widely used for chemotherapy of head and neck squamous cell carcinoma. However, details of the molecular mechanism responsible for cisplatin resistance are still unclear. The aim of this study was to identify the expression of genes related to cisplatin resistance in oral squamous cell carcinoma cells. Methods A cisplatin-resistant cell line, Tca/cisplatin, was established from a cisplatin-sensitive cell line, Tca8113, which was derived from moderately-differe...

  12. Second-order quadrupolar line shapes under molecular dynamics: An additional transition in the extremely fast regime.

    Science.gov (United States)

    Hung, Ivan; Wu, Gang; Gan, Zhehong

    NMR spectroscopy is a powerful tool for probing molecular dynamics. For the classic case of two-site exchange, NMR spectra go through the transition from exchange broadening through coalescence and then motional narrowing as the exchange rate increases passing through the difference between the resonance frequencies of the two sites. For central-transition spectra of half-integer quadrupolar nuclei in solids, line shape change due to molecular dynamics occurs in two stages. The first stage occurs when the exchange rate is comparable to the second-order quadrupolar interaction. The second spectral transition comes at a faster exchange rate which approaches the Larmor frequency and generally reduces the isotropic quadrupolar shift. Such a two-stage transition phenomenon is unique to half-integer quadrupolar nuclei. A quantum mechanical formalism in full Liouville space is presented to explain the physical origin of the two-stage phenomenon and for use in spectral simulations. Variable-temperature 17 O NMR of solid NaNO 3 in which the NO 3 - ion undergoes 3-fold jumps confirms the two-stage transition process. The spectra of NaNO 3 acquired in the temperature range of 173-413K agree well with simulations using the quantum mechanical formalism. The rate constants for the 3-fold NO 3 - ion jumps span eight orders of magnitude (10 2 -10 10 s -1 ) covering both transitions of the dynamic 17 O line shape. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. Using molecular tools to identify the geographical origin of a case of human brucellosis.

    Science.gov (United States)

    Muchowski, J K; Koylass, M S; Dainty, A C; Stack, J A; Perrett, L; Whatmore, A M; Perrier, C; Chircop, S; Demicoli, N; Gatt, A B; Caruana, P A; Gopaul, K K

    2015-10-01

    Although Malta is historically linked with the zoonosis brucellosis, there had not been a case of the disease in either the human or livestock population for several years. However, in July 2013 a case of human brucellosis was identified on the island. To determine whether this recent case originated in Malta, four isolates from this case were subjected to molecular analysis. Molecular profiles generated using multilocus sequence analysis and multilocus variable number tandem repeat for the recent human case isolates and 11 Brucella melitensis strains of known Maltese origin were compared with others held on in-house and global databases. While the 11 isolates of Maltese origin formed a distinct cluster, the recent human isolation was not associated with these strains but instead clustered with isolates originating from the Horn of Africa. These data was congruent with epidemiological trace-back showed that the individual had travelled to Malta from Eritrea. This work highlights the potential of using molecular typing data to aid in epidemiological trace-back of Brucella isolations and assist in monitoring of the effectiveness of brucellosis control schemes.

  14. Production and molecular characterization of bread wheat lines with reduced amount of α-type gliadins.

    Science.gov (United States)

    Camerlengo, Francesco; Sestili, Francesco; Silvestri, Marco; Colaprico, Giuseppe; Margiotta, Benedetta; Ruggeri, Roberto; Lupi, Roberta; Masci, Stefania; Lafiandra, Domenico

    2017-12-19

    Among wheat gluten proteins, the α-type gliadins are the major responsible for celiac disease, an autoimmune disorder that affects about 1% of the world population. In fact, these proteins contain several toxic and immunogenic epitopes that trigger the onset of the disease. The α-type gliadins are a multigene family, encoded by genes located at the complex Gli-2 loci. Here, three bread wheat deletion lines (Gli-A2, Gli-D2 and Gli-A2/Gli-D2) at the Gli-2 loci were generated by the introgression in the bread wheat cultivar Pegaso of natural mutations, detected in different bread wheat cultivars. The molecular characterization of these lines allowed the isolation of 49 unique expressed genes coding α-type gliadins, that were assigned to each of the three Gli-2 loci. The number and the amount of α-type gliadin transcripts were drastically reduced in the deletion lines. In particular, the line Gli-A2/Gli-D2 contained only 12 active α-type gliadin genes (-75.6% respect to the cv. Pegaso) and a minor level of transcripts (-80% compared to cv. Pegaso). Compensatory pleiotropic effects were observed in the two other classes of gliadins (ω- and γ-gliadins) either at gene expression or protein levels. Although the comparative analysis of the deduced amino acid sequences highlighted the typical structural features of α-type gliadin proteins, substantial differences were displayed among the 49 proteins for the presence of toxic and immunogenic epitopes. The deletion line Gli-A2/Gli-D2 did not contain the 33-mer peptide, one of the major epitopes triggering the celiac disease, representing an interesting material to develop less "toxic" wheat varieties.

  15. Gene expression profiling identifies FYN as an important molecule in tamoxifen resistance and a predictor of early recurrence in patients treated with endocrine therapy

    DEFF Research Database (Denmark)

    Elias, D; (Hansen) Vever, Henriette; Lænkholm, A-V

    2015-01-01

    To elucidate the molecular mechanisms of tamoxifen resistance in breast cancer, we performed gene array analyses and identified 366 genes with altered expression in four unique tamoxifen-resistant (TamR) cell lines vs the parental tamoxifen-sensitive MCF-7/S0.5 cell line. Most of these genes were...

  16. Derivation and Osmotolerance Characterization of Three Immortalized Tilapia (Oreochromis mossambicus) Cell Lines

    Science.gov (United States)

    Gardell, Alison M.; Qin, Qin; Rice, Robert H.; Li, Johnathan; Kültz, Dietmar

    2014-01-01

    Fish cell cultures are becoming more widely used models for investigating molecular mechanisms of physiological response to environmental challenge. In this study, we derived two immortalized Mozambique tilapia (Oreochromis mossambicus) cell lines from brain (OmB) and lip epithelium (OmL), and compared them to a previously immortalized bulbus arteriosus (TmB) cell line. The OmB and OmL cell lines were generated without or with Rho-associated kinase (ROCK) inhibitor/3T3 feeder layer supplementation. Although both approaches were successful, ROCK inhibitor/feeder layer supplementation was found to offer the advantages of selecting for epithelial-like cell type and decreasing time to immortalization. After immortalization (≥ passage 5), we characterized the proteomes of the newly derived cell lines (OmB and OmL) using LCMS and identified several unique cell markers for each line. Subsequently, osmotolerance for each of the three cell lines following acute exposure to elevated sodium chloride was evaluated. The acute maximum osmotolerance of these tilapia cell lines (>700 mOsm/kg) was markedly higher than that of any other known vertebrate cell line, but was significantly higher in the epithelial-like OmL cell line. To validate the physiological relevance of these tilapia cell lines, we quantified the effects of acute hyperosmotic challenge (450 mOsm/kg and 700 mOsm/kg) on the transcriptional regulation of two enzymes involved in biosynthesis of the compatible organic osmolyte, myo-inositol. Both enzymes were found to be robustly upregulated in all three tilapia cell lines. Therefore, the newly established tilapia cells lines represent valuable tools for studying molecular mechanisms involved in the osmotic stress response of euryhaline fish. PMID:24797371

  17. The millimeter IRAM-30 m line survey toward IK Tauri

    Science.gov (United States)

    Velilla Prieto, L.; Sánchez Contreras, C.; Cernicharo, J.; Agúndez, M.; Quintana-Lacaci, G.; Bujarrabal, V.; Alcolea, J.; Balança, C.; Herpin, F.; Menten, K. M.; Wyrowski, F.

    2017-01-01

    Aims: We aim to investigate the physical and chemical properties of the molecular envelope of the oxygen-rich AGB star IK Tau. Methods: We carried out a millimeter wavelength line survey between 79 and 356 GHz with the IRAM-30 m telescope. We analysed the molecular lines detected in IK Tau using the population diagram technique to derive rotational temperatures and column densities. We conducted a radiative transfer analysis of the SO2 lines, which also helped us to verify the validity of the approximated method of the population diagram for the rest of the molecules. Results: For the first time in this source we detected rotational lines in the ground vibrational state of HCO+, NS, NO, and H2CO, as well as several isotopologues of molecules previously identified, namely, C18O, Si17O, Si18O, 29SiS, 30SiS, Si34S, H13CN, 13CS, C34S, H234S, 34SO, and 34SO2. We also detected several rotational lines in vibrationally excited states of SiS and SiO isotopologues, as well as rotational lines of H2O in the vibrationally excited state ν2 = 2. We have also increased the number of rotational lines detected of molecules that were previously identified toward IK Tau, including vibrationally excited states, enabling a detailed study of the molecular abundances and excitation temperatures. In particular, we highlight the detection of NS and H2CO with fractional abundances of f(NS) 10-8 and f(H2CO) [10-7-10-8]. Most of the molecules display rotational temperatures between 15 and 40 K. NaCl and SiS isotopologues display rotational temperatures higher than the average ( 65 K). In the case of SO2 a warm component with Trot 290 K is also detected. Conclusions: With a total of 350 lines detected of 34 different molecular species (including different isotopologues), IK Tau displays a rich chemistry for an oxygen-rich circumstellar envelope. The detection of carbon bearing molecules like H2CO, as well as the discrepancies found between our derived abundances and the predictions from

  18. FIMS Wavelength Calibration via Airglow Line Observations

    Directory of Open Access Journals (Sweden)

    Dae-Hee Lee

    2004-12-01

    Full Text Available Far-ultraviolet Imaging Spectrograph (FIMS is the main payload of the Korea's first scientific micro satellite STSAT-1, which was launched at Sep. 27 2003 successfully. Major objective of FIMS is observing hot gas in the Galaxy in FUV bands to diagnose the energy flow models of the interstellar medium. Supernova remnants, molecular clouds, and Aurora emission in the geomagnetic pole regions are specific targets for pointing observation. Although the whole system was calibrated before launch, it is essential to perform on-orbit calibration for data analysis. For spectral calibration, we observed airglow lines in the atmosphere since they provide good spectral references. We identify and compare the observed airglow lines with model calculations, and correct the spectral distortion appeared in the detector system to improve the spectral resolution of the system.

  19. Line emission processes in atomic and molecular shocks

    International Nuclear Information System (INIS)

    Shull, J.M.

    1988-01-01

    The review discusses the observations and theoretical models of interstellar shock waves in diffuse and molecular clouds. After summarizing the relevant gas dynamics, atomic, molecular and grain processes, and physics of radiative and magnetic precursors, the author describes observational diagnostics of shocks. This paper concludes with a discussion of two topics: unstable or non-steady shocks and thermal conduction in metal-rich shocks

  20. Spectral shapes of Ar-broadened HCl lines in the fundamental band by classical molecular dynamics simulations and comparison with experiments

    Energy Technology Data Exchange (ETDEWEB)

    Tran, H., E-mail: ha.tran@lisa.u-pec.fr [Laboratoire Interuniversitaire des Systèmes Atmosphériques, UMR CNRS 7583, Université Paris Est Créteil, Université Paris Diderot, Institut Pierre-Simon Laplace, 94010 Créteil Cedex (France); Domenech, J.-L. [Instituto de Estructura de la Materia, Consejo Superior de Investigaciones Cientificas, (IEM-CSIC), Serrano 123, 28006 Madrid (Spain)

    2014-08-14

    Spectral shapes of isolated lines of HCl perturbed by Ar are investigated for the first time using classical molecular dynamics simulations (CMDS). Using reliable intermolecular potentials taken from the literature, these CMDS provide the time evolution of the auto-correlation function of the dipole moment, whose Fourier-Laplace transform leads to the absorption spectrum. In order to test these calculations, room temperature spectra of various lines in the fundamental band of HCl diluted in Ar are measured, in a large pressure range, with a difference-frequency laser spectrometer. Comparisons between measured and calculated spectra show that the CMDS are able to predict the large Dicke narrowing effect on the shape of HCl lines and to satisfactorily reproduce the shapes of HCl spectra at different pressures and for various rotational quantum numbers.

  1. CHEMICAL ANALYSIS OF A DIFFUSE CLOUD ALONG A LINE OF SIGHT TOWARD W51: MOLECULAR FRACTION AND COSMIC-RAY IONIZATION RATE

    Energy Technology Data Exchange (ETDEWEB)

    Indriolo, Nick; Neufeld, D. A. [Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD 21218 (United States); Gerin, M. [LERMA, CNRS, Observatoire de Paris and ENS, F-75231 Paris Cedex 05 (France); Geballe, T. R. [Gemini Observatory, Hilo, HI 96720 (United States); Black, J. H. [Department of Earth and Space Sciences, Chalmers University of Technology, Onsala Space Observatory, SE-43992 Onsala (Sweden); Menten, K. M. [MPI fuer Radioastronomie, D-53121 Bonn (Germany); Goicoechea, J. R. [Departamento de Astrofisica, Centro de Astrobiologia (CSIC-INTA), E-28850 Madrid (Spain)

    2012-10-20

    Absorption lines from the molecules OH{sup +}, H{sub 2}O{sup +}, and H{sup +} {sub 3} have been observed in a diffuse molecular cloud along a line of sight near W51 IRS2. We present the first chemical analysis that combines the information provided by all three of these species. Together, OH{sup +} and H{sub 2}O{sup +} are used to determine the molecular hydrogen fraction in the outskirts of the observed cloud, as well as the cosmic-ray ionization rate of atomic hydrogen. H{sup +} {sub 3} is used to infer the cosmic-ray ionization rate of H{sub 2} in the molecular interior of the cloud, which we find to be {zeta}{sub 2} = (4.8 {+-} 3.4) Multiplication-Sign 10{sup -16} s{sup -1}. Combining the results from all three species we find an efficiency factor-defined as the ratio of the formation rate of OH{sup +} to the cosmic-ray ionization rate of H-of {epsilon} = 0.07 {+-} 0.04, much lower than predicted by chemical models. This is an important step in the future use of OH{sup +} and H{sub 2}O{sup +} on their own as tracers of the cosmic-ray ionization rate.

  2. Carbon K-shell photoionization of CO: Molecular frame angular distributions of normal and conjugate shakeup satellites

    International Nuclear Information System (INIS)

    Jahnke, T.; Titze, J.; Foucar, L.; Wallauer, R.; Osipov, T.; Benis, E.P.; Jagutzki, O.; Arnold, W.; Czasch, A.; Staudte, A.; Schoeffler, M.; Alnaser, A.; Weber, T.; Prior, M.H.; Schmidt-Boecking, H.; Doerner, R.

    2011-01-01

    We have measured the molecular frame angular distributions of photoelectrons emitted from the Carbon K-shell of fixed-in-space CO molecules for the case of simultaneous excitation of the remaining molecular ion. Normal and conjugate shakeup states are observed. Photoelectrons belonging to normal Σ-satellite lines show an angular distribution resembling that observed for the main photoline at the same electron energy. Surprisingly a similar shape is found for conjugate shakeup states with Π-symmetry. In our data we identify shake rather than electron scattering (PEVE) as the mechanism producing the conjugate lines. The angular distributions clearly show the presence of a Σ shape resonance for all of the satellite lines.

  3. Biomolecule-loaded chitosan nanoparticles induce apoptosis and molecular changes in cancer cell line (SiHa).

    Science.gov (United States)

    Sujima Anbu, Anbu; Velmurugan, Palanivel; Lee, Jeong-Ho; Oh, Byung-Taek; Venkatachalam, Perumal

    2016-07-01

    The present study reports on the synthesis of chitosan nanoparticles (CNPs) using methanol extracts of Gymnema sylvestre (GS) leaves and Cinnamomum zeylanicum (CZ) bark. Biomolecule-loaded nanoparticles induced apoptosis in a human cervical cancer (SiHa) cell line, and experiments were carried out to elucidate the underlying molecular mechanisms. FT-IR and XRD showed possible functional groups of the biomolecules and the crystalline nature of CNPs, respectively. Transmission electron microscopy images revealed that synthesized GSCNPs and CZCNPs had a smooth spherical shape with average sizes of about 58-80 and 60-120nm, respectively. Dynamic light scattering studies indicated that both GSCNPs and CZCNs were structurally stable with homogenous and heterogeneous natures, respectively. Furthermore, synthesized GSCNPs and CZCNPs exhibited dose-dependent cytotoxicity against the SiHa cancer cell line, with inhibitory concentration (IC50) values of 102.17μg/ml, 87.75μg/ml, 132.74μg/ml and 90.35μg/ml for GS leaf extract, GSCNPs, CZBE and CZCNPs, respectively. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Micro RNAs as molecular markers of glioblastoma multiform

    Energy Technology Data Exchange (ETDEWEB)

    Farace, M G [Department Experimental Medicine and Biochemical Sciences, University of Tor Vergata, Rome (Italy); Finocchiaro, G [Istituto Neurologico Besta, Milan (Italy); Ricci Vitiani, L [Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanita, Rome (Italy)

    2009-07-01

    The aim of this project was to unravel the role that miR-221 and miR-222, of which we had already demonstrated the specific differential expression in glioblastoma multiforme compared to normal brain, play in the control of cell proliferation, with the ultimate goal to provide new insights in the molecular basis of cancer. The results of our research allowed to identify an important molecular target for miRNA-221 and miR-222, highly expressed in glioblastoma multiforme tissues and cell lines, and to precisely recognize the mRNA regions responsible for this regulation.

  5. Micro RNAs as molecular markers of glioblastoma multiform

    International Nuclear Information System (INIS)

    Farace, M.G.; Finocchiaro, G.; Ricci Vitiani, L.

    2009-01-01

    The aim of this project was to unravel the role that miR-221 and miR-222, of which we had already demonstrated the specific differential expression in glioblastoma multiforme compared to normal brain, play in the control of cell proliferation, with the ultimate goal to provide new insights in the molecular basis of cancer. The results of our research allowed to identify an important molecular target for miRNA-221 and miR-222, highly expressed in glioblastoma multiforme tissues and cell lines, and to precisely recognize the mRNA regions responsible for this regulation

  6. Molecular clouds without detectable CO

    International Nuclear Information System (INIS)

    Blitz, L.; Bazell, D.; Desert, F.X.

    1990-01-01

    The clouds identified by Desert, Bazell, and Boulanger (DBB clouds) in their search for high-latitude molecular clouds were observed in the CO (J = 1-0) line, but only 13 percent of the sample was detected. The remaining 87 percent are diffuse molecular clouds with CO abundances of about 10 to the -6th, a typical value for diffuse clouds. This hypothesis is shown to be consistent with Copernicus data. The DBB clouds are shown to be an essentially complete catalog of diffuse molecular clouds in the solar vicinity. The total molecular surface density in the vicinity of the sun is then only about 20 percent greater than the 1.3 solar masses/sq pc determined by Dame et al. (1987). Analysis of the CO detections indicates that there is a sharp threshold in extinction of 0.25 mag before CO is detectable and is derived from the IRAS I(100) micron threshold of 4 MJy/sr. This threshold is presumably where the CO abundance exhibits a sharp increase 18 refs

  7. Agronomic and molecular evaluation of induced mutant rice (oryza sativa l.) lines in Egypt

    International Nuclear Information System (INIS)

    Sshehzad, T.; Allah, A.; Aallah, E.A.; Ammar, M.H.; Abdelkhalik, A.H.

    2011-01-01

    The present study was conducted at the farm of the Rice Research and Training Center, Sakha, Kafr El-Sheikh, Egypt, during 2000-2007 rice sowing seasons. Five rice varieties viz., Giza 171, Giza 175, Giza 176, Giza 181 and GZ 1368 were the most widely grown Japonica and Indica types in Egypt during the last period, possesses at that time many positive agronomic characteristics including wide adaptability, high yield potential, tolerance to stresses and good eating quality. But with the passage of time it has lost its vigor. In Rice Research Program, Egypt, dry seeds of the above mentioned varieties were treated with different doses of gamma rays (100, 200, 300, 400, and 500 Gy) for raising M1 generation. M1 plants were established by transplanting in the year 2000 season. One hundred independent lines have been advanced to M5 generation enabling evaluation of quantitative traits by replicated trials and promising lines were selected and tested in multi-location trials as M6, M7 and M8 generations. Morphological variations at vegetative and reproductive stages including plant type and various physiological characters were observed in the five populations. The mutant lines characteristics consisted of better resistance to lodging, blast disease, high yield potential, as well as early maturity. Results from yield trials and molecular assessments indicated that the mutants differed genetically from their parents. So, these mutants could be used as a donor parents in rice breeding program and some of them can be recommended as new rice varieties suitable for rice belt in Egypt. (author)

  8. Expression of the chondroitin sulphate proteoglycan molecular complex in six human melanoma xenograft lines studied by flow cytometry and immunohistochemistry.

    Science.gov (United States)

    Nagelhus, T A; Rofstad, E K

    1993-06-01

    The expression of the chondroitin sulphate proteoglycan (CSP) molecular complex in six human melanoma xenograft lines (BEX-t, COX-t, HUX-t, ROX-t, SAX-t, WIX-t) was studied by flow cytometry and immunohistochemistry using the monoclonal antibodies 9.2.27, ME31.3, G7A5, and NKI.M6. The two methods and the four antibodies gave consistent results. The six melanoma lines could be divided into three distinct groups of two lines each; expression was high in the HUX-t and ROX-t lines and intermediate in the BEX-t and SAX-t lines, whereas the COX-t and WIX-t lines were negative. The mean number of epitopes per cell for 9.2.27 was approximately twice as high as for ME31.3, G7A5, and NKI.M6 and was estimated to range from 0.8 +/- 0.1 x 10(5) to 1.9 +/- 0.2 x 10(5) in the positive xenograft lines. The expression of the CSP complex was heterogeneous. The immunofluorescence histograms measured by flow cytometry were therefore broad for all tumour lines. A significant fraction of the HUX-t cells was negative or weakly stained. These cells appeared as clear negative patches in the immunohistochemical preparations. Moreover, most morphologically intact tumour cells adjacent to necrotic areas did not show significant expression of the CSP complex, irrespective of tumour line. These cells were probably hypoxic and thus resistant to radiation therapy. The expression of the CSP complex in the xenograft lines was similar to that reported for melanoma in man.

  9. An SSH library responsive to azadirachtin A constructed in Spodoptera litura Fabricius cell lines.

    Science.gov (United States)

    Yan, Chao; Zhang, Zhi-Xiang; Xu, Han-Hong

    2012-05-31

    The present study revealed differentially expressed genes responsive to azadirachtin A (Aza) in Spodoptera litura cell line through suppression subtractive hybridization. In the Aza-responsive SSH library, approximately 270 sequences represent 53 different identified genes encoding proteins with various predicted functions, and the percentages of the gene clusters were 26.09% (genetic information processing), 11.41% (cell growth and death), 7.07% (metabolism), 6.52% (signal transduction/transport) and 2.72% (immunity), respectively. Eleven clones homologous to identified genes were selected to be confirmed through quantitative real time polymerase chain reaction. Among the eleven clones validated, all but one transcript of lipase showed an increase in SL cell line collected from ETA, whereas the transcripts of other genes were lower in the SL cell line collected from ETA compared with that of UETA. These genes were considered to be related to the response of SL cell line to Aza. These will provide a new clue to uncover the molecular mechanisms of Aza acting on SL cell line. Copyright © 2012 Elsevier B.V. All rights reserved.

  10. Identifying molecular subtypes in human colon cancer using gene expression and DNA methylation microarray data.

    Science.gov (United States)

    Ren, Zhonglu; Wang, Wenhui; Li, Jinming

    2016-02-01

    Identifying colon cancer subtypes based on molecular signatures may allow for a more rational, patient-specific approach to therapy in the future. Classifications using gene expression data have been attempted before with little concordance between the different studies carried out. In this study we aimed to uncover subtypes of colon cancer that have distinct biological characteristics and identify a set of novel biomarkers which could best reflect the clinical and/or biological characteristics of each subtype. Clustering analysis and discriminant analysis were utilized to discover the subtypes in two different molecular levels on 153 colon cancer samples from The Cancer Genome Atlas (TCGA) Data Portal. At gene expression level, we identified two major subtypes, ECL1 (expression cluster 1) and ECL2 (expression cluster 2) and a list of signature genes. Due to the heterogeneity of colon cancer, the subtype ECL1 can be further subdivided into three nested subclasses, and HOTAIR were found upregulated in subclass 2. At DNA methylation level, we uncovered three major subtypes, MCL1 (methylation cluster 1), MCL2 (methylation cluster 2) and MCL3 (methylation cluster 3). We found only three subtypes of CpG island methylator phenotype (CIMP) in colon cancer instead of the four subtypes in the previous reports, and we found no sufficient evidence to subdivide MCL3 into two distinct subgroups.

  11. Molecular analysis of urothelial cancer cell lines for modeling tumor biology and drug response.

    Science.gov (United States)

    Nickerson, M L; Witte, N; Im, K M; Turan, S; Owens, C; Misner, K; Tsang, S X; Cai, Z; Wu, S; Dean, M; Costello, J C; Theodorescu, D

    2017-01-05

    The utility of tumor-derived cell lines is dependent on their ability to recapitulate underlying genomic aberrations and primary tumor biology. Here, we sequenced the exomes of 25 bladder cancer (BCa) cell lines and compared mutations, copy number alterations (CNAs), gene expression and drug response to BCa patient profiles in The Cancer Genome Atlas (TCGA). We observed a mutation pattern associated with altered CpGs and APOBEC-family cytosine deaminases similar to mutation signatures derived from somatic alterations in muscle-invasive (MI) primary tumors, highlighting a major mechanism(s) contributing to cancer-associated alterations in the BCa cell line exomes. Non-silent sequence alterations were confirmed in 76 cancer-associated genes, including mutations that likely activate oncogenes TERT and PIK3CA, and alter chromatin-associated proteins (MLL3, ARID1A, CHD6 and KDM6A) and established BCa genes (TP53, RB1, CDKN2A and TSC1). We identified alterations in signaling pathways and proteins with related functions, including the PI3K/mTOR pathway, altered in 60% of lines; BRCA DNA repair, 44%; and SYNE1-SYNE2, 60%. Homozygous deletions of chromosome 9p21 are known to target the cell cycle regulators CDKN2A and CDKN2B. This loci was commonly lost in BCa cell lines and we show the deletions extended to the polyamine enzyme methylthioadenosine (MTA) phosphorylase (MTAP) in 36% of lines, transcription factor DMRTA1 (27%) and antiviral interferon epsilon (IFNE, 19%). Overall, the BCa cell line genomic aberrations were concordant with those found in BCa patient tumors. We used gene expression and copy number data to infer pathway activities for cell lines, then used the inferred pathway activities to build a predictive model of cisplatin response. When applied to platinum-treated patients gathered from TCGA, the model predicted treatment-specific response. Together, these data and analysis represent a valuable community resource to model basic tumor biology and to study

  12. IDEN2-A program for visual identification of spectral lines and energy levels in optical spectra of atoms and simple molecules

    Science.gov (United States)

    Azarov, V. I.; Kramida, A.; Vokhmentsev, M. Ya.

    2018-04-01

    The article describes a Java program that can be used in a user-friendly way to visually identify spectral lines observed in complex spectra with theoretically predicted transitions between atomic or molecular energy levels. The program arranges various information about spectral lines and energy levels in such a way that line identification and determination of positions of experimentally observed energy levels become much easier tasks that can be solved fast and efficiently.

  13. A suite of molecular markers for identifying species, detecting introgression and describing population structure in spadefoot toads (Spea spp.).

    Science.gov (United States)

    Pfennig, Karin S; Allenby, Ashley; Martin, Ryan A; Monroy, Anaïs; Jones, Corbin D

    2012-09-01

    Two congeneric species of spadefoot toad, Spea multiplicata and Spea bombifrons, have been the focus of hybridization studies since the 1970s. Because complex hybrids are not readily distinguished phenotypically, genetic markers are needed to identify introgressed individuals. We therefore developed a set of molecular markers (amplified fragment length polymorphism, polymerase chain reaction-restriction fragment length polymorphism and single nucleotide polymorphism) for identifying pure-species, F1 hybrids and more complex introgressed types. To do so, we tested a series of markers across both species and known hybrids using populations in both allopatry and sympatry. We retained those markers that differentiated the two pure-species and also consistently identified known species hybrids. These markers are well suited for identifying hybrids between these species. Moreover, those markers that show variation within each species can be used in conjunction with existing molecular markers in studies of population structure and gene flow. © 2012 Blackwell Publishing Ltd.

  14. A 6-gene signature identifies four molecular subgroups of neuroblastoma

    Science.gov (United States)

    2011-01-01

    Background There are currently three postulated genomic subtypes of the childhood tumour neuroblastoma (NB); Type 1, Type 2A, and Type 2B. The most aggressive forms of NB are characterized by amplification of the oncogene MYCN (MNA) and low expression of the favourable marker NTRK1. Recently, mutations or high expression of the familial predisposition gene Anaplastic Lymphoma Kinase (ALK) was associated to unfavourable biology of sporadic NB. Also, various other genes have been linked to NB pathogenesis. Results The present study explores subgroup discrimination by gene expression profiling using three published microarray studies on NB (47 samples). Four distinct clusters were identified by Principal Components Analysis (PCA) in two separate data sets, which could be verified by an unsupervised hierarchical clustering in a third independent data set (101 NB samples) using a set of 74 discriminative genes. The expression signature of six NB-associated genes ALK, BIRC5, CCND1, MYCN, NTRK1, and PHOX2B, significantly discriminated the four clusters (p INSS stage 4 and/or dead of disease, p < 0.05, Fisher's exact test). Conclusions Based on expression profiling we have identified four molecular subgroups of neuroblastoma, which can be distinguished by a 6-gene signature. The fourth subgroup has not been described elsewhere, and efforts are currently made to further investigate this group's specific characteristics. PMID:21492432

  15. Molecular and Functional Characterization of GR2-R1 Event Based Backcross Derived Lines of Golden Rice in the Genetic Background of a Mega Rice Variety Swarna.

    Directory of Open Access Journals (Sweden)

    Haritha Bollinedi

    Full Text Available Homozygous Golden Rice lines developed in the background of Swarna through marker assisted backcross breeding (MABB using transgenic GR2-R1 event as a donor for the provitamin A trait have high levels of provitamin A (up to 20 ppm but are dwarf with pale green leaves and drastically reduced panicle size, grain number and yield as compared to the recurrent parent, Swarna. In this study, we carried out detailed morphological, biochemical and molecular characterization of these lines in a quest to identify the probable reasons for their abnormal phenotype. Nucleotide blast analysis with the primer sequences used to amplify the transgene revealed that the integration of transgene disrupted the native OsAux1 gene, which codes for an auxin transmembrane transporter protein. Real time expression analysis of the transgenes (ZmPsy and CrtI driven by endosperm-specific promoter revealed the leaky expression of the transgene in the vegetative tissues. We propose that the disruption of OsAux1 disturbed the fine balance of plant growth regulators viz., auxins, gibberellic acid and abscisic acid, leading to the abnormalities in the growth and development of the lines homozygous for the transgene. The study demonstrates the conserved roles of OsAux1 gene in rice and Arabidopsis.

  16. A novel cell growth-promoting factor identified in a B cell leukemia cell line, BALL-1

    International Nuclear Information System (INIS)

    Dao, T.; Holan, V.; Minowada, J.

    1993-01-01

    A novel leukemia cell growth-promoting activity has been identified in the culture supernatant from a human B cell leukemia cell line, BALL-1. The supernatant from unstimulated cultures of the BALL-1 cells significantly promoted the growth of 16 out of 24 leukemia/lymphoma cell lines of different lineages (T, B and non-lymphoid) in a minimal concentration of fetal bovine serum (FBS), and 5 out of 12 cases of fresh leukemia cells in FBS-free medium. The growth-promoting sieve filtration and dialysis. The MW of the factor was less than 10 kDa. The growth-promoting activity was heat and acid stable and resistant to trypsin treatment. The factor isolated from the BALL-1 supernatant was distinct from known polypeptide growth factors with MW below 10 kDa, such as epidermal growth factor, transforming growth factor α, insulin-like growth factor I (IGF-I), IGF-II and insulin, as determine by specific antibodies and by cell-growth-promoting tests. The factor is the BALL-1 supernatant did not promote the proliferation of normal human fresh peripheral blood lymphocytes or mouse fibroblast cell line, BALB/C 3T3. In addition to the BALL-1 supernatant, a similar growth-promoting activity was found in the culture supernatant from 13 of 17 leukemia/lymphoma cell lines tested. The activity in these culture supernatant promoted the growth of leukemia/lymphoma cell lines in autocrine and/or paracrine fashions. These observations suggest that the low MW cell growth-promoting activity found in the BALL-1 culture supernatant is mediated by a novel factor which may be responsible for the clonal expansion of particular leukemic clones. (author)

  17. Radio molecular maser line study of symbiotic stars

    International Nuclear Information System (INIS)

    Cohen, N.L.; Ghigo, F.D.

    1980-01-01

    A sample of symbiotic stars has been searched for maser emission from the 1665- and 1667-MHz OH mainlines, the 22-GHz H 2 O line, and the 43-GHz SiO line. R Aqr remains the sole symbiotic for which maser emission has been detected. Its SiO spectrum reveals a pedestal of emission with a narrow superposed peak at V/sub LSR/ -26.4 +- 0.7 km/s. The line's existence and the pedestal feature are both characteristic of SiO lines found in late-type variables by Snyder et al. [Astrophys. J. 224, 512 (1978)]. For the other symbiotic stars, it is possible that conditions favorable for maser emission have been suppressed by the presence of a hot companion. Alternatively our findings may argue against the presence of late-type variables in symbiotic stars. In either case, R Aqr seems to be in a class by itself. We cannot confirm the suggestion that R Aqr is a binary, since the spectral feature has not shifted noticeably in the two years since the observations by Lepine, LeSqueren, and Scalise [Astrophys. J. 225, 869 (1978)]. However, we point out that monitoring the pedestal emission over a number of years is the least ambiguous way to discern any velocity shift that might result from orbital motion

  18. Treatment paradigms for patients with metastatic non small cell lung cancer (NSCLC, squamous lung cancer: first, second and third-line

    Directory of Open Access Journals (Sweden)

    Abdulaziz eAl Farsi

    2014-06-01

    Full Text Available Historically, the treatment algorithm applied to non small cell lung cancer (NSCLC was the same for all histologic subtypes. However, recent advances in our understanding of the molecular profiles of squamous and non-squamous NSCLC have changed this perspective. Histologic subtype and the presence of specific molecular abnormalities have predictive value for response to and toxicity from therapy, as well as overall survival. For patients with squamous NSCLC, a platinum agent plus gemcitabine, or paclitaxel is recommended as first-line therapy. The role of EGFR monoclonal antibodies is uncertain. Maintenance therapy is not widely recommended, although data exist for the use of erlotinib. The standard recommendation for second-line therapy is docetaxel and erlotinib should be considered as second or third-line therapy. There is ongoing research identifying molecular targets in squamous NSCLC and many agents are in early phase clinical trials. Immunotherapeutic approaches targeting programmed death 1 receptor (PD-1 and its ligand (PD-L1 appear promising.

  19. Quantitative proteomics identify molecular targets that are crucial in larval settlement and metamorphosis of bugula neritina

    KAUST Repository

    Zhang, Huoming

    2011-01-07

    The marine invertebrate Bugula neritina has a biphasic life cycle that consists of a swimming larval stage and a sessile juvenile and adult stage. The attachment of larvae to the substratum and their subsequent metamorphosis have crucial ecological consequences. Despite many studies on this species, little is known about the molecular mechanism of these processes. Here, we report a comparative study of swimming larvae and metamorphosing individuals at 4 and 24 h postattachment using label-free quantitative proteomics. We identified more than 1100 proteins at each stage, 61 of which were differentially expressed. Specifically, proteins involved in energy metabolism and structural molecules were generally down-regulated, whereas proteins involved in transcription and translation, the extracellular matrix, and calcification were strongly up-regulated during metamorphosis. Many tightly regulated novel proteins were also identified. Subsequent analysis of the temporal and spatial expressions of some of the proteins and an assay of their functions indicated that they may have key roles in metamorphosis of B. neritina. These findings not only provide molecular evidence with which to elucidate the substantial changes in morphology and physiology that occur during larval attachment and metamorphosis but also identify potential targets for antifouling treatment. © 2011 American Chemical Society.

  20. Identifying self-interstitials of bcc and fcc crystals in molecular dynamics

    Science.gov (United States)

    Bukkuru, S.; Bhardwaj, U.; Warrier, M.; Rao, A. D. P.; Valsakumar, M. C.

    2017-02-01

    Identification of self-interstitials in molecular dynamics (MD) simulations is of critical importance. There exist several criteria for identifying the self-interstitial. Most of the existing methods use an assumed cut-off value for the displacement of an atom from its lattice position to identify the self-interstitial. The results obtained are affected by the chosen cut-off value. Moreover, these chosen cut-off values are independent of temperature. We have developed a novel unsupervised learning algorithm called Max-Space Clustering (MSC) to identify an appropriate cut-off value and its dependence on temperature. This method is compared with some widely used methods such as effective sphere (ES) method and nearest neighbor sphere (NNS) method. The cut-off radius obtained using our method shows a linear variation with temperature. The value of cut-off radius and its temperature dependence is derived for five bcc (Cr, Fe, Mo, Nb, W) and six fcc (Ag, Au, Cu, Ni, Pd, Pt) crystals. It is seen that the ratio of the cut-off values "r" to the lattice constant "a" lies between 0.23 and 0.3 at 300 K and this ratio is on an average smaller for the fcc crystals. Collision cascade simulations are carried out for Primary knock-on Atom (PKA) energies of 5 keV in Fe (at 300 K and 1000 K) and W (at 300 K and 2500 K) and the results are compared using the various methods.

  1. Line radiative transfer and statistical equilibrium

    NARCIS (Netherlands)

    Kamp, Inga

    Atomic and molecular line emission from protoplanetary disks contains key information of their detailed physical and chemical structures. To unravel those structures, we need to understand line radiative transfer in dusty media and the statistical equilibrium, especially of molecules. I describe

  2. Study of Outflow and Molecular Lines from the Observations of BHR71 by The Herschel Key Program,``Dust, Ice, and Gas In Time" (DIGIT)

    Science.gov (United States)

    Yang, Yao-Lun; Green, Joel D.

    2014-07-01

    The infall and outflow processes initiated by the collapse a dense core are widely observed in Class 0 protostars, and significantly change the density and temperature structure of the prestellar core as well as the following disk and envelope evolution. Since the Class 0 protostars are usually embedded in the cold molecular envelope preventing them from being observed at visible or near-IR wavelengths, the spectral analyses of the far-IR spectra provide us a window to look through the envelope and constrain the physical properties of the envelope and the core. BHR71, a Class 0 embedded protostar, is located in an isolated neighborhood with a collimated bipolar outflow and shows a rich far-IR spectrum as observed in the DIGIT program (PI: Neal Evans) with Herschel. It has numerous molecular and atomic features that can constrain its physical properties and the density structure well. In this research, we developed a robust data reduction (Green et al. 2013a, b) and automatic line fitting package that ensures all of the molecular and atomic lines are extracted to the same standard and it can be easily used for any other protostars observed by Herschel as well. We found 44 and 28 emission lines in the central spaxel in the PACS and the SPIRE bands respectively, including CO, 13CO, OH, and H2O. The extended feature observed at low-J CO and several H2O lines are consistent to the outflow direction but less collimated and a heterogeneous environment is concluded from the rotational diagram analysis. A dust Monte Carlo radiative transfer simulation using RADMC-3D will reveal the embedded structure with a dust density profile of a flared disk and a spherical envelope with bipolar outflow cavity. We will use a line radiative transfer simulation for multiple species to constrain the chemical abundance distributions and their temperature profiles.With high sensitivity spatial resolved spectra and simulated internal structure analysis of BHR71 will provide a good test of

  3. Radiation transport and the kinematics of molecular clouds

    International Nuclear Information System (INIS)

    Kwan, J.

    1978-01-01

    We compare line profiles calculated under either the systematic mottion interpretation or the turbulent motion interpretation of the molecular line widths, with the stipulation that both the density and temperature distributions be decreasing functions of radius. In systematic motion of the form V (r) proportional/sup -alpha/, α>0, optically thin lines observed toward the center are flat-topped or double-peaked, and optically thick lines are asymmetric. In a constant collapes or outflow velocity, optically thin lines observed toward the center are double-peaked, and optically thick lines arfe flat-topped. In systematic motion of the form V (r) proportionalr/sup α/,α>0, both optically thin and optically thick lines are centrally peaked. The distinguishing feature in this case is that the width (FWHM) of the CS 3→ 2 line is considerably smaller that that of the 13 CO 1 → 0 line. In turbulent motion, the CO 1 → 0, 2 → 1, and 3 → 2 lines are marked by progressively more pronounced self-absorptions.The observations at M17 SW and the Kleinmann-Low (KL) nebula are studied. At M17 SW, they are best accounted for by a model in which turbulence dominates the central part of the molecular region but collapse prevails at the outer part. At KL, the present observations can be equally well explained by one of two models. The first model postulates that KL is at the front face of the molecular cloud and that the temperature is highest at the surface. Turbulence gives rise to the line broadening. The second model postulates that KL is deep within the molecular cloud. Systematic motion about KL accounts for the CO and 13 CO line widths, but high-density fragments at KL are required to provide excitations in other molecular lines with considerably larger spontaneous emission rates

  4. Dissecting molecular stress networks: identifying nodes of divergence between life-history phenotypes.

    Science.gov (United States)

    Schwartz, Tonia S; Bronikowski, Anne M

    2013-02-01

    The complex molecular network that underlies physiological stress response is comprised of nodes (proteins, metabolites, mRNAs, etc.) whose connections span cells, tissues and organs. Variable nodes are points in the network upon which natural selection may act. Thus, identifying variable nodes will reveal how this molecular stress network may evolve among populations in different habitats and how it might impact life-history evolution. Here, we use physiological and genetic assays to test whether laboratory-born juveniles from natural populations of garter snakes (Thamnophis elegans), which have diverged in their life-history phenotypes, vary concomitantly at candidate nodes of the stress response network, (i) under unstressed conditions and (ii) in response to an induced stress. We found that two common measures of stress (plasma corticosterone and liver gene expression of heat shock proteins) increased under stress in both life-history phenotypes. In contrast, the phenotypes diverged at four nodes both under unstressed conditions and in response to stress: circulating levels of reactive oxygen species (superoxide, H(2)O(2)); liver gene expression of GPX1 and erythrocyte DNA damage. Additionally, allele frequencies for SOD2 diverge from neutral markers, suggesting diversifying selection on SOD2 alleles. This study supports the hypothesis that these life-history phenotypes have diverged at the molecular level in how they respond to stress, particularly in nodes regulating oxidative stress. Furthermore, the differences between the life-history phenotypes were more pronounced in females. We discuss the responses to stress in the context of the associated life-history phenotype and the evolutionary pressures thought to be responsible for divergence between the phenotypes. © 2012 Blackwell Publishing Ltd.

  5. Quantitative proteomics identifies central players in erlotinib resistance of the non-small cell lung cancer cell line HCC827

    DEFF Research Database (Denmark)

    Jacobsen, Kirstine; Lund, Rikke Raaen; Beck, Hans Christian

    Background: Erlotinib (Tarceva®, Roche) has significantly changed the treatment of non-small cell lung cancer (NSCLC) as 70% of patients show significant tumor regression when treated. However, all patients relapse due to development of acquired resistance, which in 43-50% of cases are caused...... by a secondary mutation (T790M) in EGFR. Importantly, a majority of resistance cases are still unexplained. Our aim is to identify novel resistance mechanisms in erlotinib-resistant subclones of the NSCLC cell line HCC827. Materials & Methods: We established 3 erlotinib-resistant subclones (resistant to 10, 20...... or other EGFR or KRAS mutations, potentiating the identification of novel resistance mechanisms. We identified 2875 cytoplasmic proteins present in all 4 cell lines. Of these 87, 56 and 23 are upregulated >1.5 fold; and 117, 72 and 32 are downregulated >1.5 fold, respectively, in the 3 resistant clones...

  6. Study for on-line system to identify inadvertent control rod drops in PWR reactors using ex-core detector and thermocouple measures

    International Nuclear Information System (INIS)

    Souza, Thiago J.; Medeiros, Jose A.C.C.; Goncalves, Alessandro C.

    2015-01-01

    Accidental control rod drops event in PWR reactors leads to an unsafe operating condition. It is important to quickly identify the rod to minimize undesirable effects in such a scenario. In this event, there is a distortion in the power distribution and temperature in the reactor core. The goal of this study is to develop an on-line model to identify the inadvertent control rod dropped in PWR reactor. The proposed model is based on physical correlations and pattern recognition of ex-core detector responses and thermocouples measures. The results of the study demonstrated the feasibility of an on-line system, contributing to safer operation conditions and preventing undesirable effects, as its shutdown. (author)

  7. Study for on-line system to identify inadvertent control rod drops in PWR reactors using ex-core detector and thermocouple measures

    Energy Technology Data Exchange (ETDEWEB)

    Souza, Thiago J.; Medeiros, Jose A.C.C.; Goncalves, Alessandro C., E-mail: tsouza@nuclear.ufrj.br, E-mail: canedo@lmp.ufrj.br, E-mail: alessandro@nuclear.ufrj.br [Coordenacao dos Programas de Pos-Graduacao em Engenharia (COPPE/UFRJ), Rio de Janeiro, RJ (Brazil). Programa de Engenharia Nuclear

    2015-07-01

    Accidental control rod drops event in PWR reactors leads to an unsafe operating condition. It is important to quickly identify the rod to minimize undesirable effects in such a scenario. In this event, there is a distortion in the power distribution and temperature in the reactor core. The goal of this study is to develop an on-line model to identify the inadvertent control rod dropped in PWR reactor. The proposed model is based on physical correlations and pattern recognition of ex-core detector responses and thermocouples measures. The results of the study demonstrated the feasibility of an on-line system, contributing to safer operation conditions and preventing undesirable effects, as its shutdown. (author)

  8. Quantitative and molecular analyses of mutation in a pSV2gpt transformed CHO cell line

    International Nuclear Information System (INIS)

    Stankowski, L.F. Jr.; Tindall, K.R.; Hsie, A.W.

    1983-01-01

    Following NDA-mediated gene transfer we have isolated a cell line useful for studying gene mutation at the molecular level. This line, AS52, derived from a hypoxanthine-guanine phosphoribosyl transferase (HGPRT) deficient Chinese hamster ovary (CHO) cell line, carries a single copy of the E. coli xanthine-guanine phosphoribosyl transferase (XGPRT) gene (gpt) and exhibits a spontaneous mutant frequency of 20 TG/sup r/ mutants/10 6 clonable cells. As with HGPRT - mutants, XGPRT - mutants can be selected in 6-thioguanine. AS52 (XGPRT + ) and wild type CHO (HGPRT + ) cell exhibit almost identical cytotoxic responses to various agents. We observed significant differences in mutation induction by UV light and ethyl methanesulfonate (EMS). Ratios of XGPRT - to HGPRT - mutants induced per unit dose (J/m 2 for UV light and μg/ml for EMS) are 1.4 and 0.70, respectively. Preliminary Southern blot hybridization analyses has been performed on 30 XGPRT - AS52 mutants. A majority of spontaneous mutants have deletions ranging in size from 1 to 4 kilobases (9/19) to complete loss of gpt sequences (4/19); the remainder have no detectable (5/19) or only minor (1/19) alterations. 5/5 UV-induced and 5/6 EMS-induced mutants do not show a detectable change. Similar analyses are underway for mutations induced by x-irradiation and ICR 191 treatment

  9. Molecular characterization of the CRa gene conferring clubroot resistance in Brassica rapa.

    Science.gov (United States)

    Ueno, Hiroki; Matsumoto, Etsuo; Aruga, Daisuke; Kitagawa, Satoshi; Matsumura, Hideo; Hayashida, Nobuaki

    2012-12-01

    Clubroot disease is one of the major diseases affecting Brassicaceae crops, and a number of these crops grown commercially, such as Chinese cabbage (Brassica rapa L. ssp. pekinensis), are known to be highly susceptible to clubroot disease. To provide protection from this disease, plant breeders have introduced genes for resistance to clubroot from the European turnip into susceptible lines. The CRa gene confers specific resistance to the clubroot pathogen Plasmodiophora brassicae isolate M85. Fine mapping of the CRa locus using synteny to the Arabidopsis thaliana genome and partial genome sequences of B. rapa revealed a candidate gene encoding a TIR-NBS-LRR protein. Several structural differences in this candidate gene were found between susceptible and resistant lines, and CRa expression was observed only in the resistant line. Four mutant lines lacking clubroot resistance were obtained by the UV irradiation of pollen from a resistant line, and all of these mutant lines carried independent mutations in the candidate TIR-NBS-LRR gene. This genetic and molecular evidence strongly suggests that the identified gene is CRa. This is the first report on the molecular characterization of a clubroot Resistance gene in Brassicaceae and of the disease resistance gene in B. rapa.

  10. Molecular defects identified by whole exome sequencing in a child with Fanconi anemia.

    Science.gov (United States)

    Zheng, Zhaojing; Geng, Juan; Yao, Ru-En; Li, Caihua; Ying, Daming; Shen, Yongnian; Ying, Lei; Yu, Yongguo; Fu, Qihua

    2013-11-10

    Fanconi anemia is a rare genetic disease characterized by bone marrow failure, multiple congenital malformations, and an increased susceptibility to malignancy. At least 15 genes have been identified that are involved in the pathogenesis of Fanconi anemia. However, it is still a challenge to assign the complementation group and to characterize the molecular defects in patients with Fanconi anemia. In the current study, whole exome sequencing was used to identify the affected gene(s) in a boy with Fanconi anemia. A recurring, non-synonymous mutation was found (c.3971C>T, p.P1324L) as well as a novel frameshift mutation (c.989_995del, p.H330LfsX2) in FANCA gene. Our results indicate that whole exome sequencing may be useful in clinical settings for rapid identification of disease-causing mutations in rare genetic disorders such as Fanconi anemia. © 2013 Elsevier B.V. All rights reserved.

  11. A comprehensive molecular study on Coffin-Siris and Nicolaides-Baraitser syndromes identifies a broad molecular and clinical spectrum converging on altered chromatin remodeling.

    Science.gov (United States)

    Wieczorek, Dagmar; Bögershausen, Nina; Beleggia, Filippo; Steiner-Haldenstätt, Sabine; Pohl, Esther; Li, Yun; Milz, Esther; Martin, Marcel; Thiele, Holger; Altmüller, Janine; Alanay, Yasemin; Kayserili, Hülya; Klein-Hitpass, Ludger; Böhringer, Stefan; Wollstein, Andreas; Albrecht, Beate; Boduroglu, Koray; Caliebe, Almuth; Chrzanowska, Krystyna; Cogulu, Ozgur; Cristofoli, Francesca; Czeschik, Johanna Christina; Devriendt, Koenraad; Dotti, Maria Teresa; Elcioglu, Nursel; Gener, Blanca; Goecke, Timm O; Krajewska-Walasek, Malgorzata; Guillén-Navarro, Encarnación; Hayek, Joussef; Houge, Gunnar; Kilic, Esra; Simsek-Kiper, Pelin Özlem; López-González, Vanesa; Kuechler, Alma; Lyonnet, Stanislas; Mari, Francesca; Marozza, Annabella; Mathieu Dramard, Michèle; Mikat, Barbara; Morin, Gilles; Morice-Picard, Fanny; Ozkinay, Ferda; Rauch, Anita; Renieri, Alessandra; Tinschert, Sigrid; Utine, G Eda; Vilain, Catheline; Vivarelli, Rossella; Zweier, Christiane; Nürnberg, Peter; Rahmann, Sven; Vermeesch, Joris; Lüdecke, Hermann-Josef; Zeschnigk, Michael; Wollnik, Bernd

    2013-12-20

    Chromatin remodeling complexes are known to modify chemical marks on histones or to induce conformational changes in the chromatin in order to regulate transcription. De novo dominant mutations in different members of the SWI/SNF chromatin remodeling complex have recently been described in individuals with Coffin-Siris (CSS) and Nicolaides-Baraitser (NCBRS) syndromes. Using a combination of whole-exome sequencing, NGS-based sequencing of 23 SWI/SNF complex genes, and molecular karyotyping in 46 previously undescribed individuals with CSS and NCBRS, we identified a de novo 1-bp deletion (c.677delG, p.Gly226Glufs*53) and a de novo missense mutation (c.914G>T, p.Cys305Phe) in PHF6 in two individuals diagnosed with CSS. PHF6 interacts with the nucleosome remodeling and deacetylation (NuRD) complex implicating dysfunction of a second chromatin remodeling complex in the pathogenesis of CSS-like phenotypes. Altogether, we identified mutations in 60% of the studied individuals (28/46), located in the genes ARID1A, ARID1B, SMARCB1, SMARCE1, SMARCA2, and PHF6. We show that mutations in ARID1B are the main cause of CSS, accounting for 76% of identified mutations. ARID1B and SMARCB1 mutations were also found in individuals with the initial diagnosis of NCBRS. These individuals apparently belong to a small subset who display an intermediate CSS/NCBRS phenotype. Our proposed genotype-phenotype correlations are important for molecular screening strategies.

  12. Exact ground-state correlation functions of an atomic-molecular Bose–Einstein condensate model

    Science.gov (United States)

    Links, Jon; Shen, Yibing

    2018-05-01

    We study the ground-state properties of an atomic-molecular Bose–Einstein condensate model through an exact Bethe Ansatz solution. For a certain range of parameter choices, we prove that the ground-state Bethe roots lie on the positive real-axis. We then use a continuum limit approach to obtain a singular integral equation characterising the distribution of these Bethe roots. Solving this equation leads to an analytic expression for the ground-state energy. The form of the expression is consistent with the existence of a line of quantum phase transitions, which has been identified in earlier studies. This line demarcates a molecular phase from a mixed phase. Certain correlation functions, which characterise these phases, are then obtained through the Hellmann–Feynman theorem.

  13. Identifying self-interstitials of bcc and fcc crystals in molecular dynamics

    International Nuclear Information System (INIS)

    Bukkuru, S.; Bhardwaj, U.; Warrier, M.; Rao, A.D.P.; Valsakumar, M.C.

    2017-01-01

    Identification of self-interstitials in molecular dynamics (MD) simulations is of critical importance. There exist several criteria for identifying the self-interstitial. Most of the existing methods use an assumed cut-off value for the displacement of an atom from its lattice position to identify the self-interstitial. The results obtained are affected by the chosen cut-off value. Moreover, these chosen cut-off values are independent of temperature. We have developed a novel unsupervised learning algorithm called Max-Space Clustering (MSC) to identify an appropriate cut-off value and its dependence on temperature. This method is compared with some widely used methods such as effective sphere (ES) method and nearest neighbor sphere (NNS) method. The cut-off radius obtained using our method shows a linear variation with temperature. The value of cut-off radius and its temperature dependence is derived for five bcc (Cr, Fe, Mo, Nb, W) and six fcc (Ag, Au, Cu, Ni, Pd, Pt) crystals. It is seen that the ratio of the cut-off values “r” to the lattice constant “a” lies between 0.23 and 0.3 at 300 K and this ratio is on an average smaller for the fcc crystals. Collision cascade simulations are carried out for Primary knock-on Atom (PKA) energies of 5 keV in Fe (at 300 K and 1000 K) and W (at 300 K and 2500 K) and the results are compared using the various methods. - Highlights: • Max-Space Clustering (MSC) method is developed to identify interstitials in crystals. • MSC provides a structured way to identify the temperature dependent cut-off radius. • It is compared with widely used sphere methods and found to be better. • MSC coupled with graph tree optimization can be used to obtain diffusion trajectory. • Cascade simulations of Fe, W are carried out and results are compared with various methods.

  14. Identifying self-interstitials of bcc and fcc crystals in molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Bukkuru, S., E-mail: srinivasaraobukkuru@gmail.com [Dept. of Nuclear Physics, Andhra University, Visakhapatnam 530003 (India); Bhardwaj, U., E-mail: haptork@gmail.com [Computational Analysis Division, BARC, Visakhapatnam 530012, Andhra Pradesh (India); Warrier, M., E-mail: manoj.warrier@gmail.com [Computational Analysis Division, BARC, Visakhapatnam 530012, Andhra Pradesh (India); Rao, A.D.P., E-mail: adp_rao_99@yahoo.com [Dept. of Nuclear Physics, Andhra University, Visakhapatnam 530003 (India); Valsakumar, M.C., E-mail: mc.valsakumar@gmail.com [IIT Palakkad, Kozhippara P.O., Palakkad 678557, Kerala (India)

    2017-02-15

    Identification of self-interstitials in molecular dynamics (MD) simulations is of critical importance. There exist several criteria for identifying the self-interstitial. Most of the existing methods use an assumed cut-off value for the displacement of an atom from its lattice position to identify the self-interstitial. The results obtained are affected by the chosen cut-off value. Moreover, these chosen cut-off values are independent of temperature. We have developed a novel unsupervised learning algorithm called Max-Space Clustering (MSC) to identify an appropriate cut-off value and its dependence on temperature. This method is compared with some widely used methods such as effective sphere (ES) method and nearest neighbor sphere (NNS) method. The cut-off radius obtained using our method shows a linear variation with temperature. The value of cut-off radius and its temperature dependence is derived for five bcc (Cr, Fe, Mo, Nb, W) and six fcc (Ag, Au, Cu, Ni, Pd, Pt) crystals. It is seen that the ratio of the cut-off values “r” to the lattice constant “a” lies between 0.23 and 0.3 at 300 K and this ratio is on an average smaller for the fcc crystals. Collision cascade simulations are carried out for Primary knock-on Atom (PKA) energies of 5 keV in Fe (at 300 K and 1000 K) and W (at 300 K and 2500 K) and the results are compared using the various methods. - Highlights: • Max-Space Clustering (MSC) method is developed to identify interstitials in crystals. • MSC provides a structured way to identify the temperature dependent cut-off radius. • It is compared with widely used sphere methods and found to be better. • MSC coupled with graph tree optimization can be used to obtain diffusion trajectory. • Cascade simulations of Fe, W are carried out and results are compared with various methods.

  15. ALMA MULTI-LINE IMAGING OF THE NEARBY STARBURST NGC 253

    Energy Technology Data Exchange (ETDEWEB)

    Meier, David S. [New Mexico Institute of Mining and Technology, 801 Leroy Place, Socorro, NM 87801 (United States); Walter, Fabian; Zschaechner, Laura K. [Max-Planck Institut für Astronomie, Königstuhl 17, D-69117 Heidelberg (Germany); Bolatto, Alberto D.; Veilleux, Sylvain; Warren, Steven R. [Department of Astronomy and Joint Space-Science Institute, University of Maryland, College Park, MD 20742 (United States); Leroy, Adam K. [National Radio Astronomy Observatory, 520 Edgemont Road, Charlottesville, VA 22903 (United States); Ott, Jürgen [National Radio Astronomy Observatory, Pete V. Domenici Array Science Center, P.O. Box O, Socorro, NM 87801 (United States); Rosolowsky, Erik [Department of Physics, University of Alberta, Edmonton, AB T6G 2E1 (Canada); Weiß, Axel [Max Planck Institut für Radioastronomie, Auf dem Hügel 69, D-53121 Bonn (Germany); Zwaan, Martin A., E-mail: dmeier@nmt.edu [European Southern Observatory, Karl-Schwarzschild-Str. 2, D-85748 Garching bei München (Germany)

    2015-03-01

    We present spatially resolved (∼50 pc) imaging of molecular gas species in the central kiloparsec of the nearby starburst galaxy NGC 253, based on observations taken with the Atacama Large Millimeter/submillimeter Array. A total of 50 molecular lines are detected over a 13 GHz bandwidth imaged in the 3 mm band. Unambiguous identifications are assigned for 27 lines. Based on the measured high CO/C{sup 17}O isotopic line ratio (≳350), we show that {sup 12}CO(1-0) has moderate optical depths. A comparison of the HCN and HCO{sup +} with their {sup 13}C-substituted isotopologues shows that the HCN(1-0) and HCO{sup +}(1-0) lines have optical depths at least comparable to CO(1-0). H{sup 13}CN/H{sup 13}CO{sup +} (and H{sup 13}CN/HN{sup 13}C) line ratios provide tighter constraints on dense gas properties in this starburst. SiO has elevated abundances across the nucleus. HNCO has the most distinctive morphology of all the bright lines, with its global luminosity dominated by the outer parts of the central region. The dramatic variation seen in the HNCO/SiO line ratio suggests that some of the chemical signatures of shocked gas are being erased in the presence of dominating central radiation fields (traced by C{sub 2}H and CN). High density molecular gas tracers (including HCN, HCO{sup +}, and CN) are detected at the base of the molecular outflow. We also detect hydrogen β recombination lines that, like their α counterparts, show compact, centrally peaked morphologies, distinct from the molecular gas tracers. A number of sulfur based species are mapped (CS, SO, NS, C{sub 2}S, H{sub 2}CS, and CH{sub 3}SH) and have morphologies similar to SiO.

  16. Development of a model system to identify differences in spring and winter oat.

    Science.gov (United States)

    Chawade, Aakash; Lindén, Pernilla; Bräutigam, Marcus; Jonsson, Rickard; Jonsson, Anders; Moritz, Thomas; Olsson, Olof

    2012-01-01

    Our long-term goal is to develop a Swedish winter oat (Avena sativa). To identify molecular differences that correlate with winter hardiness, a winter oat model comprising of both non-hardy spring lines and winter hardy lines is needed. To achieve this, we selected 294 oat breeding lines, originating from various Russian, German, and American winter oat breeding programs and tested them in the field in south- and western Sweden. By assaying for winter survival and agricultural properties during four consecutive seasons, we identified 14 breeding lines of different origins that not only survived the winter but also were agronomically better than the rest. Laboratory tests including electrolytic leakage, controlled crown freezing assay, expression analysis of the AsVrn1 gene and monitoring of flowering time suggested that the American lines had the highest freezing tolerance, although the German lines performed better in the field. Finally, six lines constituting the two most freezing tolerant lines, two intermediate lines and two spring cultivars were chosen to build a winter oat model system. Metabolic profiling of non-acclimated and cold acclimated leaf tissue samples isolated from the six selected lines revealed differential expression patterns of 245 metabolites including several sugars, amino acids, organic acids and 181 hitherto unknown metabolites. The expression patterns of 107 metabolites showed significant interactions with either a cultivar or a time-point. Further identification, characterisation and validation of these metabolites will lead to an increased understanding of the cold acclimation process in oats. Furthermore, by using the winter oat model system, differential sequencing of crown mRNA populations would lead to identification of various biomarkers to facilitate winter oat breeding.

  17. Drought Tolerance in Pinus halepensis Seed Sources As Identified by Distinctive Physiological and Molecular Markers

    OpenAIRE

    Taïbi, Khaled; Campo, Antonio D. del; Vilagrosa Carmona, Alberto; Bellés, José M.; López-Gresa, María Pilar; Pla, Davinia; Calvete, Juan J.; López-Nicolás, José M.; Mulet, José M.

    2017-01-01

    Drought is one of the main constraints determining forest species growth, survival and productivity, and therefore one of the main limitations for reforestation or afforestation. The aim of this study is to characterize the drought response at the physiological and molecular level of different Pinus halepensis (common name Aleppo pine) seed sources, previously characterized in field trials as drought-sensitive or drought-tolerant. This approach aims to identify different traits capable of pre...

  18. Footpoints of the giant molecular loops in the Galactic center region

    Science.gov (United States)

    Riquelme, D.; Amo-Baladrón, M. A.; Martín-Pintado, J.; Mauersberger, R.; Martín, S.; Burton, M.; Cunningham, M.; Jones, P. A.; Menten, K. M.; Bronfman, L.; Güsten, R.

    2018-05-01

    Aims: We aim to reveal the morphology, chemical composition, kinematics, and to establish the main processes prevalent in the gas at the footpoints of the giant molecular loops (GMLs) in the Galactic center region. Methods: Using the 22-m Mopra telescope, we mapped the M-3.8+0.9 molecular cloud, placed at the footpoints of a GML, in 3-mm range molecular lines. To derive the molecular hydrogen column density, we also observed the 13CO(2 - 1) line at 1 mm using the 12-m APEX telescope. From the 3 mm observations 12 molecular species were detected, namely HCO+, HCN, H13CN, HNC, SiO, CS, CH3OH, N2H+, SO, HNCO, OCS, and HC3N. Results: Maps revealing the morphology and kinematics of the M-3.8+0.9 molecular cloud in different molecules are presented. We identify six main molecular complexes. We derive fractional abundances in 11 selected positions of the different molecules assuming local thermodynamical equilibrium. Conclusions: Most of the fractional abundances derived for the M-3.8+0.9 molecular cloud are very similar over the whole cloud. However, the fractional abundances of some molecules show significant difference with respect to those measured in the central molecular zone (CMZ). The abundances of the shock tracer SiO are very similar between the GMLs and the CMZ. The methanol emission is the most abundant species in the GMLs. This indicates that the gas is likely affected by moderate 30 km s-1 or even high velocity (50 km s-1) shocks, consistent with the line profile observed toward one of the studied position. The origin of the shocks is likely related to the flow of the gas throughout the GMLs towards the footpoints. OPRA and APEX final data cubes (FITS) are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/613/A42

  19. Proteomic-Biostatistic Integrated Approach for Finding the Underlying Molecular Determinants of Hypertension in Human Plasma.

    Science.gov (United States)

    Gajjala, Prathibha R; Jankowski, Vera; Heinze, Georg; Bilo, Grzegorz; Zanchetti, Alberto; Noels, Heidi; Liehn, Elisa; Perco, Paul; Schulz, Anna; Delles, Christian; Kork, Felix; Biessen, Erik; Narkiewicz, Krzysztof; Kawecka-Jaszcz, Kalina; Floege, Juergen; Soranna, Davide; Zidek, Walter; Jankowski, Joachim

    2017-08-01

    Despite advancements in lowering blood pressure, the best approach to lower it remains controversial because of the lack of information on the molecular basis of hypertension. We, therefore, performed plasma proteomics of plasma from patients with hypertension to identify molecular determinants detectable in these subjects but not in controls and vice versa. Plasma samples from hypertensive subjects (cases; n=118) and controls (n=85) from the InGenious HyperCare cohort were used for this study and performed mass spectrometric analysis. Using biostatistical methods, plasma peptides specific for hypertension were identified, and a model was developed using least absolute shrinkage and selection operator logistic regression. The underlying peptides were identified and sequenced off-line using matrix-assisted laser desorption ionization orbitrap mass spectrometry. By comparison of the molecular composition of the plasma samples, 27 molecular determinants were identified differently expressed in cases from controls. Seventy percent of the molecular determinants selected were found to occur less likely in hypertensive patients. In cross-validation, the overall R 2 was 0.434, and the area under the curve was 0.891 with 95% confidence interval 0.8482 to 0.9349, P hypertensive patients were found to be -2.007±0.3568 and 3.383±0.2643, respectively, P hypertensives and normotensives. The identified molecular determinants may be the starting point for further studies to clarify the molecular causes of hypertension. © 2017 American Heart Association, Inc.

  20. International bulletin on atomic and molecular data for fusion. No. 66, August 2007

    International Nuclear Information System (INIS)

    Humbert, D.; Bannister, M.E.; Fuhr, J.; Gilbody, H.B.

    2007-08-01

    Information in this Bulletin is presented in four parts. The Atomic and Molecular Data Information System (AMDIS) of the International Atomic Energy Agency is presented in Part 1. The indexed papers are listed separately for structure and spectra, atomic and molecular collisions, and surface interactions in Part 2. The structure and spectra indexation lines are grouped by process. The first column gives the process, the second one the reactants and then the character of the data contained (Th for theoretical, Ex for experimental, and E/T for both experimental and theoretical). The number in the last column is the reference number in Part 3 of the Bulletin. The atomic and molecular indexation lines are grouped by one collision partner (photon, electron or heavy particle). The first column gives the reactants, the second column gives the process, the third column gives the energy range with the appropriate units, and the last two columns are the same as in the structure and spectra indexation lines. The particle-surface interactions indexation lines are grouped by process. The first column gives the reactants, the second the energy range with the appropriate units, and the last two columns are the same as in the previous cases. Part 3 contains all the bibliographic data for both the indexed and non-indexed references. Those references which are indexed in Part 1 are identified by the repeated indexation lines. The Author Index (Part 4) refers to the bibliographic references contained in Part 3

  1. International bulletin on atomic and molecular data for fusion. No. 68, December 2009

    International Nuclear Information System (INIS)

    Chung, H.K.; Humbert, D.

    2009-12-01

    Information in this Bulletin is presented in four parts. The Atomic and Molecular Data Information System (AMDIS) of the International Atomic Energy Agency is presented in Part 1. The indexed papers are listed separately for structure and spectra, atomic and molecular collisions, and surface interactions in Part 2. The structure and spectra index lines are grouped by process. The first column gives the reactants, the second one the process and then the character of the data contained (Th for theoretical, Ex for experimental, and E/T for both experimental and theoretical). The number in the last column is the reference number in Part 3 of the Bulletin. The atomic and molecular index lines are grouped by one collision partner (photon, electron or heavy particle). The first column gives the reactants, the second column gives the process, the third column gives the energy range with the appropriate units, and the last two columns are the same as in the structure and spectra index lines. The particle-surface interactions index lines are grouped by process. The first column gives the reactants, the second the energy range with the appropriate units, and the last two columns are the same as in the previous cases. Part 3 contains all the bibliographic data for both the indexed and non-indexed references. Those references which are indexed in Part 1 are identified by the repeated index lines. The Author Index (Part 4) refers to the bibliographic references contained in Part 3

  2. International Bulletin on Atomic and Molecular Data for Fusion. No. 67, December 2008

    International Nuclear Information System (INIS)

    Humbert, D.

    2008-12-01

    Information in this Bulletin is presented in four parts. The Atomic and Molecular Data Information System (AMDIS) of the International Atomic Energy Agency is presented in Part 1. The indexed papers are listed separately for structure and spectra, atomic and molecular collisions, and surface interactions in Part 2. The structure and spectra indexation lines are grouped by process. The first column gives the process, the second one the reactants and then the character of the data contained (Th for theoretical, Ex for experimental, and E/T for both experimental and theoretical). The number in the last column is the reference number in Part 3 of the Bulletin. The atomic and molecular indexation lines are grouped by one collision partner (photon, electron or heavy particle). The first column gives the reactants, the second column gives the process, the third column gives the energy range with the appropriate units, and the last two columns are the same as in the structure and spectra indexation lines. The particle-surface interactions indexation lines are grouped by process. The first column gives the reactants, the second the energy range with the appropriate units, and the last two columns are the same as in the previous cases. Part 3 contains all the bibliographic data for both the indexed and non-indexed references. Those references which are indexed in Part 1 are identified by the repeated indexation lines. The Author Index (Part 4) refers to the bibliographic references contained in Part 3.

  3. LINE-1 couples EMT programming with acquisition of oncogenic phenotypes in human bronchial epithelial cells.

    Science.gov (United States)

    Reyes-Reyes, Elsa M; Aispuro, Ivan; Tavera-Garcia, Marco A; Field, Matthew; Moore, Sara; Ramos, Irma; Ramos, Kenneth S

    2017-11-28

    Although several lines of evidence have established the central role of epithelial-to-mesenchymal-transition (EMT) in malignant progression of non-small cell lung cancers (NSCLCs), the molecular events connecting EMT to malignancy remain poorly understood. This study presents evidence that Long Interspersed Nuclear Element-1 (LINE-1) retrotransposon couples EMT programming with malignancy in human bronchial epithelial cells (BEAS-2B). This conclusion is supported by studies showing that: 1) activation of EMT programming by TGF-β1 increases LINE-1 mRNAs and protein; 2) the lung carcinogen benzo(a)pyrene coregulates TGF-β1 and LINE-1 mRNAs, with LINE-1 positioned downstream of TGF-β1 signaling; and, 3) forced expression of LINE-1 in BEAS-2B cells recapitulates EMT programming and induces malignant phenotypes and tumorigenesis in vivo . These findings identify a TGFβ1-LINE-1 axis as a critical effector pathway that can be targeted for the development of precision therapies during malignant progression of intractable NSCLCs.

  4. Phosphoproteomic Analysis Identifies Signaling Pathways Regulated by Curcumin in Human Colon Cancer Cells.

    Science.gov (United States)

    Sato, Tatsuhiro; Higuchi, Yutaka; Shibagaki, Yoshio; Hattori, Seisuke

    2017-09-01

    Curcumin, a major polyphenol of the spice turmeric, acts as a potent chemopreventive and chemotherapeutic agent in several cancer types, including colon cancer. Although various proteins have been shown to be affected by curcumin, how curcumin exerts its anticancer activity is not fully understood. Phosphoproteomic analyses were performed using SW480 and SW620 human colon cancer cells to identify curcumin-affected signaling pathways. Curcumin inhibited the growth of the two cell lines in a dose-dependent manner. Thirty-nine curcumin-regulated phosphoproteins were identified, five of which are involved in cancer signaling pathways. Detailed analyses revealed that the mTORC1 and p53 signaling pathways are main targets of curcumin. Our results provide insight into the molecular mechanisms of the anticancer activities of curcumin and future molecular targets for its clinical application. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

  5. 3D scan line method for identifying void fabric of granular materials

    Directory of Open Access Journals (Sweden)

    Theocharis Alexandros I.

    2017-01-01

    Full Text Available Among other processes measuring the void phase of porous or fractured media, scan line approach is a simplified “graphical” method, mainly used in image processing related procedures. In soil mechanics, the application of scan line method is related to the soil fabric, which is important in characterizing the anisotropic mechanical response of soils. Void fabric is of particular interest, since graphical approaches are well defined experimentally and most of them can also be easily used in numerical experiments, like the scan line method. This is in contrast to the definition of fabric based on contact normal vectors that are extremely difficult to determine, especially considering physical experiments. The scan line method has been proposed by Oda et al [1] and implemented again by Ghedia and O’Sullivan [2]. A modified method based on DEM analysis instead of image measurements of fabric has been previously proposed and implemented by the authors in a 2D scheme [3-4]. In this work, a 3D extension of the modified scan line definition is presented using PFC 3D®. The results show clearly similar trends with the 2D case and the same behaviour of fabric anisotropy is presented.

  6. Identifying molecular targets of lifestyle modifications in colon cancer prevention

    Directory of Open Access Journals (Sweden)

    Molly Marie Derry

    2013-05-01

    Full Text Available One in four deaths in the United States is cancer-related, and colorectal cancer (CRC is the second leading cause of cancer-associated deaths. Screening strategies are utilized but have not reduced disease incidence or mortality. In this regard, there is an interest in cancer preventive strategies focusing on lifestyle intervention, where specific etiologic factors involved in cancer initiation, promotion, and progression could be targeted. For example, exposure to dietary carcinogens, such as nitrosamines and polycyclic aromatic hydrocarbons influences colon carcinogenesis. Furthermore, dietary deficiencies could alter sensitivity to genetic damage and influence carcinogen metabolism contributing to CRC. High alcohol consumption increases the risk of mutations including the fact that acetaldehyde, an ethanol metabolite, is classified as a group 1 carcinogen. Tobacco smoke exposure is also a risk factor for cancer development; ~20% of CRCs are associated with smoking. Additionally, obese patients have a higher risk of cancer development, which is further supported by the fact that physical activity decreases CRC risk by 55%. Similarly, chronic inflammatory conditions also increase the risk of CRC development. Moreover, the circadian clock alters digestion and regulates other biochemical, physiological and behavioral processes that could positively influence CRC. Taken together, colon carcinogenesis involves a number of etiological factors, and therefore, to create effective preventive strategies, molecular targets need to be identified and beleaguered prior to disease progression. With this in mind, the following is a comprehensive review identifying downstream target proteins of the above lifestyle risk factors, which are modulated during colon carcinogenesis and could be targeted for CRC prevention by novel agents including phytochemicals.

  7. A 6-gene signature identifies four molecular subgroups of neuroblastoma

    Directory of Open Access Journals (Sweden)

    Kogner Per

    2011-04-01

    Full Text Available Abstract Background There are currently three postulated genomic subtypes of the childhood tumour neuroblastoma (NB; Type 1, Type 2A, and Type 2B. The most aggressive forms of NB are characterized by amplification of the oncogene MYCN (MNA and low expression of the favourable marker NTRK1. Recently, mutations or high expression of the familial predisposition gene Anaplastic Lymphoma Kinase (ALK was associated to unfavourable biology of sporadic NB. Also, various other genes have been linked to NB pathogenesis. Results The present study explores subgroup discrimination by gene expression profiling using three published microarray studies on NB (47 samples. Four distinct clusters were identified by Principal Components Analysis (PCA in two separate data sets, which could be verified by an unsupervised hierarchical clustering in a third independent data set (101 NB samples using a set of 74 discriminative genes. The expression signature of six NB-associated genes ALK, BIRC5, CCND1, MYCN, NTRK1, and PHOX2B, significantly discriminated the four clusters (p ALK, BIRC5, and PHOX2B, and was significantly associated with higher tumour stage, poor outcome and poor survival compared to the Type 1-corresponding favourable group (INSS stage 4 and/or dead of disease, p Conclusions Based on expression profiling we have identified four molecular subgroups of neuroblastoma, which can be distinguished by a 6-gene signature. The fourth subgroup has not been described elsewhere, and efforts are currently made to further investigate this group's specific characteristics.

  8. A Molecular-line Study of the Interstellar Bullet Engine IRAS05506+2414

    Science.gov (United States)

    Sahai, Raghvendra; Lee, Chin-Fei; Sánchez Contreras, Carmen; Patel, Nimesh; Morris, Mark R.; Claussen, Mark

    2017-12-01

    We present interferometric and single-dish molecular line observations of the interstellar bullet-outflow source IRAS 05506+2414, whose wide-angle bullet spray is similar to the Orion BN/KL explosive outflow and likely arises from an entirely different mechanism than the classical accretion-disk-driven bipolar flows in young stellar objects. The bullet-outflow source is associated with a large pseudo-disk and three molecular outflows—a high-velocity outflow (HVO), a medium-velocity outflow (MVO), and a slow, extended outflow (SEO). The size (mass) of the pseudo-disk is 10,350 au × 6400 au (0.64-0.17 M ⊙) from a model-fit assuming infall and rotation, we derive a central stellar mass of 8-19 M ⊙. The HVO (MVO) has an angular size ˜5180 (˜3330) au and a projected outflow velocity of ˜140 km s-1 (˜30 km s-1). The SEO size (outflow speed) is ˜0.9 pc (˜6 km s-1). The HVO’s axis is aligned with (orthogonal to) that of the SEO (pseudo-disk). The velocity structure of the MVO is unresolved. The scalar momenta in the HVO and SEO are very similar, suggesting that the SEO has resulted from the HVO interacting with ambient-cloud material. The bullet spray shares a common axis with the pseudo-disk and has an age comparable to that of MVO (few hundred years), suggesting that these three structures are intimately linked. We discuss several models for the outflows in IRAS 05506+2414 (including dynamical decay of a stellar cluster, chance encounter of a runaway star with a dense cloud, and close passage of two protostars), and conclude that second-epoch imaging to derive proper motions of the bullets and nearby stars can help to discriminate between them.

  9. Analysis of Hα(Dα) Line Shape Xu Wei & Li Yan

    Indian Academy of Sciences (India)

    Abstract. The particles energy distribution is derived directly from the Hα(Dα) line shape, which is measured by two sets of OMA. The dissociative excitation of molecular is dominating when the local elec- tron temperature is >10eV. The Dα line shape is also simulated by the Monte–Carlo method, the molecular dissociation ...

  10. High molecular weight hyaluronic acid increases the differentiation potential of the murine chondrocytic ATDC5 cell line.

    Science.gov (United States)

    Sato, Eiichi; Ando, Takashi; Ichikawa, Jiro; Okita, Genki; Sato, Nobutaka; Wako, Masanori; Ohba, Tetsuro; Ochiai, Satoshi; Hagino, Tetsuo; Jacobson, Richard; Haro, Hirotaka

    2014-12-01

    Osteoarthritis (OA) is a group of common, chronic, and painful inflammatory joint diseases. One important finding in OA patients is a remarkable decrease in the molecular weight of hyaluronic acid (HA) in the synovial fluid of affected joints. Therapeutic HA is available to patients in most parts of the world as a viscosupplementation product for the treatment of OA. Previous clinical reports show that high molecular weight HA (HMWHA) more effectively relieves pain than low molecular weight HA (LMWHA). However, the mechanism behind this finding remains unclear. In this study, we investigated whether a LMWHA (Low-0.9 MDa) and two types of HMWHA (High-1.9 MDa and 6 MDa) differentially affected chondroregulatory action. We tested this using ATDC5 cell, a murine chondrocytic cell line widely used in culture systems to study chondrogenic differentiation. We found that HMWHA, especially hylan G-F 20 (High-6 MDa), significantly induced aggrecan and proteoglycan accumulation, nodule formation, and mRNA expression of chondrogenic differentiation markers in a time- and dose-dependent manner. In addition, we showed that HMWHA prevented TNF-α induced inhibition of chondrogenic differentiation, with no effect on cell proliferation or viability. These results reveal that HMWHA significantly promotes chondrogenic differentiation of ATDC5 cells in vitro, and suggest that HMWHA plays a significant chondroregulatory role in vivo. © 2014 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

  11. NFATC3-PLA2G15 Fusion Transcript Identified by RNA Sequencing Promotes Tumor Invasion and Proliferation in Colorectal Cancer Cell Lines.

    Science.gov (United States)

    Jang, Jee-Eun; Kim, Hwang-Phill; Han, Sae-Won; Jang, Hoon; Lee, Si-Hyun; Song, Sang-Hyun; Bang, Duhee; Kim, Tae-You

    2018-06-14

    This study was designed to identify novel fusion transcripts (FTs) and their functional significance in colorectal cancer lines. We performed paired-end RNA sequencing of 28 colorectal cancer (CRC) cell lines. FT candidates were identified using TopHat-fusion, ChimeraScan, and FusionMap tools and further experimental validation was conducted through reverse transcription-polymerase chain reaction and Sanger sequencing. FT was depleted in human CRC line and the effects on cell proliferation, cell migration, and cell invasion were analyzed. 1,380 FT candidates were detected through bioinformatics filtering. We selected 6 candidate FTs, including 4 inter-chromosomal and 2 intra-chromosomal FTs and each FT was found in at least 1 of the 28 cell lines. Moreover, when we tested 19 pairs of CRC tumor and adjacent normal tissue samples, NFATC3-PLA2G15 FT was found in 2. Knockdown of NFATC3-PLA2G15 using siRNA reduced mRNA expression of epithelial-mesenchymal transition (EMT) markers such as vimentin, twist, and fibronectin and increased mesenchymal-epithelial transition markers of E-cadherin, claudin-1, and FOXC2 in colo-320 cell line harboring NFATC3-PLA2G15 FT. The NFATC3-PLA2G15 knockdown also inhibited invasion, colony formation capacity, and cell proliferation. These results suggest that that NFATC3-PLA2G15 FTs may contribute to tumor progression by enhancing invasion by EMT and proliferation.

  12. Unraveling molecular mechanistic differences in liver metabolism between lean and fat lines of Pekin duck (Anas platyrhynchos domestica): a proteomic study.

    Science.gov (United States)

    Zheng, Aijuan; Chang, Wenhuan; Hou, Shuisheng; Zhang, Shu; Cai, Huiyi; Chen, Guilan; Lou, Ruiying; Liu, Guohua

    2014-02-26

    Duck is one of the major poultry meat sources for human consumption. To satisfy different eating habits, lean and fat strains of Pekin ducks have been developed. The objective of this study was to determine the molecular mechanistic differences in liver metabolism between two duck strains. The liver proteome of the Pekin duck lines was compared on days 1, 14, 28, and 42 posthatching using 2-DE based proteomics. There was a different abundance of 76 proteins in the livers of the two duck lines. Fat ducks strongly expressed proteins related to pathways of glycolysis, ATP synthesis, and protein catabolism, suggesting enhanced fat deposition rather than protein retention. In contrast, highly expressed proteins in lean ducks improved protein anabolism and reduced protein catabolism, resulting in an enhancement of lean meat deposition. Along with the decrease in fat deposition, the immune system of the lean duck strain may be enhanced by enhanced expression of proteins involved in stress response, immune defense, and antioxidant functions. These results indicate that selection pressure has shaped the two duck lines differently resulting in different liver metabolic capacities. These observed variations between the two strains at the molecular level are matched with physiological changes in growth performance and meat production. This information may have beneficial impacts in areas such as genetic modification through the manipulation of target proteins or genes in specific pathways to improve the efficiency of duck meat production. The objective of this study was to unravel molecular mechanistic differences in liver metabolism between lean and fat Pekin duck (Anas platyrhynchos domestica) strains. There was a different abundance of 76 proteins in the livers of the two duck lines. Enhanced protein expression in the fat ducks related to pathways of glycolysis, ATP synthesis and protein catabolism suggesting increased fat deposition rather than protein retention. In

  13. Yield QTL analysis of Oryza sativa x O. glumaepatula introgression lines

    Directory of Open Access Journals (Sweden)

    Priscila Nascimento Rangel

    2013-03-01

    Full Text Available The objective of this work was to evaluate the yield performance of two generations (BC2F2 and BC2F9 of introgression lines developed from the interspecific cross between Oryza sativa and O. glumaepatula, and to identify the SSR markers associated to yield. The wild accession RS‑16 (O. glumaepatula was used as donor parent in the backcross with the high yielding cultivar Cica‑8 (O. sativa. A set of 114 BC2F1 introgression lines was genotyped with 141 polymorphic SSR loci distributed across the whole rice genome. Molecular analysis showed that in average 22% of the O. glumaepatula genome was introgressed into BC2F1 generation. Nine BC2F9 introgression lines had a significantly higher yield than the genitor Cica‑8, thus showing a positive genome interaction among cultivated rice and the wild O. glumaepatula. Seven QTL were identified in the overall BC2F2, with one marker interval (4879‑EST20 of great effect on yield. The alleles with positive effect on yield came from the cultivated parent Cica‑8.

  14. New technique of identifying the hierarchy of dynamic domains in proteins using a method of molecular dynamics simulations

    Directory of Open Access Journals (Sweden)

    Yesylevskyy S. O.

    2010-04-01

    Full Text Available Aim. Despite a large number of existing domain identification techniques there is no universally accepted method, which identifies the hierarchy of dynamic domains using the data of molecular dynamics (MD simulations. The goal of this work is to develop such technique. Methods. The dynamic domains are identified by eliminating systematic motions from MD trajectories recursively in a model-free manner. Results. The technique called the Hierarchical Domain-Wise Alignment (HDWA to identify hierarchically organized dynamic domains in proteins using the MD trajectories has been developed. Conclusion. A new method of domain identification in proteins is proposed

  15. Probing molecular mechanisms of the Hsp90 chaperone: biophysical modeling identifies key regulators of functional dynamics.

    Directory of Open Access Journals (Sweden)

    Anshuman Dixit

    Full Text Available Deciphering functional mechanisms of the Hsp90 chaperone machinery is an important objective in cancer biology aiming to facilitate discovery of targeted anti-cancer therapies. Despite significant advances in understanding structure and function of molecular chaperones, organizing molecular principles that control the relationship between conformational diversity and functional mechanisms of the Hsp90 activity lack a sufficient quantitative characterization. We combined molecular dynamics simulations, principal component analysis, the energy landscape model and structure-functional analysis of Hsp90 regulatory interactions to systematically investigate functional dynamics of the molecular chaperone. This approach has identified a network of conserved regions common to the Hsp90 chaperones that could play a universal role in coordinating functional dynamics, principal collective motions and allosteric signaling of Hsp90. We have found that these functional motifs may be utilized by the molecular chaperone machinery to act collectively as central regulators of Hsp90 dynamics and activity, including the inter-domain communications, control of ATP hydrolysis, and protein client binding. These findings have provided support to a long-standing assertion that allosteric regulation and catalysis may have emerged via common evolutionary routes. The interaction networks regulating functional motions of Hsp90 may be determined by the inherent structural architecture of the molecular chaperone. At the same time, the thermodynamics-based "conformational selection" of functional states is likely to be activated based on the nature of the binding partner. This mechanistic model of Hsp90 dynamics and function is consistent with the notion that allosteric networks orchestrating cooperative protein motions can be formed by evolutionary conserved and sparsely connected residue clusters. Hence, allosteric signaling through a small network of distantly connected

  16. IN SILICO MODELLING OF CYTOTOXIC BEHAVIOUR OF ANTI-LEUKEMIC COMPOUNDS ON HL-60 CELL LINE

    Directory of Open Access Journals (Sweden)

    David Ebuka Arthur

    2016-05-01

    Full Text Available This research employs multiple linear regression technique in the modelling of some potent anti-leukemic compounds using paDEL molecular descriptor software calculator, to identify the best relationship between the chemical structure and toxicities of the anticancer datasets against some leukemic cell lines (HL-60. Statistical parameters such as Q2 and R2pred (test set were computed to validate the strength of the model, while Williams plot was used to assess its applicability domain. The mean effects of the molecular descriptors in the models were calculated to illuminate the principal properties of the molecules responsible for their cytotoxicity.

  17. Survey for C-Band High Spectral Lines with the Arecibo Telescope

    Science.gov (United States)

    Tan, Wei Siang

    High-mass stars have masses greater than 8 solar masses and are the main source of heavy elements such as iron in the interstellar medium. This type of stars form in giant molecular clouds. Studying the molecular environment in star-forming regions is crucial to understand the physical structure and conditions that lead to the formation of high-mass stars. This thesis presents observations conducted with the 305m Arecibo Telescope in Puerto Rico of twelve high-mass star forming regions. Every source was observed in multiple transitions of molecular species including CH, CH3OH, H2CS, and OH lines, and a radio recombination line. The observations were conducted with the C-Band High receiver of the Arecibo Telescope in the frequency range of 6.0 to 7.4GHz. The goals of the observations were to investigate the detectability of different molecular species (including new possible molecular masers) and obtain high sensitivity observations of the 6.7GHz CH3OH line to detect absorption and use it as a probe of the kinematics of the molecular material with respect to the ionized gas. Among the results of the observations, we report detection of 6.7GHz CH3OH masers toward nine regions, OH masers toward five sources, 6.7GHz CH3OH absorption toward four sources (including tentative detections), and detection of H2CS toward the star forming region G34.26+0.15. We also found a variable and recurrent 6.7GHz CH3OH maser in G45.12+0.13. The 6.7GHz CH 3OH and 6278.65MHz H2CS absorption lines were modeled using the radiative transfer code RADEX to investigate the physical conditions of the molecular clouds responsible for the absorption lines. Our analysis of the absorption lines supports the interpretation that the spectral lines are tracing molecular envelopes of HII regions. In the case of 6.7GHz CH 3OH absorption, our results and data from an extensive literature review indicate that absorption is rare, but that a population of 6.7GHz CH 3OH absorbers may be present at levels

  18. Shocked molecular hydrogen in the supernova remnant IC 443

    International Nuclear Information System (INIS)

    Burton, M.G.; Brand, P.W.J.L.; Webster, A.S.

    1988-01-01

    Emission from the υ = 1-0 S(1) line of molecular hydrogen has been mapped over a section of the supernova remnant IC 443. The emission originates in a sinuous ridge where the expanding shell of the SNR is interacting with a molecular cloud. The relative intensities of the 1-0 S(1), 1-0 S(0) and 2-1 S(1) lines at 2.1-2.2 μm were measured and found to be characteristic of shock-excitation of the gas. The ridge shows bright spots which are possibly density enhancements in the molecular cloud. The total luminosity of the molecular hydrogen lines in the mapped region is estimated to be about 1000 times the solar luminosity, making IC 443 one of the most luminous galactic molecular hydrogen sources yet detected. (author)

  19. Determination of edge plasma parameters by a genetic algorithm analysis of spectral line shapes

    Energy Technology Data Exchange (ETDEWEB)

    Marandet, Y.; Genesio, P.; Godbert-Mouret, L.; Koubiti, M.; Stamm, R. [Universite de Provence (PIIM), Centre de Saint-Jerome, 13 - Marseille (France); Capes, H.; Guirlet, R. [Association Euratom-CEA Cadarache, 13 - Saint-Paul-lez-Durance (France). Dept. de Recherches sur la Fusion Controlee

    2003-07-01

    Comparing an experimental and a theoretical line shape can be achieved by a genetic algorithm (GA) based on an analogy to the mechanisms of natural selection. Such an algorithm is able to deal with complex non-linear models, and can avoid local minima. We have used this optimization tool in the context of edge plasma spectroscopy, for a determination of the temperatures and fractions of the various populations of neutral deuterium emitting the D{sub {alpha}} line in 2 configurations of Tore-Supra: ergodic divertor and toroidal pumped limiter. Using the GA fit, the neutral emitters are separated into up to 4 populations which can be identified as resulting from molecular dissociation reactions, charge exchange, or reflection. In all the edge plasmas studied, a significant fraction of neutrals emit in the line wings, leading to neutrals with a temperature up to a few hundreds eV if a Gaussian line shape is assumed. This conclusion could be modified if the line wing exhibits a non Gaussian behavior.

  20. Determination of edge plasma parameters by a genetic algorithm analysis of spectral line shapes

    International Nuclear Information System (INIS)

    Marandet, Y.; Genesio, P.; Godbert-Mouret, L.; Koubiti, M.; Stamm, R.; Capes, H.; Guirlet, R.

    2003-01-01

    Comparing an experimental and a theoretical line shape can be achieved by a genetic algorithm (GA) based on an analogy to the mechanisms of natural selection. Such an algorithm is able to deal with complex non-linear models, and can avoid local minima. We have used this optimization tool in the context of edge plasma spectroscopy, for a determination of the temperatures and fractions of the various populations of neutral deuterium emitting the D α line in 2 configurations of Tore-Supra: ergodic divertor and toroidal pumped limiter. Using the GA fit, the neutral emitters are separated into up to 4 populations which can be identified as resulting from molecular dissociation reactions, charge exchange, or reflection. In all the edge plasmas studied, a significant fraction of neutrals emit in the line wings, leading to neutrals with a temperature up to a few hundreds eV if a Gaussian line shape is assumed. This conclusion could be modified if the line wing exhibits a non Gaussian behavior

  1. Molecular HIV screening.

    Science.gov (United States)

    Bourlet, Thomas; Memmi, Meriam; Saoudin, Henia; Pozzetto, Bruno

    2013-09-01

    Nuclear acid testing is more and more used for the diagnosis of infectious diseases. This paper focuses on the use of molecular tools for HIV screening. The term 'screening' will be used under the meaning of first-line HIV molecular techniques performed on a routine basis, which excludes HIV molecular tests designed to confirm or infirm a newly discovered HIV-seropositive patient or other molecular tests performed for the follow-up of HIV-infected patients. The following items are developed successively: i) presentation of the variety of molecular tools used for molecular HIV screening, ii) use of HIV molecular tools for the screening of blood products, iii) use of HIV molecular tools for the screening of organs and tissue from human origin, iv) use of HIV molecular tools in medically assisted procreation and v) use of HIV molecular tools in neonates from HIV-infected mothers.

  2. Deciphering the Correlation between Breast Tumor Samples and Cell Lines by Integrating Copy Number Changes and Gene Expression Profiles

    Directory of Open Access Journals (Sweden)

    Yi Sun

    2015-01-01

    Full Text Available Breast cancer is one of the most common cancers with high incident rate and high mortality rate worldwide. Although different breast cancer cell lines were widely used in laboratory investigations, accumulated evidences have indicated that genomic differences exist between cancer cell lines and tissue samples in the past decades. The abundant molecular profiles of cancer cell lines and tumor samples deposited in the Cancer Cell Line Encyclopedia and The Cancer Genome Atlas now allow a systematical comparison of the breast cancer cell lines with breast tumors. We depicted the genomic characteristics of breast primary tumors based on the copy number variation and gene expression profiles and the breast cancer cell lines were compared to different subgroups of breast tumors. We identified that some of the breast cancer cell lines show high correlation with the tumor group that agrees with previous knowledge, while a big part of them do not, including the most used MCF7, MDA-MB-231, and T-47D. We presented a computational framework to identify cell lines that mostly resemble a certain tumor group for the breast tumor study. Our investigation presents a useful guide to bridge the gap between cell lines and tumors and helps to select the most suitable cell line models for personalized cancer studies.

  3. Megamasers: Molecular Diagnostics of the Nuclear Ism

    Science.gov (United States)

    Baan, Willem A.; Klöckner, Hans-R.

    2005-01-01

    Molecular emissions are powerful tracers of intense heating and star-formation processes in galactic nuclei. In this paper we consider the characteristics of molecular Megamaser emission among the population of (Ultra-) Luminous Infrared Galaxies that are powered by intense star-formation or accretion onto a massive compact object. In addition, we consider the systematic behavior of the line emission of high-density tracer molecules. An evolutionary scenario is presented for ULIRGs that may explain the molecular line ratios observed in the population of FIR galaxies.

  4. Integrated analysis of breast cancer cell lines reveals unique signaling pathways

    Energy Technology Data Exchange (ETDEWEB)

    Heiser, Laura M.; Wang, Nicholas J.; Talcott, Carolyn L.; Laderoute, Keith R.; Knapp, Merrill; Guan, Yinghui; Hu, Zhi; Ziyad, Safiyyah; Weber, Barbara L.; Laquerre, Sylvie; Jackson, Jeffrey R.; Wooster, Richard F.; Kuo, Wen-Lin; Gray, Joe W.; Spellman, Paul T.

    2009-03-31

    Cancer is a heterogeneous disease resulting from the accumulation of genetic defects that negatively impact control of cell division, motility, adhesion and apoptosis. Deregulation in signaling along the EGFR-MAPK pathway is common in breast cancer, though the manner in which deregulation occurs varies between both individuals and cancer subtypes. We were interested in identifying subnetworks within the EGFR-MAPK pathway that are similarly deregulated across subsets of breast cancers. To that end, we mapped genomic, transcriptional and proteomic profiles for 30 breast cancer cell lines onto a curated Pathway Logic symbolic systems model of EGFR-MEK signaling. This model was comprised of 539 molecular states and 396 rules governing signaling between active states. We analyzed these models and identified several subtype specific subnetworks, including one that suggested PAK1 is particularly important in regulating the MAPK cascade when it is over-expressed. We hypothesized that PAK1 overexpressing cell lines would have increased sensitivity to MEK inhibitors. We tested this experimentally by measuring quantitative responses of 20 breast cancer cell lines to three MEK inhibitors. We found that PAK1 over-expressing luminal breast cancer cell lines are significantly more sensitive to MEK inhibition as compared to those that express PAK1 at low levels. This indicates that PAK1 over-expression may be a useful clinical marker to identify patient populations that may be sensitive to MEK inhibitors. All together, our results support the utility of symbolic system biology models for identification of therapeutic approaches that will be effective against breast cancer subsets.

  5. Integrated analysis of breast cancer cell lines reveals unique signaling pathways.

    Science.gov (United States)

    Heiser, Laura M; Wang, Nicholas J; Talcott, Carolyn L; Laderoute, Keith R; Knapp, Merrill; Guan, Yinghui; Hu, Zhi; Ziyad, Safiyyah; Weber, Barbara L; Laquerre, Sylvie; Jackson, Jeffrey R; Wooster, Richard F; Kuo, Wen Lin; Gray, Joe W; Spellman, Paul T

    2009-01-01

    Cancer is a heterogeneous disease resulting from the accumulation of genetic defects that negatively impact control of cell division, motility, adhesion and apoptosis. Deregulation in signaling along the EgfR-MAPK pathway is common in breast cancer, though the manner in which deregulation occurs varies between both individuals and cancer subtypes. We were interested in identifying subnetworks within the EgfR-MAPK pathway that are similarly deregulated across subsets of breast cancers. To that end, we mapped genomic, transcriptional and proteomic profiles for 30 breast cancer cell lines onto a curated Pathway Logic symbolic systems model of EgfR-MAPK signaling. This model was composed of 539 molecular states and 396 rules governing signaling between active states. We analyzed these models and identified several subtype-specific subnetworks, including one that suggested Pak1 is particularly important in regulating the MAPK cascade when it is over-expressed. We hypothesized that Pak1 over-expressing cell lines would have increased sensitivity to Mek inhibitors. We tested this experimentally by measuring quantitative responses of 20 breast cancer cell lines to three Mek inhibitors. We found that Pak1 over-expressing luminal breast cancer cell lines are significantly more sensitive to Mek inhibition compared to those that express Pak1 at low levels. This indicates that Pak1 over-expression may be a useful clinical marker to identify patient populations that may be sensitive to Mek inhibitors. All together, our results support the utility of symbolic system biology models for identification of therapeutic approaches that will be effective against breast cancer subsets.

  6. APRIL is a novel clinical chemo-resistance biomarker in colorectal adenocarcinoma identified by gene expression profiling

    International Nuclear Information System (INIS)

    Petty, Russell D; Wang, Weiguang; Gilbert, Fiona; Semple, Scot; Collie-Duguid, Elaina SR; Samuel, Leslie M; Murray, Graeme I; MacDonald, Graham; O'Kelly, Terrence; Loudon, Malcolm; Binnie, Norman; Aly, Emad; McKinlay, Aileen

    2009-01-01

    5-Fluorouracil(5FU) and oral analogues, such as capecitabine, remain one of the most useful agents for the treatment of colorectal adenocarcinoma. Low toxicity and convenience of administration facilitate use, however clinical resistance is a major limitation. Investigation has failed to fully explain the molecular mechanisms of resistance and no clinically useful predictive biomarkers for 5FU resistance have been identified. We investigated the molecular mechanisms of clinical 5FU resistance in colorectal adenocarcinoma patients in a prospective biomarker discovery project utilising gene expression profiling. The aim was to identify novel 5FU resistance mechanisms and qualify these as candidate biomarkers and therapeutic targets. Putative treatment specific gene expression changes were identified in a transcriptomics study of rectal adenocarcinomas, biopsied and profiled before and after pre-operative short-course radiotherapy or 5FU based chemo-radiotherapy, using microarrays. Tumour from untreated controls at diagnosis and resection identified treatment-independent gene expression changes. Candidate 5FU chemo-resistant genes were identified by comparison of gene expression data sets from these clinical specimens with gene expression signatures from our previous studies of colorectal cancer cell lines, where parental and daughter lines resistant to 5FU were compared. A colorectal adenocarcinoma tissue microarray (n = 234, resected tumours) was used as an independent set to qualify candidates thus identified. APRIL/TNFSF13 mRNA was significantly upregulated following 5FU based concurrent chemo-radiotherapy and in 5FU resistant colorectal adenocarcinoma cell lines but not in radiotherapy alone treated colorectal adenocarcinomas. Consistent withAPRIL's known function as an autocrine or paracrine secreted molecule, stromal but not tumour cell protein expression by immunohistochemistry was correlated with poor prognosis (p = 0.019) in the independent set

  7. Transcriptome sequencing and de novo analysis of a cytoplasmic male sterile line and its near-isogenic restorer line in chili pepper (Capsicum annuum L..

    Directory of Open Access Journals (Sweden)

    Chen Liu

    Full Text Available BACKGROUND: The use of cytoplasmic male sterility (CMS in F1 hybrid seed production of chili pepper is increasingly popular. However, the molecular mechanisms of cytoplasmic male sterility and fertility restoration remain poorly understood due to limited transcriptomic and genomic data. Therefore, we analyzed the difference between a CMS line 121A and its near-isogenic restorer line 121C in transcriptome level using next generation sequencing technology (NGS, aiming to find out critical genes and pathways associated with the male sterility. RESULTS: We generated approximately 53 million sequencing reads and assembled de novo, yielding 85,144 high quality unigenes with an average length of 643 bp. Among these unigenes, 27,191 were identified as putative homologs of annotated sequences in the public protein databases, 4,326 and 7,061 unigenes were found to be highly abundant in lines 121A and 121C, respectively. Many of the differentially expressed unigenes represent a set of potential candidate genes associated with the formation or abortion of pollen. CONCLUSIONS: Our study profiled anther transcriptomes of a chili pepper CMS line and its restorer line. The results shed the lights on the occurrence and recovery of the disturbances in nuclear-mitochondrial interaction and provide clues for further investigations.

  8. Evaluation of Mungbean Mutant Lines to Drought Stress and Their Genetic Relationships Using SSR Markers

    Directory of Open Access Journals (Sweden)

    Yuliasti

    2015-12-01

    Full Text Available Development of mungbean cultivarstolerant to drought stress through mutation breeding approach would enable us to anticipate the crop yield-reducing effects of climate changes. The objective of this research was to evaluate the yield performance of mungbean mutant lines that showed tolerance to drought stress, and to analyze their genetic diversity and relationship among mutant lines using SSR markers. The study was conducted during the dry season of 2012 in the Muneng experimental farm, Probolinggo, East Java. The experiment was laid out in a randomized block design with four replications. Five mutant lines and two parental lines as control were tested for evaluation of yield and drought tolerance under twoenvironments of two irrigation systems as treatment. The two environmental conditions consisted of optimal irrigation (at least three times: at planting, flowering and during pod filling and suboptimal irrigation (two times at planting and flowering. To evaluate genetic variation among selected mutant lines and their discrimination from parental lines in molecular level, a cluster analysis was performed using Unweighted Pair Group Method with Arithmetic Mean (UPGMA in the NTSYS software. The results showed that three mutant lines, including PsJ30, PsJ31, PsJ32 produced the highest grain yields of 1.17, 1.01, and 1.04 ton/ha, respectively, compared to the other mutant lines and the parents Gelatik (0.85 ton/ha and Perkutut (0.87 ton/ha as control check. Of those mutant lines, PSJ31 was the most tolerant to drought with sensitivity index value of 0.47. The PSJ31 has now been officially released as a new variety ( 2013, named as Muri which was identified to have high yield and tolerant to drought. Based on 23 SSR markers used for clustering analysis of those 3 selected mutant lines,9SSR markers (MBSS R033; satt137; MBSSR008; MBSSR203; MBSSR013; MBSSR021; MBSSR016; MBSSR136; and DMBSSR013 were successfully identified the three mungbean mutant

  9. A molecular line survey toward the nearby galaxies NGC 1068, NGC 253, and IC 342 at 3 mm with the Nobeyama 45 m radio telescope: Impact of an AGN on 1 kpc scale molecular abundances

    Science.gov (United States)

    Nakajima, Taku; Takano, Shuro; Kohno, Kotaro; Harada, Nanase; Herbst, Eric

    2018-01-01

    It is important to investigate the relationships between the power sources and the chemical compositions of galaxies in order to understand the scenario of galaxy evolution. We carried out an unbiased molecular line survey towards active galactic nucleus (AGN) host galaxy NGC1068, and prototypical starburst galaxies, NGC 253 and IC 342, with the Nobeyama 45 m telescope in the 3 mm band. The advantage of this line survey is that the obtained spectra have the highest angular resolution ever obtained with single-dish telescopes. In particular, the beam size of this telescope is ˜15″-19″, which is able to separate spatially the nuclear molecular emission from that of the starburst ring (d ˜ 30″) in NGC 1068. We successfully detected approximately 23 molecular species in each galaxy, and calculated rotation temperatures and column densities. We estimate the molecular fractional abundances with respect to 13CO and CS molecules and compare them among three galaxies in order to investigate the chemical signatures of an AGN environment. As a result, we found clear trends in the abundances of molecules surrounding the AGN on a 1-kpc scale. HCN, H13CN, CN, 13CN, and HC3N are more abundant, and CH3CCH is deficient in NGC 1068 compared with the starburst galaxies. High abundances of HCN, H13CN, and HC3N suggest that the circumnuclear disk in NGC 1068 is in a high-temperature environment. The reason for the non-detection of CH3CCH is likely to be dissociation by high-energy radiation or less sublimation of a precursor of CH3CCH from grains.

  10. The Molecular Gas Environment in the 20 km s{sup −1} Cloud in the Central Molecular Zone

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Xing; Gu, Qiusheng [School of Astronomy and Space Science, Nanjing University, Nanjing, Jiangsu 210093 (China); Zhang, Qizhou; Battersby, Cara [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Kauffmann, Jens; Pillai, Thushara [Max Planck Institut für Radioastronomie, Auf dem Hügel 69, D-53121 Bonn (Germany); Longmore, Steven N. [Astrophysics Research Institute, Liverpool John Moores University, 146 Brownlow Hill, Liverpool L3 5RF (United Kingdom); Kruijssen, J. M. Diederik [Astronomisches Rechen-Institut, Zentrum für Astronomie der Universität Heidelberg, Mönchhofstraße 12-14, D-69120 Heidelberg (Germany); Liu, Hauyu Baobab; Zhang, Zhi-Yu [European Southern Observatory, Karl-Schwarzschild-Straße 2, D-85748 Garching (Germany); Ginsburg, Adam [National Radio Astronomy Observatory, Socorro, NM 87801 (United States); Mills, Elisabeth A. C., E-mail: xinglv.nju@gmail.com [Department of Physics and Astronomy, San Jose State University, One Washington Square, San Jose, CA 95192 (United States)

    2017-04-10

    We recently reported a population of protostellar candidates in the 20 km s{sup −1} cloud in the Central Molecular Zone of the Milky Way, traced by H{sub 2}O masers in gravitationally bound dense cores. In this paper, we report molecular line studies with high angular resolution (∼3″) of the environment of star formation in this cloud. Maps of various molecular line transitions as well as the continuum at 1.3 mm are obtained using the Submillimeter Array. Five NH{sub 3} inversion lines and the 1.3 cm continuum are observed with the Karl G. Jansky Very Large Array. The interferometric observations are complemented with single-dish data. We find that the CH{sub 3}OH, SO, and HNCO lines, which are usually shock tracers, are better correlated spatially with the compact dust emission from dense cores among the detected lines. These lines also show enhancement in intensities with respect to SiO intensities toward the compact dust emission, suggesting the presence of slow shocks or hot cores in these regions. We find gas temperatures of ≳100 K at 0.1 pc scales based on RADEX modeling of the H{sub 2}CO and NH{sub 3} lines. Although no strong correlations between temperatures and linewidths/H{sub 2}O maser luminosities are found, in high-angular-resolution maps we note several candidate shock-heated regions offset from any dense cores, as well as signatures of localized heating by protostars in several dense cores. Our findings suggest that at 0.1 pc scales in this cloud star formation and strong turbulence may together affect the chemistry and temperature of the molecular gas.

  11. Agronomic and molecular evaluation of maize inbred lines for drought tolerance

    International Nuclear Information System (INIS)

    Mikić, S.; Zorić, M.; Stanisavljević, D.; Kondić-Špika, A.; Brbaklić, L.; Kobiljski, B.; Nastasić, A.; Mitrović, B.; Šurlan-Momirović, G.

    2016-01-01

    Drought is a severe threat to maize yield stability in Serbia and other temperate Southeast European countries occurring occasionally but with significant yield losses. The development of resilient genotypes that perform well under drought is one of the main focuses of maize breeding programmes. To test the tolerance of newly developed elite maize inbred lines to drought stress, field trials for grain yield performance and anthesis silk interval (ASI) were set in drought stressed environments in 2011 and 2012. Inbred lines performing well under drought, clustered into a group with short ASI and a smaller group with long ASI, were considered as a potential source for tolerance. The former contained inbreds from different heterotic groups and with a proportion of local germplasm. The latter consisted of genotypes with mixed exotic and Lancaster germplasm, which performed better in more drought-affected environments. Three inbreds were selected for their potential drought tolerance, showing an above-average yield and small ASI in all environments. Association analysis indicated significant correlations between ASI and grain yield and three microsatellites (bnlg1525, bnlg238 and umc1025). Eight alleles were selected for their favourable concurrent effect on yield increase and ASI decrease. The proportion of phenotypic variation explained by the markers varied across environments from 5.7% to 22.4% and from 4.6% to 8.1% for ASI and yield, respectively. The alleles with strongest effect on performance of particular genotypes and their interactions in specific environments were identified by the mean of partial least square interactions analysis indicating potential suitability of the makers for tolerant genotype selection.

  12. Agronomic and molecular evaluation of maize inbred lines for drought tolerance

    Energy Technology Data Exchange (ETDEWEB)

    Mikić, S.; Zorić, M.; Stanisavljević, D.; Kondić-Špika, A.; Brbaklić, L.; Kobiljski, B.; Nastasić, A.; Mitrović, B.; Šurlan-Momirović, G.

    2016-07-01

    Drought is a severe threat to maize yield stability in Serbia and other temperate Southeast European countries occurring occasionally but with significant yield losses. The development of resilient genotypes that perform well under drought is one of the main focuses of maize breeding programmes. To test the tolerance of newly developed elite maize inbred lines to drought stress, field trials for grain yield performance and anthesis silk interval (ASI) were set in drought stressed environments in 2011 and 2012. Inbred lines performing well under drought, clustered into a group with short ASI and a smaller group with long ASI, were considered as a potential source for tolerance. The former contained inbreds from different heterotic groups and with a proportion of local germplasm. The latter consisted of genotypes with mixed exotic and Lancaster germplasm, which performed better in more drought-affected environments. Three inbreds were selected for their potential drought tolerance, showing an above-average yield and small ASI in all environments. Association analysis indicated significant correlations between ASI and grain yield and three microsatellites (bnlg1525, bnlg238 and umc1025). Eight alleles were selected for their favourable concurrent effect on yield increase and ASI decrease. The proportion of phenotypic variation explained by the markers varied across environments from 5.7% to 22.4% and from 4.6% to 8.1% for ASI and yield, respectively. The alleles with strongest effect on performance of particular genotypes and their interactions in specific environments were identified by the mean of partial least square interactions analysis indicating potential suitability of the makers for tolerant genotype selection.

  13. Program of telluric lines monitoring

    Directory of Open Access Journals (Sweden)

    Vince I.

    2006-01-01

    Full Text Available A new observational program of telluric lines monitoring was introduced at Belgrade Astronomical Observatory. The ultimate goal of this program is to investigate the properties of Earth’s atmosphere through modeling the observed profiles of telluric lines. The program is intend to observe infrared molecular oxygen lines that were selected according to spectral sensitivity of the available CCD camera. In this paper we give the initial and the final selection criteria for spectral lines included in the program the description of equipment and procedures used for observations and reduction, a review of preliminary observational results with the estimated precision, and a short discussion on the comparison of the theoretical predictions and the measurements.

  14. MALT90 Kinematic Distances to Dense Molecular Clumps

    Energy Technology Data Exchange (ETDEWEB)

    Whitaker, J. Scott [Physics Department, Boston University, 590 Commonwealth Avenue, Boston, MA 02215 (United States); Jackson, James M.; Sanhueza, Patricio; Stephens, Ian W. [Institute for Astrophysical Research, Boston University, Boston, MA 02215 (United States); Rathborne, J. M. [CSIRO Astronomy and Space Science, P.O. Box 76, Epping NSW 1710 (Australia); Foster, J. B. [Department of Astronomy, Yale University, P.O. Box 28101, New Haven, CT 06520-8101 (United States); Contreras, Y. [Leiden Observatory, Leiden University, P.O. Box 9513, 2300 RA Leiden (Netherlands); Longmore, S. N., E-mail: scott@bu.edu [Astrophysics Research Institute, Liverpool John Moores University, Egerton Wharf, Birkenhead CH41 1LD (United Kingdom)

    2017-10-01

    Using molecular-line data from the Millimetre Astronomy Legacy Team 90 GHz Survey (MALT90), we have estimated kinematic distances to 1905 molecular clumps identified in the ATLASGAL 870 μ m continuum survey over the longitude range 295° <  l  < 350°. The clump velocities were determined using a flux-weighted average of the velocities obtained from Gaussian fits to the HCO{sup +}, HNC, and N{sub 2}H{sup +} (1–0) transitions. The near/far kinematic distance ambiguity was addressed by searching for the presence or absence of absorption or self-absorption features in 21 cm atomic hydrogen spectra from the Southern Galactic Plane Survey. Our algorithm provides an estimation of the reliability of the ambiguity resolution. The Galactic distribution of the clumps indicates positions where the clumps are bunched together, and these locations probably trace the locations of spiral arms. Several clumps fall at the predicted location of the far side of the Scutum–Centaurus arm. Moreover, a number of clumps with positive radial velocities are unambiguously located on the far side of the Milky Way at galactocentric radii beyond the solar circle. The measurement of these kinematic distances, in combination with continuum or molecular-line data, now enables the determination of fundamental parameters such as mass, size, and luminosity for each clump.

  15. ExoMol molecular line lists - XXVI: spectra of SH and NS

    Science.gov (United States)

    Yurchenko, Sergei N.; Bond, Wesley; Gorman, Maire N.; Lodi, Lorenzo; McKemmish, Laura K.; Nunn, William; Shah, Rohan; Tennyson, Jonathan

    2018-07-01

    Line lists for the sulphur-containing molecules SH (the mercapto radical) and NS are computed as part of the ExoMol project. These line lists consider transitions within the X2Π ground state for 32SH, 33SH, 34SH,36SH and, 32SD, and 14N32S, 14N33S, 14N34S, 14N36S, and 15N32S. Ab initio potential energy (PEC) and spin-orbit coupling (SOC) curves are computed and then improved by fitting to experimentally observed transitions. Fully ab initio dipole moment curves (DMCs) computed at high level of theory are used to produce the final line lists. For SH, our fit gives a root-mean-square (rms) error of 0.03 cm-1 between the observed (vmax = 4, Jmax = 34.5) and calculated transitions wavenumbers; this is extrapolated such that all X2Π rotational-vibrational-electronic (rovibronic) bound states are considered. For 32SH the resulting line list contains about 81 000 transitions and 2300 rovibronic states, considering levels up to vmax = 14 and Jmax = 60.5. For NS the refinement used a combination of experimentally determined frequencies and energy levels and led to an rms-fitting error of 0.002 cm-1. Each NS-calculated line list includes around 2.8 million transitions and 31 000 rovibronic states with a vibrational range up to v = 53 and rotational range up to J = 235.5, which covers up to 23 000 cm-1. Both line lists should be complete for temperatures up to 5000 K. Example spectra simulated using this line list are shown and comparisons made to the existing data in the CDMS data base. The line lists are available from the CDS (http://cdsarc.u-strasbg.fr) and ExoMol (www.exomol.com) data bases.

  16. ExoMol molecular line lists - XXVI: spectra of SH and NS

    Science.gov (United States)

    Yurchenko, Sergei N.; Bond, Wesley; Gorman, Maire N.; Lodi, Lorenzo; McKemmish, Laura K.; Nunn, William; Shah, Rohan; Tennyson, Jonathan

    2018-04-01

    Line lists for the sulphur-containing molecules SH (the mercapto radical) and NS are computed as part of the ExoMol project. These line lists consider transitions within the X 2Π ground state for 32SH, 33SH, 34SH and 32SD, and 14N32S, 14N33S, 14N34S, 14N36S and 15N32S. Ab initio potential energy (PEC) and spin-orbit coupling (SOC) curves are computed and then improved by fitting to experimentally observed transitions. Fully ab initio dipole moment curves (DMCs) computed at high level of theory are used to produce the final line lists. For SH, our fit gives a root-mean-square (rms) error of 0.03 cm-1 between the observed (vmax = 4, Jmax = 34.5) and calculated transitions wavenumbers; this is extrapolated such that all X 2Π rotational-vibrational-electronic (rovibronic) bound states are considered. For 32SH the resulting line list contains about 81 000 transitions and 2 300 rovibronic states, considering levels up to vmax = 14 and Jmax = 60.5. For NS the refinement used a combination of experimentally determined frequencies and energy levels and led to an rms fitting error of 0.002 cm-1. Each NS calculated line list includes around 2.8 million transitions and 31 000 rovibronic states with a vibrational range up to v = 53 and rotational range to J = 235.5, which covers up to 23 000 cm-1. Both line lists should be complete for temperatures up to 5000 K. Example spectra simulated using this line list are shown and comparisons made to the existing data in the CDMS database. The line lists are available from the CDS (http://cdsarc.u-strasbg.fr) and ExoMol (www.exomol.com) data bases.

  17. A 6-gene signature identifies four molecular subgroups of neuroblastoma

    LENUS (Irish Health Repository)

    Abel, Frida

    2011-04-14

    Abstract Background There are currently three postulated genomic subtypes of the childhood tumour neuroblastoma (NB); Type 1, Type 2A, and Type 2B. The most aggressive forms of NB are characterized by amplification of the oncogene MYCN (MNA) and low expression of the favourable marker NTRK1. Recently, mutations or high expression of the familial predisposition gene Anaplastic Lymphoma Kinase (ALK) was associated to unfavourable biology of sporadic NB. Also, various other genes have been linked to NB pathogenesis. Results The present study explores subgroup discrimination by gene expression profiling using three published microarray studies on NB (47 samples). Four distinct clusters were identified by Principal Components Analysis (PCA) in two separate data sets, which could be verified by an unsupervised hierarchical clustering in a third independent data set (101 NB samples) using a set of 74 discriminative genes. The expression signature of six NB-associated genes ALK, BIRC5, CCND1, MYCN, NTRK1, and PHOX2B, significantly discriminated the four clusters (p < 0.05, one-way ANOVA test). PCA clusters p1, p2, and p3 were found to correspond well to the postulated subtypes 1, 2A, and 2B, respectively. Remarkably, a fourth novel cluster was detected in all three independent data sets. This cluster comprised mainly 11q-deleted MNA-negative tumours with low expression of ALK, BIRC5, and PHOX2B, and was significantly associated with higher tumour stage, poor outcome and poor survival compared to the Type 1-corresponding favourable group (INSS stage 4 and\\/or dead of disease, p < 0.05, Fisher\\'s exact test). Conclusions Based on expression profiling we have identified four molecular subgroups of neuroblastoma, which can be distinguished by a 6-gene signature. The fourth subgroup has not been described elsewhere, and efforts are currently made to further investigate this group\\'s specific characteristics.

  18. Multi-scale strategies for dealing with moving contact lines

    Science.gov (United States)

    Smith, Edward R.; Theodorakis, Panagiotis; Craster, Richard V.; Matar, Omar K.

    2017-11-01

    Molecular dynamics (MD) has great potential to elucidate the dynamics of the moving contact line. As a more fundamental model, it can provide a priori results for fluid-liquid interfaces, surface tension, viscosity, phase change, and near wall stick-slip behaviour which typically show very good agreement to experimental results. However, modelling contact line motion combines all this complexity in a single problem. In this talk, MD simulations of the contact line are compared to the experimental results obtained from studying the dynamics of a sheared liquid bridge. The static contact angles are correctly matched to the experimental data for a range of different electro-wetting results. The moving contact line results are then compared for each of these electro-wetting values. Despite qualitative agreement, there are notable differences between the simulation and experiments. Many MD simulation have studied contact lines, and the sheared liquid bridge, so it is of interest to review the limitations of this setup in light of this discrepancy. A number of factors are discussed, including the inter-molecular interaction model, molecular-scale surface roughness, model of electro-wetting and, perhaps most importantly, the limited system sizes possible using MD simulation. EPSRC, UK, MEMPHIS program Grant (EP/K003976/1), RAEng Research Chair (OKM).

  19. Visual detection of glial cell line-derived neurotrophic factor based on a molecular translator and isothermal strand-displacement polymerization reaction.

    Science.gov (United States)

    Zhang, Li-Yong; Xing, Tao; Du, Li-Xin; Li, Qing-Min; Liu, Wei-Dong; Wang, Ji-Yue; Cai, Jing

    2015-01-01

    Glial cell line-derived neurotrophic factor (GDNF) is a small protein that potently promotes the survival of many types of neurons. Detection of GDNF is vital to monitoring the survival of sympathetic and sensory neurons. However, the specific method for GDNF detection is also un-discovered. The purpose of this study is to explore the method for protein detection of GDNF. A novel visual detection method based on a molecular translator and isothermal strand-displacement polymerization reaction (ISDPR) has been proposed for the detection of GDNF. In this study, a molecular translator was employed to convert the input protein to output deoxyribonucleic acid signal, which was further amplified by ISDPR. The product of ISDPR was detected by a lateral flow biosensor within 30 minutes. This novel visual detection method based on a molecular translator and ISDPR has very high sensitivity and selectivity, with a dynamic response ranging from 1 pg/mL to 10 ng/mL, and the detection limit was 1 pg/mL of GDNF. This novel visual detection method exhibits high sensitivity and selectivity, which is very simple and universal for GDNF detection to help disease therapy in clinical practice.

  20. Proteomic analysis of cell lines to identify the irinotecan resistance ...

    Indian Academy of Sciences (India)

    MADHU

    was selected from the wild-type LoVo cell line by chronic exposure to irinotecan ... dose–effect curves of anticancer drugs were drawn on semilogarithm .... alcohol metabolites daunorubicinol (Forrest and Gonzalez. 2000; Mordente et al. ..... Chen L, Huang C and Wei Y 2007 Proteomic analysis of liver cancer cells treated ...

  1. Retinal ganglion cells with distinct directional preferences differ in molecular identity, structure, and central projections.

    Science.gov (United States)

    Kay, Jeremy N; De la Huerta, Irina; Kim, In-Jung; Zhang, Yifeng; Yamagata, Masahito; Chu, Monica W; Meister, Markus; Sanes, Joshua R

    2011-05-25

    The retina contains ganglion cells (RGCs) that respond selectively to objects moving in particular directions. Individual members of a group of ON-OFF direction-selective RGCs (ooDSGCs) detect stimuli moving in one of four directions: ventral, dorsal, nasal, or temporal. Despite this physiological diversity, little is known about subtype-specific differences in structure, molecular identity, and projections. To seek such differences, we characterized mouse transgenic lines that selectively mark ooDSGCs preferring ventral or nasal motion as well as a line that marks both ventral- and dorsal-preferring subsets. We then used the lines to identify cell surface molecules, including Cadherin 6, CollagenXXVα1, and Matrix metalloprotease 17, that are selectively expressed by distinct subsets of ooDSGCs. We also identify a neuropeptide, CART (cocaine- and amphetamine-regulated transcript), that distinguishes all ooDSGCs from other RGCs. Together, this panel of endogenous and transgenic markers distinguishes the four ooDSGC subsets. Patterns of molecular diversification occur before eye opening and are therefore experience independent. They may help to explain how the four subsets obtain distinct inputs. We also demonstrate differences among subsets in their dendritic patterns within the retina and their axonal projections to the brain. Differences in projections indicate that information about motion in different directions is sent to different destinations.

  2. Diversity in host clone performance within a Chinese hamster ovary cell line.

    Science.gov (United States)

    O'Callaghan, Peter M; Berthelot, Maud E; Young, Robert J; Graham, James W A; Racher, Andrew J; Aldana, Dulce

    2015-01-01

    Much effort has been expended to improve the capabilities of individual Chinese hamster ovary (CHO) host cell lines to synthesize recombinant therapeutic proteins (rPs). However, given the increasing variety in rP molecular types and formats it may be advantageous to employ a toolbox of CHO host cell lines in biomanufacturing. Such a toolbox would contain a panel of hosts with specific capabilities to synthesize certain molecular types at high volumetric concentrations and with the correct product quality (PQ). In this work, we examine a panel of clonally derived host cell lines isolated from CHOK1SV for the ability to manufacture two model proteins, an IgG4 monoclonal antibody (Mab) and an Fc-fusion protein (etanercept). We show that these host cell lines vary in their relative ability to synthesize these proteins in transient and stable pool production format. Furthermore, we examined the PQ attributes of the stable pool-produced Mab and etanercept (by N-glycan ultra performance liquid chromatography (UPLC) and liquid chromatography - tandem mass spectrometry (LC-MS/MS), respectively), and uncovered substantial variation between the host cell lines in Mab N-glycan micro-heterogeneity and etanercept N and O-linked macro-heterogeneity. To further investigate the capabilities of these hosts to act as cell factories, we examined the glycosylation pathway gene expression profiles as well as the levels of endoplasmic reticulum (ER) and mitochondria in the untransfected hosts. We uncovered a moderate correlation between ER mass and the volumetric product concentration in transient and stable pool Mab production. This work demonstrates the utility of leveraging diversity within the CHOK1SV pool to identify new host cell lines with different performance characteristics. © 2015 American Institute of Chemical Engineers.

  3. DNA methylation profiles of ovarian epithelial carcinoma tumors and cell lines.

    Directory of Open Access Journals (Sweden)

    Sahar Houshdaran

    2010-02-01

    Full Text Available Epithelial ovarian carcinoma is a significant cause of cancer mortality in women worldwide and in the United States. Epithelial ovarian cancer comprises several histological subtypes, each with distinct clinical and molecular characteristics. The natural history of this heterogeneous disease, including the cell types of origin, is poorly understood. This study applied recently developed methods for high-throughput DNA methylation profiling to characterize ovarian cancer cell lines and tumors, including representatives of three major histologies.We obtained DNA methylation profiles of 1,505 CpG sites (808 genes in 27 primary epithelial ovarian tumors and 15 ovarian cancer cell lines. We found that the DNA methylation profiles of ovarian cancer cell lines were markedly different from those of primary ovarian tumors. Aggregate DNA methylation levels of the assayed CpG sites tended to be higher in ovarian cancer cell lines relative to ovarian tumors. Within the primary tumors, those of the same histological type were more alike in their methylation profiles than those of different subtypes. Supervised analyses identified 90 CpG sites (68 genes that exhibited 'subtype-specific' DNA methylation patterns (FDR<1% among the tumors. In ovarian cancer cell lines, we estimated that for at least 27% of analyzed autosomal CpG sites, increases in methylation were accompanied by decreases in transcription of the associated gene.The significant difference in DNA methylation profiles between ovarian cancer cell lines and tumors underscores the need to be cautious in using cell lines as tumor models for molecular studies of ovarian cancer and other cancers. Similarly, the distinct methylation profiles of the different histological types of ovarian tumors reinforces the need to treat the different histologies of ovarian cancer as different diseases, both clinically and in biomarker studies. These data provide a useful resource for future studies, including those of

  4. Integration of genomic, transcriptomic and proteomic data identifies two biologically distinct subtypes of invasive lobular breast cancer.

    Science.gov (United States)

    Michaut, Magali; Chin, Suet-Feung; Majewski, Ian; Severson, Tesa M; Bismeijer, Tycho; de Koning, Leanne; Peeters, Justine K; Schouten, Philip C; Rueda, Oscar M; Bosma, Astrid J; Tarrant, Finbarr; Fan, Yue; He, Beilei; Xue, Zheng; Mittempergher, Lorenza; Kluin, Roelof J C; Heijmans, Jeroen; Snel, Mireille; Pereira, Bernard; Schlicker, Andreas; Provenzano, Elena; Ali, Hamid Raza; Gaber, Alexander; O'Hurley, Gillian; Lehn, Sophie; Muris, Jettie J F; Wesseling, Jelle; Kay, Elaine; Sammut, Stephen John; Bardwell, Helen A; Barbet, Aurélie S; Bard, Floriane; Lecerf, Caroline; O'Connor, Darran P; Vis, Daniël J; Benes, Cyril H; McDermott, Ultan; Garnett, Mathew J; Simon, Iris M; Jirström, Karin; Dubois, Thierry; Linn, Sabine C; Gallagher, William M; Wessels, Lodewyk F A; Caldas, Carlos; Bernards, Rene

    2016-01-05

    Invasive lobular carcinoma (ILC) is the second most frequently occurring histological breast cancer subtype after invasive ductal carcinoma (IDC), accounting for around 10% of all breast cancers. The molecular processes that drive the development of ILC are still largely unknown. We have performed a comprehensive genomic, transcriptomic and proteomic analysis of a large ILC patient cohort and present here an integrated molecular portrait of ILC. Mutations in CDH1 and in the PI3K pathway are the most frequent molecular alterations in ILC. We identified two main subtypes of ILCs: (i) an immune related subtype with mRNA up-regulation of PD-L1, PD-1 and CTLA-4 and greater sensitivity to DNA-damaging agents in representative cell line models; (ii) a hormone related subtype, associated with Epithelial to Mesenchymal Transition (EMT), and gain of chromosomes 1q and 8q and loss of chromosome 11q. Using the somatic mutation rate and eIF4B protein level, we identified three groups with different clinical outcomes, including a group with extremely good prognosis. We provide a comprehensive overview of the molecular alterations driving ILC and have explored links with therapy response. This molecular characterization may help to tailor treatment of ILC through the application of specific targeted, chemo- and/or immune-therapies.

  5. Immortalized human myotonic dystrophy muscle cell lines to assess therapeutic compounds

    Science.gov (United States)

    Arandel, Ludovic; Polay Espinoza, Micaela; Matloka, Magdalena; Bazinet, Audrey; De Dea Diniz, Damily; Naouar, Naïra; Rau, Frédérique; Jollet, Arnaud; Edom-Vovard, Frédérique; Mamchaoui, Kamel; Tarnopolsky, Mark; Puymirat, Jack; Battail, Christophe; Boland, Anne; Deleuze, Jean-Francois; Mouly, Vincent; Klein, Arnaud F.

    2017-01-01

    ABSTRACT Myotonic dystrophy type 1 (DM1) and type 2 (DM2) are autosomal dominant neuromuscular diseases caused by microsatellite expansions and belong to the family of RNA-dominant disorders. Availability of cellular models in which the DM mutation is expressed within its natural context is essential to facilitate efforts to identify new therapeutic compounds. Here, we generated immortalized DM1 and DM2 human muscle cell lines that display nuclear RNA aggregates of expanded repeats, a hallmark of myotonic dystrophy. Selected clones of DM1 and DM2 immortalized myoblasts behave as parental primary myoblasts with a reduced fusion capacity of immortalized DM1 myoblasts when compared with control and DM2 cells. Alternative splicing defects were observed in differentiated DM1 muscle cell lines, but not in DM2 lines. Splicing alterations did not result from differentiation delay because similar changes were found in immortalized DM1 transdifferentiated fibroblasts in which myogenic differentiation has been forced by overexpression of MYOD1. As a proof-of-concept, we show that antisense approaches alleviate disease-associated defects, and an RNA-seq analysis confirmed that the vast majority of mis-spliced events in immortalized DM1 muscle cells were affected by antisense treatment, with half of them significantly rescued in treated DM1 cells. Immortalized DM1 muscle cell lines displaying characteristic disease-associated molecular features such as nuclear RNA aggregates and splicing defects can be used as robust readouts for the screening of therapeutic compounds. Therefore, immortalized DM1 and DM2 muscle cell lines represent new models and tools to investigate molecular pathophysiological mechanisms and evaluate the in vitro effects of compounds on RNA toxicity associated with myotonic dystrophy mutations. PMID:28188264

  6. Immortalized human myotonic dystrophy muscle cell lines to assess therapeutic compounds

    Directory of Open Access Journals (Sweden)

    Ludovic Arandel

    2017-04-01

    Full Text Available Myotonic dystrophy type 1 (DM1 and type 2 (DM2 are autosomal dominant neuromuscular diseases caused by microsatellite expansions and belong to the family of RNA-dominant disorders. Availability of cellular models in which the DM mutation is expressed within its natural context is essential to facilitate efforts to identify new therapeutic compounds. Here, we generated immortalized DM1 and DM2 human muscle cell lines that display nuclear RNA aggregates of expanded repeats, a hallmark of myotonic dystrophy. Selected clones of DM1 and DM2 immortalized myoblasts behave as parental primary myoblasts with a reduced fusion capacity of immortalized DM1 myoblasts when compared with control and DM2 cells. Alternative splicing defects were observed in differentiated DM1 muscle cell lines, but not in DM2 lines. Splicing alterations did not result from differentiation delay because similar changes were found in immortalized DM1 transdifferentiated fibroblasts in which myogenic differentiation has been forced by overexpression of MYOD1. As a proof-of-concept, we show that antisense approaches alleviate disease-associated defects, and an RNA-seq analysis confirmed that the vast majority of mis-spliced events in immortalized DM1 muscle cells were affected by antisense treatment, with half of them significantly rescued in treated DM1 cells. Immortalized DM1 muscle cell lines displaying characteristic disease-associated molecular features such as nuclear RNA aggregates and splicing defects can be used as robust readouts for the screening of therapeutic compounds. Therefore, immortalized DM1 and DM2 muscle cell lines represent new models and tools to investigate molecular pathophysiological mechanisms and evaluate the in vitro effects of compounds on RNA toxicity associated with myotonic dystrophy mutations.

  7. Immortalized human myotonic dystrophy muscle cell lines to assess therapeutic compounds.

    Science.gov (United States)

    Arandel, Ludovic; Polay Espinoza, Micaela; Matloka, Magdalena; Bazinet, Audrey; De Dea Diniz, Damily; Naouar, Naïra; Rau, Frédérique; Jollet, Arnaud; Edom-Vovard, Frédérique; Mamchaoui, Kamel; Tarnopolsky, Mark; Puymirat, Jack; Battail, Christophe; Boland, Anne; Deleuze, Jean-Francois; Mouly, Vincent; Klein, Arnaud F; Furling, Denis

    2017-04-01

    Myotonic dystrophy type 1 (DM1) and type 2 (DM2) are autosomal dominant neuromuscular diseases caused by microsatellite expansions and belong to the family of RNA-dominant disorders. Availability of cellular models in which the DM mutation is expressed within its natural context is essential to facilitate efforts to identify new therapeutic compounds. Here, we generated immortalized DM1 and DM2 human muscle cell lines that display nuclear RNA aggregates of expanded repeats, a hallmark of myotonic dystrophy. Selected clones of DM1 and DM2 immortalized myoblasts behave as parental primary myoblasts with a reduced fusion capacity of immortalized DM1 myoblasts when compared with control and DM2 cells. Alternative splicing defects were observed in differentiated DM1 muscle cell lines, but not in DM2 lines. Splicing alterations did not result from differentiation delay because similar changes were found in immortalized DM1 transdifferentiated fibroblasts in which myogenic differentiation has been forced by overexpression of MYOD1. As a proof-of-concept, we show that antisense approaches alleviate disease-associated defects, and an RNA-seq analysis confirmed that the vast majority of mis-spliced events in immortalized DM1 muscle cells were affected by antisense treatment, with half of them significantly rescued in treated DM1 cells. Immortalized DM1 muscle cell lines displaying characteristic disease-associated molecular features such as nuclear RNA aggregates and splicing defects can be used as robust readouts for the screening of therapeutic compounds. Therefore, immortalized DM1 and DM2 muscle cell lines represent new models and tools to investigate molecular pathophysiological mechanisms and evaluate the in vitro effects of compounds on RNA toxicity associated with myotonic dystrophy mutations. © 2017. Published by The Company of Biologists Ltd.

  8. Identification and characterization of mobile genetic elements LINEs from Brassica genome.

    Science.gov (United States)

    Nouroz, Faisal; Noreen, Shumaila; Khan, Muhammad Fiaz; Ahmed, Shehzad; Heslop-Harrison, J S Pat

    2017-09-05

    Among transposable elements (TEs), the LTR retrotransposons are abundant followed by non-LTR retrotransposons in plant genomes, the lateral being represented by LINEs and SINEs. Computational and molecular approaches were used for the characterization of Brassica LINEs, their diversity and phylogenetic relationships. Four autonomous and four non-autonomous LINE families were identified and characterized from Brassica. Most of the autonomous LINEs displayed two open reading frames, ORF1 and ORF2, where ORF1 is a gag protein domain, while ORF2 encodes endonuclease (EN) and a reverse transcriptase (RT). Three of four families encoded an additional RNase H (RH) domain in pol gene common to 'R' and 'I' type of LINEs. The PCR analyses based on LINEs RT fragments indicate their high diversity and widespread occurrence in tested 40 Brassica cultivars. Database searches revealed the homology in LINE sequences in closely related genera Arabidopsis indicating their origin from common ancestors predating their separation. The alignment of 58 LINEs RT sequences from Brassica, Arabidopsis and other plants depicted 4 conserved domains (domain II-V) showing similarity to previously detected domains. Based on RT alignment of Brassica and 3 known LINEs from monocots, Brassicaceae LINEs clustered in separate clade, further resolving 4 Brassica-Arabidopsis specific families in 2 sub-clades. High similarities were observed in RT sequences in the members of same family, while low homology was detected in members across the families. The investigation led to the characterization of Brassica specific LINE families and their diversity across Brassica species and their cultivars. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. ExoMol molecular line lists - XXIII. Spectra of PO and PS

    Science.gov (United States)

    Prajapat, Laxmi; Jagoda, Pawel; Lodi, Lorenzo; Gorman, Maire N.; Yurchenko, Sergei N.; Tennyson, Jonathan

    2017-12-01

    Comprehensive line lists for phosphorus monoxide (31P16O) and phosphorus monosulphide (31P32S) in their X 2Π electronic ground state are presented. The line lists are based on new ab initio potential energy (PEC), spin-orbit (SOC) and dipole moment (DMC) curves computed using the MRCI+Q-r method with aug-cc-pwCV5Z and aug-cc-pV5Z basis sets. The nuclear motion equations (i.e. the rovibronic Schrödinger equations for each molecule) are solved using the program DUO. The PECs and SOCs are refined in least-squares fits to available experimental data. Partition functions, Q(T), are computed up to T = 5000 K, the range of validity of the line lists. These line lists are the most comprehensive available for either molecule. The characteristically sharp peak of the Q-branches from the spin-orbit split components gives useful diagnostics for both PO and PS in spectra at infrared wavelengths. These line lists should prove useful for analysing observations and setting up models of environments such as brown dwarfs, low-mass stars, O-rich circumstellar regions and potentially for exoplanetary retrievals. Since PS is yet to be detected in space, the role of the two lowest excited electronic states (a 4Π and B 2Π) are also considered. An approximate line list for the PS X-B electronic transition, which predicts a number of sharp vibrational bands in the near ultraviolet, is also presented. The line lists are available from the CDS (http://cdsarc.u-strasbg.fr) and ExoMol (www.exomol.com) data bases.

  10. Establishment, characterization and chemosensitivity of three mismatch repair deficient cell lines from sporadic and inherited colorectal carcinomas.

    Directory of Open Access Journals (Sweden)

    Claudia Maletzki

    Full Text Available BACKGROUND: Colorectal cancer (CRC represents a morphologic and molecular heterogenic disease. This heterogeneity substantially impairs drug effectiveness and prognosis. The subtype of mismatch repair deficient (MMR-D CRCs, accounting for about 15% of all cases, shows particular differential responses up to resistance towards currently approved cytostatic drugs. Pre-clinical in vitro models representing molecular features of MMR-D tumors are thus mandatory for identifying biomarkers that finally help to predict responses towards new cytostatic drugs. Here, we describe the successful establishment and characterization of three patient-derived MMR-D cell lines (HROC24, HROC87, and HROC113 along with their corresponding xenografts. METHODOLOGY: MMR-D cell lines (HROC24, HROC87, and HROC113 were established from a total of ten clinicopathological well-defined MMR-D cases (120 CRC cases in total. Cells were comprehensively characterized by phenotype, morphology, growth kinetics, invasiveness, and molecular profile. Additionally, response to clinically relevant chemotherapeutics was examined in vitro and in vivo. PRINCIPAL FINDINGS: Two MMR-D lines showing CIMP-H derived from sporadic CRC (HROC24: K-ras(wt, B-raf(mut, HROC87: K-ras(wt, B-raf(mut, whereas the HROC113 cell line (K-ras(mut, B-raf(wt was HNPCC-associated. A diploid DNA-status could be verified by flow cytometry and SNP Array analysis. All cell lines were characterized as epithelial (EpCAM(+ tumor cells, showing surface tumor marker expression (CEACAM(+. MHC-class II was inducible by Interferon-γ stimulation. Growth kinetics as well as invasive potential was quite heterogeneous between individual lines. Besides, MMR-D cell lines exhibited distinct responsiveness towards chemotherapeutics, even when comparing in vitro and in vivo sensitivity. CONCLUSIONS: These newly established and well-characterized, low-passage MMR-D cell lines provide a useful tool for future investigations on the

  11. Alternative splicing enriched cDNA libraries identify breast cancer-associated transcripts

    Science.gov (United States)

    2010-01-01

    Background Alternative splicing (AS) is a central mechanism in the generation of genomic complexity and is a major contributor to transcriptome and proteome diversity. Alterations of the splicing process can lead to deregulation of crucial cellular processes and have been associated with a large spectrum of human diseases. Cancer-associated transcripts are potential molecular markers and may contribute to the development of more accurate diagnostic and prognostic methods and also serve as therapeutic targets. Alternative splicing-enriched cDNA libraries have been used to explore the variability generated by alternative splicing. In this study, by combining the use of trapping heteroduplexes and RNA amplification, we developed a powerful approach that enables transcriptome-wide exploration of the AS repertoire for identifying AS variants associated with breast tumor cells modulated by ERBB2 (HER-2/neu) oncogene expression. Results The human breast cell line (C5.2) and a pool of 5 ERBB2 over-expressing breast tumor samples were used independently for the construction of two AS-enriched libraries. In total, 2,048 partial cDNA sequences were obtained, revealing 214 alternative splicing sequence-enriched tags (ASSETs). A subset with 79 multiple exon ASSETs was compared to public databases and reported 138 different AS events. A high success rate of RT-PCR validation (94.5%) was obtained, and 2 novel AS events were identified. The influence of ERBB2-mediated expression on AS regulation was evaluated by capillary electrophoresis and probe-ligation approaches in two mammary cell lines (Hb4a and C5.2) expressing different levels of ERBB2. The relative expression balance between AS variants from 3 genes was differentially modulated by ERBB2 in this model system. Conclusions In this study, we presented a method for exploring AS from any RNA source in a transcriptome-wide format, which can be directly easily adapted to next generation sequencers. We identified AS transcripts

  12. Drought Tolerance in Pinus halepensis Seed Sources As Identified by Distinctive Physiological and Molecular Markers.

    Science.gov (United States)

    Taïbi, Khaled; Del Campo, Antonio D; Vilagrosa, Alberto; Bellés, José M; López-Gresa, María Pilar; Pla, Davinia; Calvete, Juan J; López-Nicolás, José M; Mulet, José M

    2017-01-01

    Drought is one of the main constraints determining forest species growth, survival and productivity, and therefore one of the main limitations for reforestation or afforestation. The aim of this study is to characterize the drought response at the physiological and molecular level of different Pinus halepensis (common name Aleppo pine) seed sources, previously characterized in field trials as drought-sensitive or drought-tolerant. This approach aims to identify different traits capable of predicting the ability of formerly uncharacterized seedlings to cope with drought stress. Gas-exchange, water potential, photosynthetic pigments, soluble sugars, free amino acids, glutathione and proteomic analyses were carried out on control and drought-stressed seedlings in greenhouse conditions. Gas-exchange determinations were also assessed in field-planted seedlings in order to validate the greenhouse experimental conditions. Drought-tolerant seed sources presented higher values of photosynthetic rates, water use efficiency, photosynthetic pigments and soluble carbohydrates concentrations. We observed the same pattern of variation of photosynthesis rate and maximal efficiency of PSII in field. Interestingly drought-tolerant seed sources exhibited increased levels of glutathione, methionine and cysteine. The proteomic profile of drought tolerant seedlings identified two heat shock proteins and an enzyme related to methionine biosynthesis that were not present in drought sensitive seedlings, pointing to the synthesis of sulfur amino acids as a limiting factor for drought tolerance in Pinus halepensis . Our results established physiological and molecular traits useful as distinctive markers to predict drought tolerance in Pinus halepensis provenances that could be reliably used in reforestation programs in drought prone areas.

  13. Drought Tolerance in Pinus halepensis Seed Sources As Identified by Distinctive Physiological and Molecular Markers

    Directory of Open Access Journals (Sweden)

    Khaled Taïbi

    2017-07-01

    Full Text Available Drought is one of the main constraints determining forest species growth, survival and productivity, and therefore one of the main limitations for reforestation or afforestation. The aim of this study is to characterize the drought response at the physiological and molecular level of different Pinus halepensis (common name Aleppo pine seed sources, previously characterized in field trials as drought-sensitive or drought-tolerant. This approach aims to identify different traits capable of predicting the ability of formerly uncharacterized seedlings to cope with drought stress. Gas-exchange, water potential, photosynthetic pigments, soluble sugars, free amino acids, glutathione and proteomic analyses were carried out on control and drought-stressed seedlings in greenhouse conditions. Gas-exchange determinations were also assessed in field-planted seedlings in order to validate the greenhouse experimental conditions. Drought-tolerant seed sources presented higher values of photosynthetic rates, water use efficiency, photosynthetic pigments and soluble carbohydrates concentrations. We observed the same pattern of variation of photosynthesis rate and maximal efficiency of PSII in field. Interestingly drought-tolerant seed sources exhibited increased levels of glutathione, methionine and cysteine. The proteomic profile of drought tolerant seedlings identified two heat shock proteins and an enzyme related to methionine biosynthesis that were not present in drought sensitive seedlings, pointing to the synthesis of sulfur amino acids as a limiting factor for drought tolerance in Pinus halepensis. Our results established physiological and molecular traits useful as distinctive markers to predict drought tolerance in Pinus halepensis provenances that could be reliably used in reforestation programs in drought prone areas.

  14. A systems biology pipeline identifies new immune and disease related molecular signatures and networks in human cells during microgravity exposure.

    Science.gov (United States)

    Mukhopadhyay, Sayak; Saha, Rohini; Palanisamy, Anbarasi; Ghosh, Madhurima; Biswas, Anupriya; Roy, Saheli; Pal, Arijit; Sarkar, Kathakali; Bagh, Sangram

    2016-05-17

    Microgravity is a prominent health hazard for astronauts, yet we understand little about its effect at the molecular systems level. In this study, we have integrated a set of systems-biology tools and databases and have analysed more than 8000 molecular pathways on published global gene expression datasets of human cells in microgravity. Hundreds of new pathways have been identified with statistical confidence for each dataset and despite the difference in cell types and experiments, around 100 of the new pathways are appeared common across the datasets. They are related to reduced inflammation, autoimmunity, diabetes and asthma. We have identified downregulation of NfκB pathway via Notch1 signalling as new pathway for reduced immunity in microgravity. Induction of few cancer types including liver cancer and leukaemia and increased drug response to cancer in microgravity are also found. Increase in olfactory signal transduction is also identified. Genes, based on their expression pattern, are clustered and mathematically stable clusters are identified. The network mapping of genes within a cluster indicates the plausible functional connections in microgravity. This pipeline gives a new systems level picture of human cells under microgravity, generates testable hypothesis and may help estimating risk and developing medicine for space missions.

  15. A systems biology pipeline identifies new immune and disease related molecular signatures and networks in human cells during microgravity exposure

    Science.gov (United States)

    Mukhopadhyay, Sayak; Saha, Rohini; Palanisamy, Anbarasi; Ghosh, Madhurima; Biswas, Anupriya; Roy, Saheli; Pal, Arijit; Sarkar, Kathakali; Bagh, Sangram

    2016-05-01

    Microgravity is a prominent health hazard for astronauts, yet we understand little about its effect at the molecular systems level. In this study, we have integrated a set of systems-biology tools and databases and have analysed more than 8000 molecular pathways on published global gene expression datasets of human cells in microgravity. Hundreds of new pathways have been identified with statistical confidence for each dataset and despite the difference in cell types and experiments, around 100 of the new pathways are appeared common across the datasets. They are related to reduced inflammation, autoimmunity, diabetes and asthma. We have identified downregulation of NfκB pathway via Notch1 signalling as new pathway for reduced immunity in microgravity. Induction of few cancer types including liver cancer and leukaemia and increased drug response to cancer in microgravity are also found. Increase in olfactory signal transduction is also identified. Genes, based on their expression pattern, are clustered and mathematically stable clusters are identified. The network mapping of genes within a cluster indicates the plausible functional connections in microgravity. This pipeline gives a new systems level picture of human cells under microgravity, generates testable hypothesis and may help estimating risk and developing medicine for space missions.

  16. Atomic and molecular excitation mechanisms in the interstellar medium

    International Nuclear Information System (INIS)

    Sternberg, A.

    1986-01-01

    The detailed infrared response of dense molecular hydrogen gas to intense ultraviolet radiation fields in photodissociation regions is presented. The thermal and chemical structures of photodissociation regions are analyzed, and the relationship between the emission by molecular hydrogen and trace atomic and molecular species is explored. The ultraviolet spectrum of radiation generated by cosmic rays inside dense molecular clouds is presented, and the resulting rates of photodissociation for a variety of interstellar molecules are calculated. Effects of this radiation on the chemistry of dense molecular clouds are discussed, and it is argued that the cosmic ray induced photons will significantly inhibit the production of complex molecular species. It is argued that the annihilation of electrons and positrons at the galactic center may result in observable infrared line emission by atomic hydrogen. A correlation between the intensity variations of the 511 keV line and the hydrogen infrared lines emitted by the annihilation region is predicted. The observed infrared fluxes from compact infrared sources at the galactic center may be used to constrain theories of pair production there

  17. The HITRAN2016 molecular spectroscopic database

    Energy Technology Data Exchange (ETDEWEB)

    Gordon, I. E.; Rothman, L. S.; Hill, C.; Kochanov, R. V.; Tan, Y.; Bernath, P. F.; Birk, M.; Boudon, V.; Campargue, A.; Chance, K. V.; Drouin, B. J.; Flaud, J. -M.; Gamache, R. R.; Hodges, J. T.; Jacquemart, D.; Perevalov, V. I.; Perrin, A.; Shine, K. P.; Smith, M. -A. H.; Tennyson, J.; Toon, G. C.; Tran, H.; Tyuterev, V. G.; Barbe, A.; Császár, A. G.; Devi, V. M.; Furtenbacher, T.; Harrison, J. J.; Hartmann, J. -M.; Jolly, A.; Johnson, T. J.; Karman, T.; Kleiner, I.; Kyuberis, A. A.; Loos, J.; Lyulin, O. M.; Massie, S. T.; Mikhailenko, S. N.; Moazzen-Ahmadi, N.; Müller, H. S. P.; Naumenko, O. V.; Nikitin, A. V.; Polyansky, O. L.; Rey, M.; Rotger, M.; Sharpe, S. W.; Sung, K.; Starikova, E.; Tashkun, S. A.; Auwera, J. Vander; Wagner, G.; Wilzewski, J.; Wcisło, P.; Yu, S.; Zak, E. J.

    2017-12-01

    This paper describes the contents of the 2016 edition of the HITRAN molecular spectroscopic compilation. The new edition replaces the previous HITRAN edition of 2012 and its updates during the intervening years. The HITRAN molecular absorption compilation is comprised of five major components: the traditional line-by-line spectroscopic parameters required for high-resolution radiative-transfer codes, infrared absorption cross-sections for molecules not yet amenable to representation in a line-by-line form, collision-induced absorption data, aerosol indices of refraction, and general tables such as partition sums that apply globally to the data. The new HITRAN is greatly extended in terms of accuracy, spectral coverage, additional absorption phenomena, added line-shape formalisms, and validity. Moreover, molecules, isotopologues, and perturbing gases have been added that address the issues of atmospheres beyond the Earth. Of considerable note, experimental IR cross-sections for almost 200 additional significant molecules have been added to the database.

  18. Determination of the Molecular Weight of Low-Molecular-Weight Heparins by Using High-Pressure Size Exclusion Chromatography on Line with a Triple Detector Array and Conventional Methods

    Directory of Open Access Journals (Sweden)

    Antonella Bisio

    2015-03-01

    Full Text Available The evaluation of weight average molecular weight (Mw and molecular weight distribution represents one of the most controversial aspects concerning the characterization of low molecular weight heparins (LMWHs. As the most commonly used method for the measurement of such parameters is high performance size exclusion chromatography (HP-SEC, the soundness of results mainly depends on the appropriate calibration of the chromatographic columns used. With the aim of meeting the requirement of proper Mw standards for LMWHs, in the present work the determination of molecular weight parameters (Mw and Mn by HP-SEC combined with a triple detector array (TDA was performed. The HP-SEC/TDA technique permits the evaluation of polymeric samples by exploiting the combined and simultaneous action of three on-line detectors: light scattering detectors (LALLS/RALLS; refractometer and viscometer. Three commercial LMWH samples, enoxaparin, tinzaparin and dalteparin, a γ-ray depolymerized heparin (γ-Hep and its chromatographic fractions, and a synthetic pentasaccharide were analysed by HP-SEC/TDA. The same samples were analysed also with a conventional HP-SEC method employing refractive index (RI and UV detectors and two different chromatographic column set, silica gel and polymeric gel columns. In both chromatographic systems, two different calibration curves were built up by using (i γ-Hep chromatographic fractions and the corresponding Mw parameters obtained via HP-SEC/TDA; (ii the whole γ-Hep preparation with broad Mw dispersion and the corresponding cumulative distribution function calculated via HP-SEC/TDA. In addition, also a chromatographic column calibration according to European Pharmacopoeia indication was built up. By comparing all the obtained results, some important differences among Mw and size distribution values of the three LMWHs were found with the five different calibration methods and with HP-SEC/TDA method. In particular, the detection of

  19. Line radiative transfer and statistical equilibrium*

    Directory of Open Access Journals (Sweden)

    Kamp Inga

    2015-01-01

    Full Text Available Atomic and molecular line emission from protoplanetary disks contains key information of their detailed physical and chemical structures. To unravel those structures, we need to understand line radiative transfer in dusty media and the statistical equilibrium, especially of molecules. I describe here the basic principles of statistical equilibrium and illustrate them through the two-level atom. In a second part, the fundamentals of line radiative transfer are introduced along with the various broadening mechanisms. I explain general solution methods with their drawbacks and also specific difficulties encountered in solving the line radiative transfer equation in disks (e.g. velocity gradients. I am closing with a few special cases of line emission from disks: Radiative pumping, masers and resonance scattering.

  20. Systematic chemical and molecular profiling of MLL-rearranged infant acute lymphoblastic leukemia reveals efficacy of romidepsin

    Science.gov (United States)

    Cruickshank, M N; Ford, J; Cheung, L C; Heng, J; Singh, S; Wells, J; Failes, T W; Arndt, G M; Smithers, N; Prinjha, R K; Anderson, D; Carter, K W; Gout, A M; Lassmann, T; O'Reilly, J; Cole, C H; Kotecha, R S; Kees, U R

    2017-01-01

    To address the poor prognosis of mixed lineage leukemia (MLL)-rearranged infant acute lymphoblastic leukemia (iALL), we generated a panel of cell lines from primary patient samples and investigated cytotoxic responses to contemporary and novel Food and Drug Administration-approved chemotherapeutics. To characterize representation of primary disease within cell lines, molecular features were compared using RNA-sequencing and cytogenetics. High-throughput screening revealed variable efficacy of currently used drugs, however identified consistent efficacy of three novel drug classes: proteasome inhibitors, histone deacetylase inhibitors and cyclin-dependent kinase inhibitors. Gene expression of drug targets was highly reproducible comparing iALL cell lines to matched primary specimens. Histone deacetylase inhibitors, including romidepsin (ROM), enhanced the activity of a key component of iALL therapy, cytarabine (ARAC) in vitro and combined administration of ROM and ARAC to xenografted mice further reduced leukemia burden. Molecular studies showed that ROM reduces expression of cytidine deaminase, an enzyme involved in ARAC deactivation, and enhances the DNA damage–response to ARAC. In conclusion, we present a valuable resource for drug discovery, including the first systematic analysis of transcriptome reproducibility in vitro, and have identified ROM as a promising therapeutic for MLL-rearranged iALL. PMID:27443263

  1. Salt-induced root protein profile changes in seedlings of maize inbred lines with differing salt tolerances

    Directory of Open Access Journals (Sweden)

    Yujing Cheng

    2014-12-01

    Full Text Available Salt stress is one of the severest growth limited-factors to agriculture production. To gain in-depth knowledge of salt-stress response mechanisms, the proteomics analysis from two maize (Zea mays L. inbred lines was carried out using two-dimensional gel electrophoresis (2-DGE and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/TOF-MS. There were 57 salt-regulated proteins identified, 21 and 36 proteins were differentially regulated in inbred lines 'Nongda 1145' (salt-resistant and 'D340' (salt-sensitive, respectively. The identified proteins were distributed in 11 biological processes and seven molecular functions. Under salt stress, proteins related to antioxidation and lignin synthesis were increased in both inbred lines. The relative abundance of proteins involved in translation initiation, elongation, and protein proteolysis increased in 'Nongda 1145' and decreased in 'D340'. In addition, the abundance of proteins involved in carbohydrate metabolism, protein refolding, ATP synthase and transcription differed between the two inbred lines. Our results suggest that the enhanced ability of salt-tolerant inbred line 'Nongda 1145' to combat salt stress occurs via regulation of transcription factors promoting increased antioxidation and lignin biosynthesis, enhanced energy production, and acceleration of protein translation and protein proteolysis.

  2. Identification of exotic genetic components and DNA methylation pattern analysis of three cotton introgression lines from Gossypium bickii.

    Science.gov (United States)

    He, Shou-Pu; Sun, Jun-Ling; Zhang, Chao; Du, Xiong-Ming

    2011-01-01

    The impact of alien DNA fragments on plant genome has been studied in many species. However, little is known about the introgression lines of Gossypium. To study the consequences of introgression in Gossypium, we investigated 2000 genomic and 800 epigenetic sites in three typical cotton introgression lines, as well as their cultivar (Gossypium hirsutum) and wild parents (Gossypium bickii), by amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP). The results demonstrate that an average of 0.5% of exotic DNA segments from wild cotton is transmitted into the genome of each introgression line, with the addition of other forms of genetic variation. In total, an average of 0.7% of genetic variation sites is identified in introgression lines. Simultaneously, the overall cytosine methylation level in each introgression line is very close to that of the upland cotton parent (an average of 22.6%). Further dividing patterns reveal that both hypomethylation and hypermethylation occurred in introgression lines in comparison with the upland cotton parent. Sequencing of nine methylation polymorphism fragments showed that most (7 of 9) of the methylation alternations occurred in the noncoding sequences. The molecular evidence of introgression from wild cotton into introgression lines in our study is identified by AFLP. Moreover, the causes of petal variation in introgression lines are discussed.

  3. Binding sites for luminescent amyloid biomarkers from non-biased molecular dynamics simulations.

    Science.gov (United States)

    König, Carolin; Skånberg, Robin; Hotz, Ingrid; Ynnerman, Anders; Norman, Patrick; Linares, Mathieu

    2018-03-25

    A very stable binding site for the interaction between a pentameric oligothiophene and an amyloid-β(1-42) fibril has been identified by means of non-biased molecular dynamics simulations. In this site, the probe is locked in an all-trans conformation with a Coulombic binding energy of 1200 kJ mol -1 due to the interactions between the anionic carboxyl groups of the probe and the cationic ε-amino groups in the lysine side chain. Upon binding, the conformationally restricted probes show a pronounced increase in molecular planarity. This is in line with the observed changes in luminescence properties that serve as the foundation for their use as biomarkers.

  4. Attempt to identify the functional areas of the cerebral cortex on CT slices parallel to the orbito-meatal line

    Energy Technology Data Exchange (ETDEWEB)

    Tanabe, Hirotaka; Okuda, Junichiro; Nishikawa, Takashi; Nishimura, Tsuyoshi (Osaka Univ. (Japan). Faculty of Medicine); Shiraishi, Junzo

    1982-06-01

    In order to identify the functional brain areas, such as Broca's area, on computed tomography slices parallel to the orbito-meatal line, the numbers of Brodmann's cortical mapping were shown on a diagram of representative brain sections parallel to the orbito-meatal line. Also, we described a method, using cerebral sulci as anatomical landmarks, for projecting lesions shown by CT scan onto the lateral brain diagram. The procedures were as follows. The distribution of lesions on CT slices was determined by the identification of major cerebral sulci and fissures, such as the Sylvian fissure, the central sulcus, and the superior frontal sulcus. Those lesions were then projected onto the lateral diagram by comparing each CT slice with the horizontal diagrams of brain sections. The method was demonstrated in three cases developing neuropsychological symptoms.

  5. Interstellar C2, CH, and CN in translucent molecular clouds

    NARCIS (Netherlands)

    Dishoeck, van E.F.; Black, J.H.

    1989-01-01

    Optical absorption-line techniques have been applied to the study of a number of translucent molecular clouds in which the total column densities are large enough that substantial molecular abundances can be maintained. Results are presented for a survey of absorption lines of interstellar C2, CH,

  6. Mechanical feedback in the molecular ISM of luminous IR galaxies

    NARCIS (Netherlands)

    Loenen, A. F.; Spaans, M.; Baan, W. A.; Meijerink, R.

    Aims. Molecular emission lines originating in the nuclei of luminous infra-red galaxies are used to determine the physical properties of the nuclear ISM in these systems. Methods. A large observational database of molecular emission lines is compared with model predictions that include heating by UV

  7. On the widths of Stokes lines in Raman scattering from molecules adsorbed at metal surfaces and in molecular conduction junctions

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Yi, E-mail: yig057@ucsd.edu; Galperin, Michael, E-mail: migalperin@ucsd.edu [Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093 (United States); Nitzan, Abraham, E-mail: nitzan@post.tau.ac.il [Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA and School of Chemistry, Tel Aviv University, Tel Aviv 69978 (Israel)

    2016-06-28

    Within a generic model we analyze the Stokes linewidth in surface enhanced Raman scattering (SERS) from molecules embedded as bridges in molecular junctions. We identify four main contributions to the off-resonant Stokes signal and show that under zero voltage bias (a situation pertaining also to standard SERS experiments) and at low bias junctions only one of these contributions is pronounced. The linewidth of this component is determined by the molecular vibrational relaxation rate, which is dominated by interactions with the essentially bosonic thermal environment when the relevant molecular electronic energy is far from the metal(s) Fermi energy(ies). It increases when the molecular electronic level is close to the metal Fermi level so that an additional vibrational relaxation channel due to electron-hole (eh) exciton in the molecule opens. Other contributions to the Raman signal, of considerably broader linewidths, can become important at larger junction bias.

  8. Diagnosis of lubricating oil by evaluating cyanide and carbon molecular emission lines in laser induced breakdown spectra

    Science.gov (United States)

    Elnasharty, I. Y.; Kassem, A. K.; Sabsabi, M.; Harith, M. A.

    2011-08-01

    To prevent engine failure it is essential to change lubricating oil regularly before it loses its protective properties. It is also necessary to monitor the physical and chemical conditions of the oil to reliably determine the optimum oil-change intervals. The present work focuses on studying evolution of the cyanide (CN) and carbon (C 2) molecular spectral emission lines in the laser induced breakdown spectra of lubricating oil as a function of its consumption. The intensities of these molecular bands have been taken as indicator of engine oil degradation at certain mileage. Furthermore, the percentage of decay of CN and C 2 integral intensity values at the corresponding mileage was calculated in order to relate it to the degree of consumption of the motor oil. Such percentage decay of the CN and C 2 integral intensities have been found to increase gradually with increasing mileage which is accompanied with increasing depletion of engine oil. The results of using LIBS technique in the present measurements proved that it is possible to have a direct, straightforward and easy method for prediction of lubricating oil degree of consumption. This may facilitate scheduling the proper time and/or mileage intervals for changing the oil to avoid any possibility of engine failure.

  9. Diagnosis of lubricating oil by evaluating cyanide and carbon molecular emission lines in laser induced breakdown spectra

    Energy Technology Data Exchange (ETDEWEB)

    Elnasharty, I.Y.; Kassem, A.K. [National Institute of Laser Enhanced Science, Cairo University (Egypt); Sabsabi, M. [National Research Council, Industrial Material Institute, Quebec (Canada); Harith, M.A., E-mail: mharithm@niles.edu.eg [National Institute of Laser Enhanced Science, Cairo University (Egypt)

    2011-08-15

    To prevent engine failure it is essential to change lubricating oil regularly before it loses its protective properties. It is also necessary to monitor the physical and chemical conditions of the oil to reliably determine the optimum oil-change intervals. The present work focuses on studying evolution of the cyanide (CN) and carbon (C{sub 2}) molecular spectral emission lines in the laser induced breakdown spectra of lubricating oil as a function of its consumption. The intensities of these molecular bands have been taken as indicator of engine oil degradation at certain mileage. Furthermore, the percentage of decay of CN and C{sub 2} integral intensity values at the corresponding mileage was calculated in order to relate it to the degree of consumption of the motor oil. Such percentage decay of the CN and C{sub 2} integral intensities have been found to increase gradually with increasing mileage which is accompanied with increasing depletion of engine oil. The results of using LIBS technique in the present measurements proved that it is possible to have a direct, straightforward and easy method for prediction of lubricating oil degree of consumption. This may facilitate scheduling the proper time and/or mileage intervals for changing the oil to avoid any possibility of engine failure.

  10. Diagnosis of lubricating oil by evaluating cyanide and carbon molecular emission lines in laser induced breakdown spectra

    International Nuclear Information System (INIS)

    Elnasharty, I.Y.; Kassem, A.K.; Sabsabi, M.; Harith, M.A.

    2011-01-01

    To prevent engine failure it is essential to change lubricating oil regularly before it loses its protective properties. It is also necessary to monitor the physical and chemical conditions of the oil to reliably determine the optimum oil-change intervals. The present work focuses on studying evolution of the cyanide (CN) and carbon (C 2 ) molecular spectral emission lines in the laser induced breakdown spectra of lubricating oil as a function of its consumption. The intensities of these molecular bands have been taken as indicator of engine oil degradation at certain mileage. Furthermore, the percentage of decay of CN and C 2 integral intensity values at the corresponding mileage was calculated in order to relate it to the degree of consumption of the motor oil. Such percentage decay of the CN and C 2 integral intensities have been found to increase gradually with increasing mileage which is accompanied with increasing depletion of engine oil. The results of using LIBS technique in the present measurements proved that it is possible to have a direct, straightforward and easy method for prediction of lubricating oil degree of consumption. This may facilitate scheduling the proper time and/or mileage intervals for changing the oil to avoid any possibility of engine failure.

  11. CONTINUUM OBSERVATIONS AT 350 MICRONS OF HIGH-REDSHIFT MOLECULAR EMISSION LINE GALAXIES

    International Nuclear Information System (INIS)

    Wu Jingwen; Evans, Neal J.; Dunham, Michael M.; Vanden Bout, Paul A.

    2009-01-01

    We report observations of 15 high-redshift (z = 1 - 5) galaxies at 350 μm using the Caltech Submillimeter Observatory and Submillimeter High Angular Resolution Camera II array detector. Emission was detected from eight galaxies, for which far-infrared luminosities, star formation rates (SFRs), total dust masses, and minimum source size estimates are derived. These galaxies have SFRs and star formation efficiencies comparable to other high-redshift molecular emission line galaxies. The results are used to test the idea that star formation in these galaxies occurs in a large number of basic units, the units being similar to star-forming clumps in the Milky Way. The luminosity of these extreme galaxies can be reproduced in a simple model with (0.9-30)x10 6 dense clumps, each with a luminosity of 5 x 10 5 L sun , the mean value for such clumps in the Milky Way. Radiative transfer models of such clumps can provide reasonable matches to the overall spectral energy distributions (SEDs) of the galaxies. They indicate that the individual clumps are quite opaque in the far-infrared. Luminosity-to-mass ratios vary over two orders of magnitude, correlating strongly with the dust temperature derived from simple fits to the SED. The gas masses derived from the dust modeling are in remarkable agreement with those from CO luminosities, suggesting that the assumptions going into both calculations are reasonable.

  12. Molecular gas in dusty high-redshift galaxies

    Science.gov (United States)

    Sharon, Chelsea Electra

    2013-12-01

    We present high-resolution observations of carbon monoxide (CO) emission lines for three high-redshift galaxies in order to determine their molecular gas and star formation properties. These galaxies (SMM J14011+0252, SMM J00266+1708, and SDSS J0901+1814) have large infrared luminosities, which imply high dust enshrouded star formation rates and substantial molecular gas masses. We observed these sources using the Robert C. Byrd Green Bank Telescope, the Karl G. Jansky Very Large Array, the Plateau de Bure Interferometer, and the Submillimeter Array in order to obtain measurements of multiple CO spectral lines, allowing us to determine the physical conditions of the molecular gas. Our high resolution and multi-line CO mapping of SMM J00266+1708 reveals that it is a pair of merging galaxies, whose two components have different gas excitation conditions and different gas kinematics. For SMM J14011+0252 (J14011), we find a near-unity CO(3--2)/CO(1--0) intensity ratio, consistent with a single phase (i.e., a single temperature and density) of molecular gas and different from the average population value for dusty galaxies selected at submillimeter wavelengths. Our radiative transfer modeling (using the large velocity gradient approximation) indicates that converting the CO line luminosity to molecular gas mass requires a Galactic (disk-like) scale factor rather than the typical conversion factor assumed for starbursts. Despite this choice of conversion factor, J14011 falls in the same region of star formation rate surface density and gas mass surface density (the Schmidt-Kennicutt relation) as other starburst galaxies. SDSS J0901+1814 (J0901) was initially selected as a star-forming galaxy at ultraviolet wavelengths, but also has a large infrared luminosity. We use the magnification provided by the strong gravitational lensing affecting this system to examine the spatial variation of the CO excitation within J0901. We find that the CO(3--2)/CO(1--0) line ratio is

  13. Dynamic Line Rating - Technologies and Challenges of PMU on Overhead Lines

    DEFF Research Database (Denmark)

    Alvarez, David; Rosero, Javier; Silva, Filipe Miguel Faria da

    2016-01-01

    for line rating computation and monitoring are identified, these are: sensors, communications, management information system and information analysis tools, which are part of integral dynamic line rating systems. Finally, the benefits and challenges of using phasor measurement units for real time capacity...

  14. Quantitative proteomics as a tool to identify resistance mechanisms in erlotinib-resistant subclones of the non-small cell lung cancer cell line HCC827

    DEFF Research Database (Denmark)

    Jacobsen, Kirstine

    , which in 43-50% of cases are caused by a secondary mutation (T790M) in EGFR. Importantly, a majority of resistance cases are still unexplained (Lin & Bivona, 2012). Our aim is to identify novel resistance mechanisms – and potentially new drug targets - in erlotinib-resistant subclones of the NSCLC cell...... of erlotinib, and in biological triplicates on a Q-Exactive mass spectrometer. Only proteins identified with minimum 2 unique peptides and in minimum 2 of 3 replicates were accepted. Results: Importantly, the resistant clones did not acquire the T790M or other EGFR or KRAS mutations, potentiating...... the identification of novel resistance mechanisms. We identified 2875 cytoplasmic proteins present in all 4 cell lines. Of these 87, 56 and 23 are upregulated >1.5 fold; and 117, 72 and 32 are downregulated >1.5 fold, respectively, in the 3 resistant clones compared to the parental cell line. By network analysis, we...

  15. Molecular marker to identify radiolarian species -toward establishment of paleo-environmental proxy-

    Science.gov (United States)

    Ishitani, Y.

    2017-12-01

    Marine fossilized unicellular plankton are known to have many genetically divergent species (biological species) in the single morphological species and these biological species show the species-specific environments much more precisely than that of morphological species. Among these plankton, Radiolaria are one of the best candidates for time- and environmental-indicators in the modern and past oceans, because radiolarians are the only group which represent entire water column from shallow to deep waters. However, the ecology and evolution of radiolarian were traditionally studied in paleontology and paleoceanography by morphological species. Even Radiolaria has a huge potential for novel proxy of wide and deep environments, there is no criterion to identify the biological species. The motivation for this study is setting the quantitative delimitation to establish the biological species of radiolarians based on molecular data, for leading the future ecological and paleo-environmental study. Identification of the biological species by ribosomal DNA sequences are mainly based on two ways: one is the evolutionary distance of the small subunit (SSU) rDNA, the internal transcribed spacer region of ribosomal DNA (ITS1 and 2), and the large subunit (LSU) rDNA; and the other is the secondary structure of ITS2. In the present study, all four possible genetic markers (SSU, ITS1, ITS2, and LSU rDNA) were amplified from 232 individuals of five radiolarian morphological species and applied to examine the evolutionary distance and secondary structure of rDNA. Comprehensive survey clearly shows that evolutionary distance of ITS1 rDNA and the secondary structure of ITS2 is good to identify the species. Notably, evolutionary distance of ITS1 rDNA is possible to set the common delimitation to identify the biological species, as 0.225 substitution per site. The results show that the ITS1 and ITS 2 rDNA could be the criterion for radiolarian species identification.

  16. Observations of far-infrared line profiles in the Orion-KL region

    International Nuclear Information System (INIS)

    Crawford, M.K.; Lugten, J.B.; Fitelson, W.; Genzel, R.; Melnick, G.; Harvard-Smithsonian Center for Astrophysics, Cambridge, MA)

    1986-01-01

    Measurements of several far-infrared emission line profiles in the Orion-KL region are reported. The emission from the CO, OH, and forbidden O I emission lines toward the BN-KL and H2 peak 1 positions probably comes from dense, hot molecular gas in the Orion-KL shock. The CO and forbidden O I lines have similar profiles, suggesting that the high-velocity forbidden O I emission also arises in magnetohydrodynamic cloud shocks. The velocity centroids of the lines are somewhat blueshifted. The far-infrared data thus support the interpretation that the blue asymmetry of the H2 2 micron lines is not mainly due to differential dust extinction, but rather to the kinematics and geometry of the shocked gas in the Orion-KL outflow. The forbidden O I and CO lines, however, have significantly less extreme blueshifted emission than the H2 lines. Both the forbidden O I 63 micron and forbidden C II 158 micron lines have features strongly supporting a common origin near the surface of the Orion molecular cloud. 28 references

  17. Incorporation of unique molecular identifiers in TruSeq adapters improves the accuracy of quantitative sequencing.

    Science.gov (United States)

    Hong, Jungeui; Gresham, David

    2017-11-01

    Quantitative analysis of next-generation sequencing (NGS) data requires discriminating duplicate reads generated by PCR from identical molecules that are of unique origin. Typically, PCR duplicates are identified as sequence reads that align to the same genomic coordinates using reference-based alignment. However, identical molecules can be independently generated during library preparation. Misidentification of these molecules as PCR duplicates can introduce unforeseen biases during analyses. Here, we developed a cost-effective sequencing adapter design by modifying Illumina TruSeq adapters to incorporate a unique molecular identifier (UMI) while maintaining the capacity to undertake multiplexed, single-index sequencing. Incorporation of UMIs into TruSeq adapters (TrUMIseq adapters) enables identification of bona fide PCR duplicates as identically mapped reads with identical UMIs. Using TrUMIseq adapters, we show that accurate removal of PCR duplicates results in improved accuracy of both allele frequency (AF) estimation in heterogeneous populations using DNA sequencing and gene expression quantification using RNA-Seq.

  18. A mouse model of alcoholic liver fibrosis-associated acute kidney injury identifies key molecular pathways

    International Nuclear Information System (INIS)

    Furuya, Shinji; Chappell, Grace A.; Iwata, Yasuhiro; Uehara, Takeki; Kato, Yuki; Kono, Hiroshi; Bataller, Ramon; Rusyn, Ivan

    2016-01-01

    Clinical data strongly indicate that acute kidney injury (AKI) is a critical complication in alcoholic hepatitis, an acute-on-chronic form of liver failure in patients with advanced alcoholic fibrosis. Development of targeted therapies for AKI in this setting is hampered by the lack of an animal model. To enable research into molecular drivers and novel therapies for fibrosis- and alcohol-associated AKI, we aimed to combine carbon tetrachloride (CCl 4 )-induced fibrosis with chronic intra-gastric alcohol feeding. Male C57BL/6J mice were administered a low dose of CCl 4 (0.2 ml/kg 2 × week/6 weeks) followed by alcohol intragastrically (up to 25 g/kg/day for 3 weeks) and with continued CCl 4 . We observed that combined treatment with CCl 4 and alcohol resulted in severe liver injury, more pronounced than using each treatment alone. Importantly, severe kidney injury was evident only in the combined treatment group. This mouse model reproduced distinct pathological features consistent with AKI in human alcoholic hepatitis. Transcriptomic analysis of kidneys revealed profound effects in the combined treatment group, with enrichment for damage-associated pathways, such as apoptosis, inflammation, immune-response and hypoxia. Interestingly, Havcr1 and Lcn2, biomarkers of AKI, were markedly up-regulated. Overall, this study established a novel mouse model of fibrosis- and alcohol-associated AKI and identified key mechanistic pathways. - Highlights: • Acute kidney injury (AKI) is a critical complication in alcoholic hepatitis • We developed a novel mouse model of fibrosis- and alcohol-associated AKI • This model reproduces key molecular and pathological features of human AKI • This animal model can help identify new targeted therapies for alcoholic hepatitis

  19. Report of the workshop on accelerator-based atomic and molecular science

    International Nuclear Information System (INIS)

    Meyerhof, W.E.

    1981-01-01

    This Workshop, held in New London, NH on July 27-30, 1980, had a registration of 43, representing an estimated one-third of all principal investigators in the United States in this research subfield. The workshop was organized into 5 working groups for the purpose of (1) identifying some vital physics problems which experimental and theoretical atomic and molecular science can address with current and projected techniques; (2) establishing facilities and equipment needs required to realize solutions to these problems; (3) formulating suggestions for a coherent national policy concerning this discipline; (4) assessing and projecting the manpower situation; and (5) evaluating the relations of this interdisciplinary science to other fields. Recommedations deal with equipment and operating costs for small accelerator laboratories, especially at universities; instrumentation of ion beam lines dedicated to atomic and molecular science at some large accelerators; development of low-velocity, high charge-state ion sources; synchrotron light sources; improvement or replacement of tandem van de Graaff accelerators; high-energy beam lines for atomic physics; the needs for postdoctoral support in this subfield; new accelerator development; need for representatives from atomic and molecular science on program committees for large national accelerator facilities; and the contributions the field can make to applied physics problems

  20. Effects of expanding compact H II regions upon molecular clouds: Molecular dissociation waves, shock waves, and carbon ionization

    International Nuclear Information System (INIS)

    Hill, J.K.; Hollenbach, D.J.

    1978-01-01

    The effect of young expanding compact H II regions upon their molecular environments are studied, emphasizing the simultaneous evolution of the molecular hydrogen dissociation front and the shocked shell of gas surrounding the nebula. For H II regions powered by 05 stars embedded in molecular clouds of ambient density 10 3 -10 4 cm -3 the dissociation wave initially travels outward much more rapidly than the shock, but later decelerates and is swept up by the shock about 10 5 yr after the expansion begins. The 21 cm line of atomic hydrogen will be optically thick in both the preshock and postshock gas for most of this period. The most important coolant transitions are the [O I] 63 μm line and, for t> or approx. =10 5 yr, the rotational transitions of H 2 and/or the rotational transitions of CO. The vibrational transitions of H 2 are excited predominantly by ultraviolet pumping. We estimate the preshock and postshock carbon recombination-line emission measures

  1. An X-ray survey of the central molecular zone: Variability of the Fe Kα emission line

    Science.gov (United States)

    Terrier, R.; Clavel, M.; Soldi, S.; Goldwurm, A.; Ponti, G.; Morris, M. R.; Chuard, D.

    2018-05-01

    There is now abundant evidence that the luminosity of the Galactic super-massive black hole (SMBH) has not always been as low as it is nowadays. The observation of varying non-thermal diffuse X-ray emission in molecular complexes in the central 300 pc has been interpreted as delayed reflection of a past illumination by bright outbursts of the SMBH. The observation of different variability timescales of the reflected emission in the Sgr A molecular complex can be well explained if the X-ray emission of at least two distinct and relatively short events (i.e. about 10 yr or less) is currently propagating through the region. The number of such events or the presence of a long-duration illumination are open questions. Variability of the reflected emission all over of the central 300 pc, in particular in the 6.4 keV Fe Kα line, can bring strong constraints. To do so we performed a deep scan of the inner 300 pc with XMM-Newton in 2012. Together with all the archive data taken over the course of the mission, and in particular a similar albeit more shallow scan performed in 2000-2001, this allows for a detailed study of variability of the 6.4 keV line emission in the region, which we present here. We show that the overall 6.4 keV emission does not strongly vary on average, but variations are very pronounced on smaller scales. In particular, most regions showing bright reflection emission in 2000-2001 significantly decrease by 2012. We discuss those regions and present newly illuminated features. The absence of bright steady emission argues against the presence of an echo from an event of multi-centennial duration and most, if not all, of the emission can likely be explained by a limited number of relatively short (i.e. up to 10 yr) events. Images of the Fe Kα emission as FITS files are only available at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/612/A102

  2. Comparison of optical properties of chromophoric dissolved organic matter (CDOM) in alpine lakes above or below the tree line: insights into sources of CDOM.

    Science.gov (United States)

    Su, Yaling; Chen, Feizhou; Liu, Zhengwen

    2015-05-01

    Here we investigated absorption and fluorescence properties of chromophoric dissolved organic matter (CDOM) in 15 alpine lakes located below or above the tree line to determine its source and composition. The results indicate that the concentrations of CDOM in below-tree-line lakes are significantly higher than in above-tree-line lakes, as evidenced from the absorption coefficients of a250 and a365. The intensities of the protein-like and humic-like fluorescence in below-tree-line lakes are higher than in above-tree-line lakes as well. Three fluorescent components were identified using parallel factor analysis (PARAFAC) modelling. Component 1 is probably associated with biological degradation of terrestrial humic component. The terrestrial humic-like component 2 is only found in below-tree-line lakes. The protein-like or phenolic component 3 is dominant in above-tree-line lakes, which is probably more derived from autochthonous origin. In this study, (1) higher a250/a365 and S275-295 values indicate smaller molecular weights of CDOM in above-tree-line lakes than in below-tree-line lakes, and smaller molecular weights at the surface than at 2.0 m depth; (2) SUVA254 and FI255 results provide evidence of lower percent aromaticity of CDOM in above-tree-line lakes; and (3) FI310 and FI370 suggest a strong allochthonous origin at the surface in below-tree-line lakes, and more contribution from autochthonous biological and aquatic bacterial origin in above-tree-line lakes.

  3. Molecular cytogenetic characterization of alien introgressions with gene Fhb3 for resistance to Fusarium head blight disease of wheat

    Science.gov (United States)

    Fusarium head blight (FHB) resistance was identified in the alien species Leymus racemosus, and wheat-Leymus introgression lines with FHB resistance were reported previously. Detailed molecular cytogenetic analysis of alien introgressions T01, T09, and T14 and the mapping of Fhb3, a new gene for FHB...

  4. An attempt to identify the functional areas of the cerebral cortex on CT slices parallel to the orbito-meatal line

    International Nuclear Information System (INIS)

    Tanabe, Hirotaka; Okuda, Junichiro; Nishikawa, Takashi; Nishimura, Tsuyoshi; Shiraishi, Junzo.

    1982-01-01

    In order to identify the functional brain areas, such as Broca's area, on computed tomography slices parallel to the orbito-meatal line, the numbers of Brodmann's cortical mapping were shown on a diagram of representative brain sections parallel to the orbito-meatal line. Also, we described a method, using cerebral sulci as anatomical landmarks, for projecting lesions shown by CT scan onto the lateral brain diagram. The procedures were as follows. The distribution of lesions on CT slices was determined by the identification of major cerebral sulci and fissures, such as the Sylvian fissure, the central sulcus, and the superior frontal sulcus. Those lesions were then projected onto the lateral diagram by comparing each CT slice with the horizontal diagrams of brain sections. The method was demonstrated in three cases developing neuropsychological symptoms. (author)

  5. New model for gastroenteropancreatic large-cell neuroendocrine carcinoma: establishment of two clinically relevant cell lines.

    Directory of Open Access Journals (Sweden)

    Andreas Krieg

    Full Text Available Recently, a novel WHO-classification has been introduced that divided gastroenteropancreatic neuroendocrine neoplasms (GEP-NEN according to their proliferation index into G1- or G2-neuroendocrine tumors (NET and poorly differentiated small-cell or large-cell G3-neuroendocrine carcinomas (NEC. Our knowledge on primary NECs of the GEP-system is limited due to the rarity of these tumors and chemotherapeutic concepts of highly aggressive NEC do not provide convincing results. The aim of this study was to establish a reliable cell line model for NEC that could be helpful in identifying novel druggable molecular targets. Cell lines were established from liver (NEC-DUE1 or lymph node metastases (NEC-DUE2 from large cell NECs of the gastroesophageal junction and the large intestine, respectively. Morphological characteristics and expression of neuroendocrine markers were extensively analyzed. Chromosomal aberrations were mapped by array comparative genomic hybridization and DNA profiling was analyzed by DNA fingerprinting. In vitro and in vivo tumorigenicity was evaluated and the sensitivity against chemotherapeutic agents assessed. Both cell lines exhibited typical morphological and molecular features of large cell NEC. In vitro and in vivo experiments demonstrated that both cell lines retained their malignant properties. Whereas NEC-DUE1 and -DUE2 were resistant to chemotherapeutic drugs such as cisplatin, etoposide and oxaliplatin, a high sensitivity to 5-fluorouracil was observed for the NEC-DUE1 cell line. Taken together, we established and characterized the first GEP large-cell NEC cell lines that might serve as a helpful tool not only to understand the biology of these tumors, but also to establish novel targeted therapies in a preclinical setup.

  6. Molecular mechanisms of drug resistance in natural Leishmania populations vary with genetic background.

    Directory of Open Access Journals (Sweden)

    Saskia Decuypere

    Full Text Available The evolution of drug-resistance in pathogens is a major global health threat. Elucidating the molecular basis of pathogen drug-resistance has been the focus of many studies but rarely is it known whether a drug-resistance mechanism identified is universal for the studied pathogen; it has seldom been clarified whether drug-resistance mechanisms vary with the pathogen's genotype. Nevertheless this is of critical importance in gaining an understanding of the complexity of this global threat and in underpinning epidemiological surveillance of pathogen drug resistance in the field. This study aimed to assess the molecular and phenotypic heterogeneity that emerges in natural parasite populations under drug treatment pressure. We studied lines of the protozoan parasite Leishmania (L. donovani with differential susceptibility to antimonial drugs; the lines being derived from clinical isolates belonging to two distinct genetic populations that circulate in the leishmaniasis endemic region of Nepal. Parasite pathways known to be affected by antimonial drugs were characterised on five experimental levels in the lines of the two populations. Characterisation of DNA sequence, gene expression, protein expression and thiol levels revealed a number of molecular features that mark antimonial-resistant parasites in only one of the two populations studied. A final series of in vitro stress phenotyping experiments confirmed this heterogeneity amongst drug-resistant parasites from the two populations. These data provide evidence that the molecular changes associated with antimonial-resistance in natural Leishmania populations depend on the genetic background of the Leishmania population, which has resulted in a divergent set of resistance markers in the Leishmania populations. This heterogeneity of parasite adaptations provides severe challenges for the control of drug resistance in the field and the design of molecular surveillance tools for widespread

  7. Molecular Diagnostics of Supernova Remnant Shocks

    Science.gov (United States)

    Lazendic, J. S.; Wardle, M.; Green, A. J.; Whiteoak, J. B.; Burton, M. G.

    We have undertaken a study of radio and infrared molecular-line emission towards several SNRs in order to investigate molecular signatures of SNR shocks, and to test models for OH maser production in SNRs. Here we present results on G349.7+0.2.

  8. Isotope separation using molecular gases and molecular lasers

    International Nuclear Information System (INIS)

    Jetter, H.

    1975-01-01

    Isotope separation using molecular gas and molecular lasers offers several advantages over the alternative method which uses dye lasers and atomic vapour. These advantages are the easy handling of the raw material, the big isotopic shift in the IR, the good efficiency of the laser and the chemical extraction of the excited isotopes. In the case of uranium difficulties arise from the great number of superimposed lines in the absorption band of the UF 6 molecule. Several of these absorption bands were measured using laser spectrometers with ultra-high resolution. The conditions for selective excitation were estimated. (orig.) [de

  9. Identification of alternatively spliced TIMP-1 mRNA in cancer cell lines and colon cancer tissue

    DEFF Research Database (Denmark)

    Usher, Pernille Autzen; Sieuwerts, A.M.; Bartels, Annette

    2007-01-01

    TIMP-1 is a promising new candidate as a prognostic marker in colorectal and breast cancer. We now describe the discovery of two alternatively spliced variants of TIMP-1 mRNA. The two variants lacking exon 2 (del-2) and 5 (del-5), respectively, were identified in human cancer cell lines by RT......-PCR. The del-2 variant was, furthermore, detected in extracts from 12 colorectal cancer tissue samples. By western blotting additional bands of lower molecular mass than full-length TIMP-1 were identified in tumor tissue, but not in plasma samples obtained from cancer patients. The two splice variants of TIMP...

  10. Tiered High-Throughput Screening Approach to Identify ...

    Science.gov (United States)

    High-throughput screening (HTS) for potential thyroid–disrupting chemicals requires a system of assays to capture multiple molecular-initiating events (MIEs) that converge on perturbed thyroid hormone (TH) homeostasis. Screening for MIEs specific to TH-disrupting pathways is limited in the US EPA ToxCast screening assay portfolio. To fill one critical screening gap, the Amplex UltraRed-thyroperoxidase (AUR-TPO) assay was developed to identify chemicals that inhibit TPO, as decreased TPO activity reduces TH synthesis. The ToxCast Phase I and II chemical libraries, comprised of 1,074 unique chemicals, were initially screened using a single, high concentration to identify potential TPO inhibitors. Chemicals positive in the single concentration screen were retested in concentration-response. Due to high false positive rates typically observed with loss-of-signal assays such as AUR-TPO, we also employed two additional assays in parallel to identify possible sources of nonspecific assay signal loss, enabling stratification of roughly 300 putative TPO inhibitors based upon selective AUR-TPO activity. A cell-free luciferase inhibition assay was used to identify nonspecific enzyme inhibition among the putative TPO inhibitors, and a cytotoxicity assay using a human cell line was used to estimate the cellular tolerance limit. Additionally, the TPO inhibition activities of 150 chemicals were compared between the AUR-TPO and an orthogonal peroxidase oxidation assay using

  11. Multiple lines of evidence to identify sewage as the cause of water quality impairment in an urbanized tropical watershed.

    Science.gov (United States)

    Kirs, Marek; Kisand, Veljo; Wong, Mayee; Caffaro-Filho, Roberto A; Moravcik, Philip; Harwood, Valerie J; Yoneyama, Bunnie; Fujioka, Roger S

    2017-06-01

    Indicator bacteria, which are conventionally used to evaluate recreational water quality, can originate from various non-human enteric and extra-enteric sources, hence they may not be indicative of human health risk nor do they provide information on the sources of contamination. In this study we utilized traditional (enterococci and Escherichia coli) and alternative (Clostridium perfringens) indicator bacteria, F + -specific coliphage, molecular markers for microorganisms associated with human sewage (human-associated Bacteroides and polyomaviruses), and microbial community analysis tools (16S rRNA gene fragment amplicon sequencing), to identify and evaluate human sewage-related impact in the Manoa watershed in Honolulu, Hawaii. Elevated concentrations of enterococci (geometric mean ranging from 1604 to 2575 CFU 100 mL -1 ) and C. perfringens (45-77 CFU 100 mL -1 ) indicated impairment of the urbanized section of the stream, while indicator bacteria concentrations decreased downstream in the tidally influenced Ala Wai Canal. The threshold values triggering water quality violation notifications in Hawaii were exceeded in 33.3-75.0% of samples collected at sites in the urbanized section of Manoa Stream, but were not exceeded in any of the samples collected at an upstream site located in a forested area. Correlation between indicator bacteria concentrations and rainfall amounts was weak to moderate but significant (E. coli R = 0.251, P = 0.009; enterococci R = 0.369, P watershed, it was lower in the impaired section. Leaking sewer systems and illegal cross-connections are implicated in the impairment of the watershed, hence both the sewer and the storm water lines should be routinely inspected. Collectively, our data suggest that information derived from the analysis of microbial communities complements current marker-based microbial source tracking techniques and environmental monitoring programs. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Rational approach to identify newer caspase-1 inhibitors using pharmacophore based virtual screening, docking and molecular dynamic simulation studies.

    Science.gov (United States)

    Patel, Shivani; Modi, Palmi; Chhabria, Mahesh

    2018-05-01

    Caspase-1 is a key endoprotease responsible for the post-translational processing of pro-inflammatory cytokines IL-1β, 18 & 33. Excessive secretion of IL-1β leads to numerous inflammatory and autoimmune diseases. Thus caspase-1 inhibition would be considered as an important therapeutic strategy for development of newer anti-inflammatory agents. Here we have employed an integrated virtual screening by combining pharmacophore mapping and docking to identify small molecules as caspase-1 inhibitors. The ligand based 3D pharmacophore model was generated having the essential structural features of (HBA, HY & RA) using a data set of 27 compounds. A validated pharmacophore hypothesis (Hypo 1) was used to screen ZINC and Minimaybridge chemical databases. The retrieved virtual hits were filtered by ADMET properties and molecular docking analysis. Subsequently, the cross-docking study was also carried out using crystal structure of caspase-1, 3, 7 and 8 to identify the key residual interaction for specific caspase-1 inhibition. Finally, the best mapped and top scored (ZINC00885612, ZINC72003647, BTB04175 and BTB04410) molecules were subjected to molecular dynamics simulation for accessing the dynamic structure of protein after ligand binding. This study identifies the most promising hits, which can be leads for the development of novel caspase-1 inhibitors as anti-inflammatory agents. Copyright © 2018 Elsevier Inc. All rights reserved.

  13. An accelerated line-by-line option for MODTRAN combining on-the-fly generation of line center absorption within 0.1 cm-1 bins and pre-computed line tails

    Science.gov (United States)

    Berk, Alexander; Conforti, Patrick; Hawes, Fred

    2015-05-01

    A Line-By-Line (LBL) option is being developed for MODTRAN6. The motivation for this development is two-fold. Firstly, when MODTRAN is validated against an independent LBL model, it is difficult to isolate the source of discrepancies. One must verify consistency between pressure, temperature and density profiles, between column density calculations, between continuum and particulate data, between spectral convolution methods, and more. Introducing a LBL option directly within MODTRAN will insure common elements for all calculations other than those used to compute molecular transmittances. The second motivation for the LBL upgrade is that it will enable users to compute high spectral resolution transmittances and radiances for the full range of current MODTRAN applications. In particular, introducing the LBL feature into MODTRAN will enable first-principle calculations of scattered radiances, an option that is often not readily available with LBL models. MODTRAN will compute LBL transmittances within one 0.1 cm-1 spectral bin at a time, marching through the full requested band pass. The LBL algorithm will use the highly accurate, pressure- and temperature-dependent MODTRAN Padé approximant fits of the contribution from line tails to define the absorption from all molecular transitions centered more than 0.05 cm-1 from each 0.1 cm-1 spectral bin. The beauty of this approach is that the on-the-fly computations for each 0.1 cm-1 bin will only require explicit LBL summing of transitions centered within a 0.2 cm-1 spectral region. That is, the contribution from the more distant lines will be pre-computed via the Padé approximants. The status of the LBL effort will be presented. This will include initial thermal and solar radiance calculations, validation calculations, and self-validations of the MODTRAN band model against its own LBL calculations.

  14. BISQUE: locus- and variant-specific conversion of genomic, transcriptomic and proteomic database identifiers.

    Science.gov (United States)

    Meyer, Michael J; Geske, Philip; Yu, Haiyuan

    2016-05-15

    Biological sequence databases are integral to efforts to characterize and understand biological molecules and share biological data. However, when analyzing these data, scientists are often left holding disparate biological currency-molecular identifiers from different databases. For downstream applications that require converting the identifiers themselves, there are many resources available, but analyzing associated loci and variants can be cumbersome if data is not given in a form amenable to particular analyses. Here we present BISQUE, a web server and customizable command-line tool for converting molecular identifiers and their contained loci and variants between different database conventions. BISQUE uses a graph traversal algorithm to generalize the conversion process for residues in the human genome, genes, transcripts and proteins, allowing for conversion across classes of molecules and in all directions through an intuitive web interface and a URL-based web service. BISQUE is freely available via the web using any major web browser (http://bisque.yulab.org/). Source code is available in a public GitHub repository (https://github.com/hyulab/BISQUE). haiyuan.yu@cornell.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  15. Scientometric methods for identifying emerging technologies

    Science.gov (United States)

    Abercrombie, Robert K; Schlicher, Bob G; Sheldon, Frederick T

    2015-11-03

    Provided is a method of generating a scientometric model that tracks the emergence of an identified technology from initial discovery (via original scientific and conference literature), through critical discoveries (via original scientific, conference literature and patents), transitioning through Technology Readiness Levels (TRLs) and ultimately on to commercial application. During the period of innovation and technology transfer, the impact of scholarly works, patents and on-line web news sources are identified. As trends develop, currency of citations, collaboration indicators, and on-line news patterns are identified. The combinations of four distinct and separate searchable on-line networked sources (i.e., scholarly publications and citation, worldwide patents, news archives, and on-line mapping networks) are assembled to become one collective network (a dataset for analysis of relations). This established network becomes the basis from which to quickly analyze the temporal flow of activity (searchable events) for the example subject domain.

  16. Development of Elite BPH-Resistant Wide-Spectrum Restorer Lines for Three and Two Line Hybrid Rice.

    Science.gov (United States)

    Fan, Fengfeng; Li, Nengwu; Chen, Yunping; Liu, Xingdan; Sun, Heng; Wang, Jie; He, Guangcun; Zhu, Yingguo; Li, Shaoqing

    2017-01-01

    Hybrid rice has contributed significantly to the world food security. Breeding of elite high-yield, strong-resistant broad-spectrum restorer line is an important strategy for hybrid rice in commercial breeding programs. Here, we developed three elite brown planthopper (BPH)-resistant wide-spectrum restorer lines by pyramiding big-panicle gene Gn8.1 , BPH-resistant genes Bph6 and Bph9 , fertility restorer genes Rf3, Rf4, Rf5 , and Rf6 through molecular marker assisted selection. Resistance analysis revealed that the newly developed restorer lines showed stronger BPH-resistance than any of the single-gene donor parent Luoyang-6 and Luoyang-9. Moreover, the three new restorer lines had broad spectrum recovery capabilities for Honglian CMS, Wild abortive CMS and two-line GMS sterile lines, and higher grain yields than that of the recurrent parent 9,311 under nature field conditions. Importantly, the hybrid crosses also showed good performance for grain yield and BPH-resistance. Thus, the development of elite BPH-resistant wide-spectrum restorer lines has a promising future for breeding of broad spectrum BPH-resistant high-yield varieties.

  17. Herschel observations of extraordinary sources: Analysis of the full Herschel/HIFI molecular line survey of sagittarius B2(N)

    Energy Technology Data Exchange (ETDEWEB)

    Neill, Justin L.; Bergin, Edwin A.; Crockett, Nathan R.; Favre, Cécile; Anderson, Dana E.; Burkhardt, Andrew M.; McNeill, Trevor D. [Department of Astronomy, University of Michigan, 500 Church Street, Ann Arbor, MI 48109 (United States); Lis, Dariusz C.; Emprechtinger, Martin; Monje, Raquel R.; Phillips, Thomas G. [California Institute of Technology, Cahill Center for Astronomy and Astrophysics 301-17, Pasadena, CA 91125 (United States); Schilke, Peter; Comito, Claudia; Qin, Sheng-Li [Physikalisches Institut, Universität zu Köln, Zülpicher Str. 77, D-50937 Köln (Germany); Chen, Jo-Hsin [Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA 91109 (United States); Harris, Brent J.; Steber, Amanda L.; Vasyunina, Tatiana [Department of Chemistry, University of Virginia, McCormick Road, Charlottesville, VA 22904 (United States); Lord, Steven D. [National Herschel Science Center, California Institute of Technology, Pasadena, CA 91125 (United States); McGuire, Brett A., E-mail: jneill@umich.edu, E-mail: ebergin@umich.edu [Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125 (United States); and others

    2014-07-01

    A sensitive broadband molecular line survey of the Sagittarius B2(N) star-forming region has been obtained with the Heterodyne Instrument for the Far-Infrared (HIFI) instrument on the Herschel Space Observatory, offering the first high spectral resolution look at this well-studied source in a wavelength region largely inaccessible from the ground (625-157 μm). From the roughly 8000 spectral features in the survey, a total of 72 isotopologues arising from 44 different molecules have been identified, ranging from light hydrides to complex organics, and arising from a variety of environments from cold and diffuse to hot and dense gas. We present a local thermodynamic equilibrium (LTE) model to the spectral signatures of each molecule, constraining the source sizes for hot core species with complementary Submillimeter Array interferometric observations and assuming that molecules with related functional group composition are cospatial. For each molecule, a single model is given to fit all of the emission and absorption features of that species across the entire 480-1910 GHz spectral range, accounting for multiple temperature and velocity components when needed to describe the spectrum. As with other HIFI surveys toward massive star-forming regions, methanol is found to contribute more integrated line intensity to the spectrum than any other species. We discuss the molecular abundances derived for the hot core where the LTE approximation is generally found to describe the spectrum well, in comparison to abundances derived for the same molecules in the Orion KL region from a similar HIFI survey. Notably, we find significantly higher abundances of amine- and amide-bearing molecules (CH{sub 3}NH{sub 2}, CH{sub 2}NH, and NH{sub 2}CHO) toward Sgr B2(N) than Orion KL and lower abundances of some complex oxygen-bearing molecules (CH{sub 3}OCHO in particular). In addition to information on the chemical composition of the hot core, the strong far-infrared dust continuum allows

  18. Analyzing the Molecular Kinetics of Water Spreading on Hydrophobic Surfaces via Molecular Dynamics Simulation.

    Science.gov (United States)

    Zhao, Lei; Cheng, Jiangtao

    2017-09-07

    In this paper, we report molecular kinetic analyses of water spreading on hydrophobic surfaces via molecular dynamics simulation. The hydrophobic surfaces are composed of amorphous polytetrafluoroethylene (PTFE) with a static contact angle of ~112.4° for water. On the basis of the molecular kinetic theory (MKT), the influences of both viscous damping and solid-liquid retarding were analyzed in evaluating contact line friction, which characterizes the frictional force on the contact line. The unit displacement length on PTFE was estimated to be ~0.621 nm and is ~4 times as long as the bond length of C-C backbone. The static friction coefficient was found to be ~[Formula: see text] Pa·s, which is on the same order of magnitude as the dynamic viscosity of water, and increases with the droplet size. A nondimensional number defined by the ratio of the standard deviation of wetting velocity to the characteristic wetting velocity was put forward to signify the strength of the inherent contact line fluctuation and unveil the mechanism of enhanced energy dissipation in nanoscale, whereas such effect would become insignificant in macroscale. Moreover, regarding a liquid droplet on hydrophobic or superhydrophobic surfaces, an approximate solution to the base radius development was derived by an asymptotic expansion approach.

  19. Line-shape theory and molecular dynamics in collision-induced light scattering

    International Nuclear Information System (INIS)

    Balucani, U.; Tognetti, V.; Vallauri, R.

    1979-01-01

    Molecular-dynamics studies in argon at 148 amagats are presented for gaining information on the dynamical properties responsible for the depolarized light scattering from simple fluids. The total and pair-correlation functions are computed within the simple dipole--induced-dipole model of polarizability anisotropy. The pair spectral shape is derived. These results are compared with a theoretical analysis based on a continued-fraction approach. The necessary frequency moments are calculated both in the low-density limit and taking into account first-order density corrections, and compared with the molecular-dynamics data. The agreement between the theoretical spectra and molecular-dynamics data shows the validity of the memory-function approach. The comparison with the real experimental results allows one to test the relevant physical contributions to the polarizability anisotropy

  20. Glycoproteins and sialyl transferase of human B lymphoblastoid cell lines

    International Nuclear Information System (INIS)

    Lui, S.W.L.; Ng, M.H.

    1980-01-01

    We used two radiolabeling methods to study glycoproteins on the surface of lymphoblastoid cells. One of the methods affects tritiation of residues which are oxidized with galactose oxidase and the other causes tritiation of neuraminic acid residues. This approach was shown to allow a better resolution of cell surface glycoproteins than if either method were used alone. Glycoproteins of B 1 - 19 cells which harbor the Epstein-Barr virus genomes were compared with those of its parental cell line, BJAB, which does not harbor the viral genomes. These studies did not reveal a unique viral protein. A 28,000 mol. wt. glycoprotein was found to be the most prominent neuraminic acidlabeled product of B 1 - 19 cells and also of the two other cell lines, Raji and Ly38, which harbor the EBV genomes. A similar molecular weight species from BJAB cells identified by galactose oxidase labeling might be deficient in neuraminic acid residues as it was poorly labeled by the periodate oxidation method. The neuraminic acid content and level of sialyl transferase of BJAB cells were found to be lower than those of the other cell lines studied. (auth.)

  1. Genomic analysis of CD8+ NK/T cell line, ‘SRIK-NKL’, with array-based CGH (aCGH), SKY/FISH and molecular mapping

    Science.gov (United States)

    Rossi, Michael; LaDuca, Jeff; Cowell, John; Srivastava, Bejai I.S.; Matsui, Sei-ichi

    2010-01-01

    We performed aCGH, SKY /FISH, molecular mapping and expression analyses on a permanent CD8+ NK/T cell line, ‘SRIK-NKL’ established from a lymphoma (ALL) patient, in attempt to define the fundamental genetic profile of its unique NK phenotypes. aCGH revealed hemizygous deletion of 6p containing genes responsible for hematopoietic functions. The SKY demonstrated that a constitutive reciprocal translocation, rcpt(5;14)(p13.2;q11) is a stable marker. Using somatic hybrids containing der(5) derived from SRIK-NKL, we found that the breakpoint in one homologue of no. 5 is located upstream of IL7R and also that the breakpoint in no. 14 is located within TRA@. The FISH analysis using BAC which contains TRA@ and its flanking region further revealed a ~231 kb deletion within 14q11 in the der(5) but not in the normal homologue of no. 14. The RT-PCR analysis detected mRNA for TRA@ transcripts which were extending across, but not including, the deleted region. IL7R was detected at least at mRNA levels. These findings were consistent with the immunological findings that TRA@ and IL7R are both expressed at mRNA levels and TRA@ at cytoplasmic protein levels in SRIK-NKL cells. In addition to rept(5;14), aCGH identified novel copy number abnormalities suggesting that the unique phenotype of the SRIK-NKL cell line is not solely due to the TRA@ rearrangement. These findings provide supportive evidence for the notion that SRIK-NKL cells may be useful for studying not only the function of NK cells but also genetic deregulations associated with leukemiogenesis. PMID:17640729

  2. A mouse model of alcoholic liver fibrosis-associated acute kidney injury identifies key molecular pathways

    Energy Technology Data Exchange (ETDEWEB)

    Furuya, Shinji; Chappell, Grace A.; Iwata, Yasuhiro [Department of Veterinary Integrative Biosciences, Texas A& M University, College Station, TX (United States); Uehara, Takeki; Kato, Yuki [Laboratory of Veterinary Pathology, Osaka Prefecture University, Osaka (Japan); Kono, Hiroshi [First Department of Surgery, University of Yamanashi, Yamanashi (Japan); Bataller, Ramon [Division of Gastroenterology & Hepatology, Department of Medicine, University of North Carolina, Chapel Hill, NC (United States); Rusyn, Ivan, E-mail: irusyn@tamu.edu [Department of Veterinary Integrative Biosciences, Texas A& M University, College Station, TX (United States)

    2016-11-01

    Clinical data strongly indicate that acute kidney injury (AKI) is a critical complication in alcoholic hepatitis, an acute-on-chronic form of liver failure in patients with advanced alcoholic fibrosis. Development of targeted therapies for AKI in this setting is hampered by the lack of an animal model. To enable research into molecular drivers and novel therapies for fibrosis- and alcohol-associated AKI, we aimed to combine carbon tetrachloride (CCl{sub 4})-induced fibrosis with chronic intra-gastric alcohol feeding. Male C57BL/6J mice were administered a low dose of CCl{sub 4} (0.2 ml/kg 2 × week/6 weeks) followed by alcohol intragastrically (up to 25 g/kg/day for 3 weeks) and with continued CCl{sub 4}. We observed that combined treatment with CCl{sub 4} and alcohol resulted in severe liver injury, more pronounced than using each treatment alone. Importantly, severe kidney injury was evident only in the combined treatment group. This mouse model reproduced distinct pathological features consistent with AKI in human alcoholic hepatitis. Transcriptomic analysis of kidneys revealed profound effects in the combined treatment group, with enrichment for damage-associated pathways, such as apoptosis, inflammation, immune-response and hypoxia. Interestingly, Havcr1 and Lcn2, biomarkers of AKI, were markedly up-regulated. Overall, this study established a novel mouse model of fibrosis- and alcohol-associated AKI and identified key mechanistic pathways. - Highlights: • Acute kidney injury (AKI) is a critical complication in alcoholic hepatitis • We developed a novel mouse model of fibrosis- and alcohol-associated AKI • This model reproduces key molecular and pathological features of human AKI • This animal model can help identify new targeted therapies for alcoholic hepatitis.

  3. Wide-field 12CO (J=2-1) and 13CO (J=2-1) Observations toward the Aquila Rift and Serpens Molecular Cloud Complexes. I. Molecular Clouds and Their Physical Properties

    Science.gov (United States)

    Nakamura, Fumitaka; Dobashi, Kazuhito; Shimoikura, Tomomi; Tanaka, Tomohiro; Onishi, Toshikazu

    2017-03-01

    We present the results of wide-field 12CO (J=2{--}1) and 13CO (J=2{--}1) observations toward the Aquila Rift and Serpens molecular cloud complexes (25^\\circ < l< 33^\\circ and 1^\\circ < b< 6^\\circ ) at an angular resolution of 3.‧4 (≈ 0.25 pc) and at a velocity resolution of 0.079 km s-1 with velocity coverage of -5 {km} {{{s}}}-1< {V}{LSR}< 35 {km} {{{s}}}-1. We found that the 13CO emission better traces the structures seen in the extinction map, and derived the {X}{13{CO}}-factor of this region. Applying SCIMES to the 13CO data cube, we identified 61 clouds and derived their mass, radii, and line widths. The line width-radius relation of the identified clouds basically follows those of nearby molecular clouds. The majority of the identified clouds are close to virial equilibrium, although the dispersion is large. By inspecting the 12CO channel maps by eye, we found several arcs that are spatially extended to 0.°2-3° in length. In the longitude-velocity diagrams of 12CO, we also found two spatially extended components that appear to converge toward Serpens South and the W40 region. The existence of two components with different velocities and arcs suggests that large-scale expanding bubbles and/or flows play a role in the formation and evolution of the Serpens South and W40 cloud.

  4. [The role of Cd-binding proteins and phytochelatins in the formation of cadmium resistance in Nicotiana plumbaginifolia cell lines].

    Science.gov (United States)

    Fenik, S I; Solodushko, V G; Kaliniak, T B; Blium, Ia B

    2007-01-01

    Nicotiana plumbaginifolia callus lines with the equal resistance to cadmium have been produced under different selective conditions--either without inhibition of the phytochelatin synthesis (line Cd-R) or in the presence of the inhibitor butionine sulfoximine (line Cd-Ri). The level of phytochelatin synthesis in the line Cd-R five-fold exceeded the control value and in the line Cd-Ri it was twice as much as in the control. It was shown that in the control line mainly three cadmium-binding proteins are expressed of the molecular weihgts 41, 34 and 19 kD. The common feature of the both resistant lines is the expression of the cadmium-binding proteins of 40, 37 and 19 kD. The resistant lines differ with respect to the synthesis of relatively low-molecular cadmium-binding proteins. The proteins of the molecular weights 12.5, 11.5 and 9 kD are expressed in the line Cd-R, while the proteins of 13 and 10 kD are expressed in the line Cd-Ri. It was supposed that both the phytochelatins and the Cd-binding proteins contribute to the resisitance of N. plumbaginifolia callus lines to cadmium and the lack of the phytochelatins can be equilibrated by the changes in the low-molecular Cd-binding protein synthesis.

  5. An Interferometric Spectral Line and Imaging Survey of VY Canis Majoris in the 345 GHz Band

    Science.gov (United States)

    Kamiński, T.; Gottlieb, C. A.; Young, K. H.; Menten, K. M.; Patel, N. A.

    2013-12-01

    A spectral line survey of the oxygen-rich red supergiant VY Canis Majoris was made between 279 and 355 GHz with the Submillimeter Array (SMA). Two hundred twenty-three spectral features from 19 molecules (not counting isotopic species of some of them) were observed, including the rotational spectra of TiO, TiO2, and AlCl for the first time in this source. The parameters and an atlas of all spectral features are presented. Observations of each line with a synthesized beam of ~0.''9, reveal the complex kinematics and morphology of the nebula surrounding VY CMa. Many of the molecules are observed in high-lying rotational levels or in excited vibrational levels. From these, it was established that the main source of the submillimeter-wave continuum (dust) and the high-excitation molecular gas (the star) are separated by about 0.''15. Apparent coincidences between the molecular gas observed with the SMA, and some of the arcs and knots observed at infrared wavelengths and in the optical scattered light by the Hubble Space Telescope are identified. The observations presented here provide important constraints on the molecular chemistry in oxygen-dominated circumstellar environments and a deeper picture of the complex circumstellar environment of VY CMa.

  6. Molecular analysis of expansion, differentiation, and growth factor treatment of human chondrocytes identifies differentiation markers and growth-related genes.

    Science.gov (United States)

    Benz, Karin; Breit, Stephen; Lukoschek, Martin; Mau, Hans; Richter, Wiltrud

    2002-04-26

    This study is intended to optimise expansion and differentiation of cultured human chondrocytes by growth factor application and to identify molecular markers to monitor their differentiation state. We dissected the molecular consequences of matrix release, monolayer, and 3D-alginate culture, growth factor optimised expansion, and re-differentiation protocols by gene expression analysis. Among 19 common cartilage molecules assessed by cDNA array, six proved best to monitor differentiation. Instant down-regulation at release of cells from the matrix was strongest for COL 2A1, fibromodulin, and PRELP while LUM, CHI3L1, and CHI3L2 were expansion-related. Both gene sets reflected the physiologic effects of the most potent growth-inducing (PDGF-BB) and proteoglycan-inducing (BMP-4) factors. Only CRTAC1 expression correlated with 2D/3D switches while the molecular phenotype of native chondrocytes was not restored. The markers and optimised protocols we suggest can help to improve cell therapy of cartilage defects and chondrocyte differentiation from stem cell sources.

  7. Duodenoscope-Related Outbreak of a Carbapenem-Resistant Klebsiella pneumoniae Identified Using Advanced Molecular Diagnostics.

    Science.gov (United States)

    Humphries, Romney M; Yang, Shuan; Kim, Stephen; Muthusamy, Venkatara Raman; Russell, Dana; Trout, Alisa M; Zaroda, Teresa; Cheng, Quen J; Aldrovandi, Grace; Uslan, Daniel Zachary; Hemarajata, Peera; Rubin, Zachary Aaron

    2017-10-01

    Carbapenem-resistant Klebsiella pneumoniae infections are increasingly prevalent in North American hospitals. We describe an outbreak of carbapenem-resistant K. pneumoniae containing the blaOXA-232 gene transmitted by contaminated duodenoscopes during endoscopic retrograde cholangiopancreatography (ERCP) procedures. An outbreak investigation was performed when 9 patients with blaOXA-232 carbapenem-resistant K. pneumoniae infections were identified at a tertiary care hospital. The investigation included 2 case-control studies, review of duodenoscope reprocessing procedures, and culture of devices. Carbapenem-resistant Enterobacteriacieae (CRE) isolates were evaluated with polymerase chain reaction analysis for carbapenemase genes, and isolates with the blaOXA-232 gene were subjected to whole-genome sequencing and chromosome single-nucleotide polymorphism analysis. On recognition of ERCP as a key risk factor for infection, targeted patient notification and CRE screening cultures were performed. Molecular testing ultimately identified 17 patients with blaOxa-232 carbapenem-resistant K. pneumoniae isolates, including 9 with infections, 7 asymptomatic carriers who had undergone ERCP, and 1 additional patient who had been hospitalized in India and was probably the initial carrier. Two case-control studies established a point-source outbreak associated with 2 specific duodenoscopes. A field investigation of the use, reprocessing, and storage of deuodenoscopes did not identify deviations from US Food and Drug Administration or manufacturer recommendations for reprocessing. This outbreak demonstrated the previously underappreciated potential for duodenoscopes to transmit disease, even after undergoing high-level disinfection according to manufacturers' guidelines.

  8. Genome‐wide DNA methylation analysis identifies MEGF10 as a novel epigenetically repressed candidate tumor suppressor gene in neuroblastoma

    Science.gov (United States)

    Charlet, Jessica; Tomari, Ayumi; Dallosso, Anthony R.; Szemes, Marianna; Kaselova, Martina; Curry, Thomas J.; Almutairi, Bader; Etchevers, Heather C.; McConville, Carmel; Malik, Karim T. A.

    2016-01-01

    Neuroblastoma is a childhood cancer in which many children still have poor outcomes, emphasising the need to better understand its pathogenesis. Despite recent genome‐wide mutation analyses, many primary neuroblastomas do not contain recognizable driver mutations, implicating alternate molecular pathologies such as epigenetic alterations. To discover genes that become epigenetically deregulated during neuroblastoma tumorigenesis, we took the novel approach of comparing neuroblastomas to neural crest precursor cells, using genome‐wide DNA methylation analysis. We identified 93 genes that were significantly differentially methylated of which 26 (28%) were hypermethylated and 67 (72%) were hypomethylated. Concentrating on hypermethylated genes to identify candidate tumor suppressor loci, we found the cell engulfment and adhesion factor gene MEGF10 to be epigenetically repressed by DNA hypermethylation or by H3K27/K9 methylation in neuroblastoma cell lines. MEGF10 showed significantly down‐regulated expression in neuroblastoma tumor samples; furthermore patients with the lowest‐expressing tumors had reduced relapse‐free survival. Our functional studies showed that knock‐down of MEGF10 expression in neuroblastoma cell lines promoted cell growth, consistent with MEGF10 acting as a clinically relevant, epigenetically deregulated neuroblastoma tumor suppressor gene. © 2016 The Authors. Molecular Carcinogenesis Published by Wiley Periodicals, Inc. PMID:27862318

  9. Study of clumping in the Cepheus OB 3 molecular cloud

    International Nuclear Information System (INIS)

    Carr, J.S.

    1987-01-01

    A portion of the Cep OB 3 molecular cloud has been mapped in the (C-13)O (1-0) line on a completely sampled grid with a 1.5-arcmin spacing. A total of 45 individual clouds, or clumps, have been identified in the map, with masses from 3 to 300 solar mass, sizes 3 pc or smaller, and mean densities of a few hundred/cu cm. Power-law correlations are found among the clump properties, namely, M proportional to R exp 2.5 and Delta(v) exp 0.24. These exponents differ somewhat from those found for similar correlations for molecular clouds in previous studies. Determination of the virial masses for the clumps shows that the clumps are not gravitationally bound and must be expanding on a time scale of about 1 Myr. Measurements of the (C-13)O (2-1) line give volume densities of 2000-5000. Comparisons of these densities with the mean volume densities from the (C-13)O (1-0) data suggest that the gas is clumped on a small scale with a volume filling factor of 0.04-0.10. 31 references

  10. LUMINOSITY FUNCTIONS OF SPITZER-IDENTIFIED PROTOSTARS IN NINE NEARBY MOLECULAR CLOUDS

    Energy Technology Data Exchange (ETDEWEB)

    Kryukova, E.; Megeath, S. T.; Allen, T. S. [Department of Physics and Astronomy, University of Toledo, Toledo, OH (United States); Gutermuth, R. A. [Department of Astronomy, University of Massachusetts, Amherst, MA (United States); Pipher, J. [Department of Physics and Astronomy, University of Rochester, Rochester, NY (United States); Allen, L. E. [National Optical Astronomy Observatories, Tucson, AZ (United States); Myers, P. C. [Harvard-Smithsonian Center for Astrophysics, Cambridge, MA (United States); Muzerolle, J. [Space Telescope Science Institute, Baltimore, MD (United States)

    2012-08-15

    We identify protostars in Spitzer surveys of nine star-forming (SF) molecular clouds within 1 kpc: Serpens, Perseus, Ophiuchus, Chamaeleon, Lupus, Taurus, Orion, Cep OB3, and Mon R2, which combined host over 700 protostar candidates. These clouds encompass a variety of SF environments, including both low-mass and high-mass SF regions, as well as dense clusters and regions of sparsely distributed star formation. Our diverse cloud sample allows us to compare protostar luminosity functions in these varied environments. We combine near- and mid-infrared photometry from the Two Micron All Sky Survey and Spitzer to create 1-24 {mu}m spectral energy distributions (SEDs). Using protostars from the c2d survey with well-determined bolometric luminosities, we derive a relationship between bolometric luminosity, mid-IR luminosity (integrated from 1-24 {mu}m), and SED slope. Estimations of the bolometric luminosities for protostar candidates are combined to create luminosity functions for each cloud. Contamination due to edge-on disks, reddened Class II sources, and galaxies is estimated and removed from the luminosity functions. We find that luminosity functions for high-mass SF clouds (Orion, Mon R2, and Cep OB3) peak near 1 L{sub Sun} and show a tail extending toward luminosities above 100 L{sub Sun }. The luminosity functions of the low-mass SF clouds (Serpens, Perseus, Ophiuchus, Taurus, Lupus, and Chamaeleon) do not exhibit a common peak, however the combined luminosity function of these regions peaks below 1 L{sub Sun }. Finally, we examine the luminosity functions as a function of the local surface density of young stellar objects. In the Orion molecular clouds, we find a significant difference between the luminosity functions of protostars in regions of high and low stellar density, the former of which is biased toward more luminous sources. This may be the result of primordial mass segregation, although this interpretation is not unique. We compare our luminosity

  11. LUMINOSITY FUNCTIONS OF SPITZER-IDENTIFIED PROTOSTARS IN NINE NEARBY MOLECULAR CLOUDS

    International Nuclear Information System (INIS)

    Kryukova, E.; Megeath, S. T.; Allen, T. S.; Gutermuth, R. A.; Pipher, J.; Allen, L. E.; Myers, P. C.; Muzerolle, J.

    2012-01-01

    We identify protostars in Spitzer surveys of nine star-forming (SF) molecular clouds within 1 kpc: Serpens, Perseus, Ophiuchus, Chamaeleon, Lupus, Taurus, Orion, Cep OB3, and Mon R2, which combined host over 700 protostar candidates. These clouds encompass a variety of SF environments, including both low-mass and high-mass SF regions, as well as dense clusters and regions of sparsely distributed star formation. Our diverse cloud sample allows us to compare protostar luminosity functions in these varied environments. We combine near- and mid-infrared photometry from the Two Micron All Sky Survey and Spitzer to create 1-24 μm spectral energy distributions (SEDs). Using protostars from the c2d survey with well-determined bolometric luminosities, we derive a relationship between bolometric luminosity, mid-IR luminosity (integrated from 1-24 μm), and SED slope. Estimations of the bolometric luminosities for protostar candidates are combined to create luminosity functions for each cloud. Contamination due to edge-on disks, reddened Class II sources, and galaxies is estimated and removed from the luminosity functions. We find that luminosity functions for high-mass SF clouds (Orion, Mon R2, and Cep OB3) peak near 1 L ☉ and show a tail extending toward luminosities above 100 L ☉ . The luminosity functions of the low-mass SF clouds (Serpens, Perseus, Ophiuchus, Taurus, Lupus, and Chamaeleon) do not exhibit a common peak, however the combined luminosity function of these regions peaks below 1 L ☉ . Finally, we examine the luminosity functions as a function of the local surface density of young stellar objects. In the Orion molecular clouds, we find a significant difference between the luminosity functions of protostars in regions of high and low stellar density, the former of which is biased toward more luminous sources. This may be the result of primordial mass segregation, although this interpretation is not unique. We compare our luminosity functions to those

  12. AGN feedback on molecular gas reservoirs in quasars at z 2.4

    Science.gov (United States)

    Carniani, S.; Marconi, A.; Maiolino, R.; Feruglio, C.; Brusa, M.; Cresci, G.; Cano-Díaz, M.; Cicone, C.; Balmaverde, B.; Fiore, F.; Ferrara, A.; Gallerani, S.; La Franca, F.; Mainieri, V.; Mannucci, F.; Netzer, H.; Piconcelli, E.; Sani, E.; Schneider, R.; Shemmer, O.; Testi, L.

    2017-09-01

    We present new ALMA observations aimed at mapping molecular gas reservoirs through the CO(3-2) transition in three quasars at z ≃ 2.4, LBQS 0109+0213, 2QZ J002830.4-281706, and [HB89] 0329-385. Previous [Oiii]λ5007 observations of these quasars showed evidence for ionised outflows quenching star formation in their host galaxies. Systemic CO(3-2) emission has been detected only in one quasar, LBQS 0109+0213, where the CO(3-2) emission is spatially anti-correlated with the ionised outflow, suggesting that most of the molecular gas may have been dispersed or heated in the region swept by the outflow. In all three sources, including the one detected in CO, our constraints on the molecular gas mass indicate a significantly reduced reservoir compared to main-sequence galaxies at the same redshift, supporting a negative feedback scenario. In the quasar 2QZ J002830.4-281706, we tentatively detect an emission line blob blue-shifted by v - 2000 km s-1 with respect to the galaxy systemic velocity and spatially offset by 0.2'' (1.7 kpc) with respect to the ALMA continuum peak. Interestingly, such emission feature is coincident in both velocity and space with the ionised outflow as seen in [Oiii]λ5007. This tentative detection must be confirmed with deeper observations but, if real, it could represent the molecular counterpart of the ionised gas outflow driven by the Active Galactic Nucleus (AGN). Finally, in all ALMA maps we detect the presence of serendipitous line emitters within a projected distance 160 kpc from the quasars. By identifying these features with the CO(3-2) transition, we find that the serendipitous line emitters would be located within | Δv | < 500 km s-1 from the quasars, hence suggesting an overdensity of galaxies in two out of three quasars.

  13. Distinct forms of the β subunit of GTP-binding regulatory proteins identified by molecular cloning

    International Nuclear Information System (INIS)

    Fong, H.K.W.; Amatruda, T.T. III; Birren, B.W.; Simon, M.I.

    1987-01-01

    Two distinct β subunits of guanine nucleotide-binding regulatory proteins have been identified by cDNA cloning and are referred to as β 1 and β 1 subunits. The bovine transducin β subunit (β 1 ) has been cloned previously. The author now isolated and analyzed cDNA clones that encode the β 2 subunit from bovine adrenal, bovine brain, and a human myeloid leukemia cell line, HL-60. The 340-residue M/sub r/ 37,329 Β 2 protein is 90% identical with β 1 in predicted amino acid sequence, and it is also organized as a series of repetitive homologous segments. The major mRNA that encodes the bovine β 2 subunit is 1.7 kilobases in length. It is expressed at lower levels than β 1 subunit mRNA in all tissues examined. The β 1 and β 2 messages are expressed in cloned human cell lines. Hybridization of cDNA probes to bovine DNA showed that β 1 and β 2 are encoded by separate genes. The amino acid sequences for the bovine and human β 2 subunit are identical, as are the amino acid sequences for the bovine and human β 1 subunit. This evolutionary conservation suggests that the two β subunits have different roles in the signal transduction process

  14. Effects of collisions on linear and non-linear spectroscopic line shapes

    International Nuclear Information System (INIS)

    Berman, P.R.

    1978-01-01

    A fundamental physical problem is the determination of atom-atom, atom-molecule and molecule-molecule differential and total scattering cross sections. In this work, a technique for studying atomic and molecular collisions using spectroscopic line shape analysis is discussed. Collisions occurring within an atomic or molecular sample influence the sample's absorptive or emissive properties. Consequently the line shapes associated with the linear or non-linear absorption of external fields by an atomic system reflect the collisional processes occurring in the gas. Explicit line shape expressions are derived characterizing linear or saturated absorption by two-or three-level 'active' atoms which are undergoing collisions with perturber atoms. The line shapes may be broadened, shifted, narrowed, or distorted as a result of collisions which may be 'phase-interrupting' or 'velocity-changing' in nature. Systematic line shape studies can be used to obtain information on both the differential and total active atom-perturber scattering cross sections. (Auth.)

  15. Gene expression analysis to identify molecular correlates of pre- and post-conditioning derived neuroprotection.

    Science.gov (United States)

    Prasad, Shiv S; Russell, Marsha; Nowakowska, Margeryta; Williams, Andrew; Yauk, Carole

    2012-06-01

    Mild ischaemic exposures before or after severe injurious ischaemia that elicit neuroprotective responses are referred to as preconditioning and post-conditioning. The corresponding molecular mechanisms of neuroprotection are not completely understood. Identification of the genes and associated pathways of corresponding neuroprotection would provide insight into neuronal survival, potential therapeutic approaches and assessments of therapies for stroke. The objectives of this study were to use global gene expression approach to infer the molecular mechanisms in pre- and post-conditioning-derived neuroprotection in cortical neurons following oxygen and glucose deprivation (OGD) in vitro and then to apply these findings to predict corresponding functional pathways. To this end, microarray analysis was applied to rat cortical neurons with or without the pre- and post-conditioning treatments at 3-h post-reperfusion, and differentially expressed transcripts were subjected to statistical, hierarchical clustering and pathway analyses. The expression patterns of 3,431 genes altered under all conditions of ischaemia (with and without pre- or post-conditioning). We identified 1,595 genes that were commonly regulated within both the pre- and post-conditioning treatments. Cluster analysis revealed that transcription profiles clustered tightly within controls, non-conditioned OGD and neuroprotected groups. Two clusters defining neuroprotective conditions associated with up- and downregulated genes were evident. The five most upregulated genes within the neuroprotective clusters were Tagln, Nes, Ptrf, Vim and Adamts9, and the five most downregulated genes were Slc7a3, Bex1, Brunol4, Nrxn3 and Cpne4. Pathway analysis revealed that the intracellular and second messenger signalling pathways in addition to cell death were predominantly associated with downregulated pre- and post-conditioning associated genes, suggesting that modulation of cell death and signal transduction pathways

  16. Molecular Cloud Structures and Massive Star Formation in N159

    Science.gov (United States)

    Nayak, O.; Meixner, M.; Fukui, Y.; Tachihara, K.; Onishi, T.; Saigo, K.; Tokuda, K.; Harada, R.

    2018-02-01

    The N159 star-forming region is one of the most massive giant molecular clouds (GMCs) in the Large Magellanic Cloud (LMC). We show the 12CO, 13CO, CS molecular gas lines observed with ALMA in N159 west (N159W) and N159 east (N159E). We relate the structure of the gas clumps to the properties of 24 massive young stellar objects (YSOs) that include 10 newly identified YSOs based on our search. We use dendrogram analysis to identify properties of the molecular clumps, such as flux, mass, linewidth, size, and virial parameter. We relate the YSO properties to the molecular gas properties. We find that the CS gas clumps have a steeper size–linewidth relation than the 12CO or 13CO gas clumps. This larger slope could potentially occur if the CS gas is tracing shocks. The virial parameters of the 13CO gas clumps in N159W and N159E are low (<1). The threshold for massive star formation in N159W is 501 M ⊙ pc‑2, and the threshold for massive star formation in N159E is 794 M ⊙ pc‑2. We find that 13CO is more photodissociated in N159E than N159W. The most massive YSO in N159E has cleared out a molecular gas hole in its vicinity. All the massive YSO candidates in N159E have a more evolved spectral energy distribution type in comparison to the YSO candidates in N159W. These differences lead us to conclude that the giant molecular cloud complex in N159E is more evolved than the giant molecular cloud complex in N159W.

  17. Characterization of Camptothecin-induced Genomic Changes in the Camptothecin-resistant T-ALL-derived Cell Line CPT-K5

    DEFF Research Database (Denmark)

    Kjeldsen, Eigil; Nielsen, Christine J F; Roy, Amit

    2018-01-01

    -K5 and its parental cell line. We identified copy number alterations affecting genes important for maintaining genome integrity and reducing CPT-induced DNA damage. We show for the first time that short tandem repeats are targets for TOP1 cleavage, that can be differentially stimulated by CPT.......Acquisition of resistance to topoisomerase I (TOP1)-targeting camptothecin (CPT) derivatives is a major clinical problem. Little is known about the underlying chromosomal and genomic mechanisms. We characterized the CPT-K5 cell line expressing mutant CPT-resistant TOP1 and its parental T......-cell derived acute lymphoblastic leukemia CPT-sensitive RPMI-8402 cell line by karyotyping and molecular genetic methods, including subtractive oligo-based array comparative genomic hybridization (soaCGH) analysis. Karyotyping revealed that CPT-K5 cells had acquired additional structural aberrations...

  18. Production of acquired immunodeficiency syndrome-associated retrovirus in human and nonhuman cells transfected with an infectious molecular clone

    International Nuclear Information System (INIS)

    Adachi, A.; Gendelman, H.E.; Koenig, S.; Folks, T.; Willey, R.; Rabson, A.; Martin, M.A.

    1986-01-01

    The authors considered an infectious molecular clone of acquired immunodeficiency syndrome-associated retrovirus. Upon transfection, this clone directed the production of infectious virus particles in a wide variety of cells in addition to human T4 cells. The progeny, infectious virions, were synthesized in mouse, mink, monkey, and several human non-T cell lines, indicating the absence of any intracellular obstacle to viral RNA or protein production or assembly. During the course of these studies, a human colon carcinoma cell line, exquisitely sensitive to DNA transfection, was identified

  19. A Large-Scale RNAi Screen Identifies SGK1 as a Key Survival Kinase for GBM Stem Cells.

    Science.gov (United States)

    Kulkarni, Shreya; Goel-Bhattacharya, Surbhi; Sengupta, Sejuti; Cochran, Brent H

    2018-01-01

    Glioblastoma multiforme (GBM) is the most common type of primary malignant brain cancer and has a very poor prognosis. A subpopulation of cells known as GBM stem-like cells (GBM-SC) have the capacity to initiate and sustain tumor growth and possess molecular characteristics similar to the parental tumor. GBM-SCs are known to be enriched in hypoxic niches and may contribute to therapeutic resistance. Therefore, to identify genetic determinants important for the proliferation and survival of GBM stem cells, an unbiased pooled shRNA screen of 10,000 genes was conducted under normoxic as well as hypoxic conditions. A number of essential genes were identified that are required for GBM-SC growth, under either or both oxygen conditions, in two different GBM-SC lines. Interestingly, only about a third of the essential genes were common to both cell lines. The oxygen environment significantly impacts the cellular genetic dependencies as 30% of the genes required under hypoxia were not required under normoxic conditions. In addition to identifying essential genes already implicated in GBM such as CDK4, KIF11 , and RAN , the screen also identified new genes that have not been previously implicated in GBM stem cell biology. The importance of the serum and glucocorticoid-regulated kinase 1 (SGK1) for cellular survival was validated in multiple patient-derived GBM stem cell lines using shRNA, CRISPR, and pharmacologic inhibitors. However, SGK1 depletion and inhibition has little effect on traditional serum grown glioma lines and on differentiated GBM-SCs indicating its specific importance in GBM stem cell survival. Implications: This study identifies genes required for the growth and survival of GBM stem cells under both normoxic and hypoxic conditions and finds SGK1 as a novel potential drug target for GBM. Mol Cancer Res; 16(1); 103-14. ©2017 AACR . ©2017 American Association for Cancer Research.

  20. COLLAPSING HOT MOLECULAR CORES: A MODEL FOR THE DUST SPECTRUM AND AMMONIA LINE EMISSION OF THE G31.41+0.31 HOT CORE

    International Nuclear Information System (INIS)

    Osorio, Mayra; Anglada, Guillem; Lizano, Susana; D'Alessio, Paola

    2009-01-01

    We present a model aimed to reproduce the observed spectral energy distribution (SED) as well as the ammonia line emission of the G31.41+0.31 hot core. The hot core is modeled as an infalling envelope onto a massive star that is undergoing an intense accretion phase. We assume an envelope with a density and velocity structure resulting from the dynamical collapse of a singular logatropic sphere. The stellar and envelope physical properties are determined by fitting the observed SED. From these physical conditions, the emerging ammonia line emission is calculated and compared with subarcsecond resolution VLA data of the (4,4) transition taken from the literature. The only free parameter in this line fitting is the ammonia abundance. The observed intensities of the main and satellite ammonia (4,4) lines and their spatial distribution can be well reproduced provided the steep increase of the gas-phase ammonia abundance in the hotter (>100 K), inner regions of the core produced by the sublimation of icy mantles where ammonia molecules are trapped is taken into account. The model predictions for the (2,2), (4,4), and (5,5) transitions, obtained with the same set of parameters, are also reasonably in agreement, given the observational uncertainties, with the single-dish spectra of the region available in the literature. The best fit is obtained for a model with a central star of ∼25M sun , a mass accretion rate of ∼3 x 10 -3 M sun yr -1 , and a total luminosity of ∼2 x 10 5 L sun . The outer radius of the envelope is 30,000 AU, where kinetic temperatures as high as ∼40 K are reached. The gas-phase ammonia abundance ranges from ∼2 x 10 -8 in the outer region to ∼3 x 10 -6 in the inner region. To our knowledge, this is the first time that the dust and molecular line data of a hot molecular core, including subarcsecond resolution data that spatially resolve the structure of the core, have been simultaneously explained by a detailed, physically self

  1. Identifying and engineering promoters for high level and sustainable therapeutic recombinant protein production in cultured mammalian cells.

    Science.gov (United States)

    Ho, Steven C L; Yang, Yuansheng

    2014-08-01

    Promoters are essential on plasmid vectors to initiate transcription of the transgenes when generating therapeutic recombinant proteins expressing mammalian cell lines. High and sustained levels of gene expression are desired during therapeutic protein production while gene expression is useful for cell engineering. As many finely controlled promoters exhibit cell and product specificity, new promoters need to be identified, optimized and carefully evaluated before use. Suitable promoters can be identified using techniques ranging from simple molecular biology methods to modern high-throughput omics screenings. Promoter engineering is often required after identification to either obtain high and sustained expression or to provide a wider range of gene expression. This review discusses some of the available methods to identify and engineer promoters for therapeutic recombinant protein expression in mammalian cells.

  2. Genome-wide association study identifies candidate genes for starch content regulation in maize kernels

    Directory of Open Access Journals (Sweden)

    Na Liu

    2016-07-01

    Full Text Available Kernel starch content is an important trait in maize (Zea mays L. as it accounts for 65% to 75% of the dry kernel weight and positively correlates with seed yield. A number of starch synthesis-related genes have been identified in maize in recent years. However, many loci underlying variation in starch content among maize inbred lines still remain to be identified. The current study is a genome-wide association study that used a set of 263 maize inbred lines. In this panel, the average kernel starch content was 66.99%, ranging from 60.60% to 71.58% over the three study years. These inbred lines were genotyped with the SNP50 BeadChip maize array, which is comprised of 56,110 evenly spaced, random SNPs. Population structure was controlled by a mixed linear model (MLM as implemented in the software package TASSEL. After the statistical analyses, four SNPs were identified as significantly associated with starch content (P ≤ 0.0001, among which one each are located on chromosomes 1 and 5 and two are on chromosome 2. Furthermore, 77 candidate genes associated with starch synthesis were found within the 100-kb intervals containing these four QTLs, and four highly associated genes were within 20-kb intervals of the associated SNPs. Among the four genes, Glucose-1-phosphate adenylyltransferase (APS1; Gene ID GRMZM2G163437 is known as an important regulator of kernel starch content. The identified SNPs, QTLs, and candidate genes may not only be readily used for germplasm improvement by marker-assisted selection in breeding, but can also elucidate the genetic basis of starch content. Further studies on these identified candidate genes may help determine the molecular mechanisms regulating kernel starch content in maize and other important cereal crops.

  3. Spontaneous pyrogen production by mouse histiocytic and myelomonocytic tumor cell lines in vitro.

    Science.gov (United States)

    Bodel, P

    1978-05-01

    Tumor-associated fever occurs commonly in acute leukemias and lymphomas. We investigated the capacity for in vitro production of pyrogen by three mouse histiocytic lymphoma cell lines (J-774, PU5-1.8, p 388 D1), one myelomonoyctic line (WEHI-3), and tow lymphoma-derived lines, RAW-8 and R-8. Pyrogen was released spontaneously into the culture medium during growth by all cell lines with macrophage or myeloid characteristics including lysozyme production; R-8 cells, of presumed B-lymphocyte origin, did not produce pyrogen. When injected into mice, the pyrogens gave fever curves typical of endogenous pyrogen, were inactived by heating to 56 degrees C and by pronase digestion, and appeared to be secreted continuously by viable cells. Two pyrogenic molecular species produced by H-774 cells were identified by Sephadex filtration, one of mol wt approximately equal to 30,000, and the other greater than or equal to 60,000. By contrast, three carcinoma cell lines of human origin and SV-40 3T3 mouse fibroblasts did not produce pyrogen in vitro. These results suggest that some malignant cells derived from phagocytic cells of bone marrow origin retain their capacity for pyrogen production, and may spontaneously secrete pyrogen during growth.

  4. MOLECULAR DIAGNOSTICS OF YERSINIA RUCKERI

    Directory of Open Access Journals (Sweden)

    Yu. Rud

    2014-06-01

    Full Text Available Purpose. The analysis of nucleotide sequences of the 16S rDNA gene of virulent strains of Yersinia ruckeri and to develop the method of molecular diagnostic of enteric redmouth disease. Methodology. By the method of CLUSTALW algorithm in MEGA software version 6.0 the nucleotide sequences of the 16S rDNA gene of virulent strains of Yersinia ruckeri were analysed. For development of molecular diagnostic of Y. ruckeri the method of polymerase chain reaction (PCR was used. Primer selection was carried out in software VectorNTI11 and on-line-service BLAST. The PCR products were investigated by the methods of sequencing and nucleotide analysis. Findings. Based on PCR assay the method of molecular diagnostic of enteric redmouth disease agent, bacterium Y. ruckeri was developed. It was shown that specific oligonucleotide primers generated PCR products in size of 600 base pairs. PCR products were investigated by the sequencing that showed right targeting of primers in reaction. Originality. Among high-conservative gene of 16S rDNA of Y. ruckeri the fragment of DNA was determined to which the specific primers for rapid diagnostic of virulent strains were selected. Practical Value. Rapid diagnostic of yersiniosis will allow to identify an agent of this infectious disease, bacterium Y. ruckeri, and to provide the prophylactic or medical measures in the fish farming of Ukraine.

  5. Analysis of gene expression data from non-small cell lung carcinoma cell lines reveals distinct sub-classes from those identified at the phenotype level.

    Directory of Open Access Journals (Sweden)

    Andrew R Dalby

    Full Text Available Microarray data from cell lines of Non-Small Cell Lung Carcinoma (NSCLC can be used to look for differences in gene expression between the cell lines derived from different tumour samples, and to investigate if these differences can be used to cluster the cell lines into distinct groups. Dividing the cell lines into classes can help to improve diagnosis and the development of screens for new drug candidates. The micro-array data is first subjected to quality control analysis and then subsequently normalised using three alternate methods to reduce the chances of differences being artefacts resulting from the normalisation process. The final clustering into sub-classes was carried out in a conservative manner such that sub-classes were consistent across all three normalisation methods. If there is structure in the cell line population it was expected that this would agree with histological classifications, but this was not found to be the case. To check the biological consistency of the sub-classes the set of most strongly differentially expressed genes was be identified for each pair of clusters to check if the genes that most strongly define sub-classes have biological functions consistent with NSCLC.

  6. AN INTERFEROMETRIC SPECTRAL LINE AND IMAGING SURVEY OF VY CANIS MAJORIS IN THE 345 GHz BAND

    International Nuclear Information System (INIS)

    Kamiński, T.; Menten, K. M.; Gottlieb, C. A.; Young, K. H.; Patel, N. A.

    2013-01-01

    A spectral line survey of the oxygen-rich red supergiant VY Canis Majoris was made between 279 and 355 GHz with the Submillimeter Array (SMA). Two hundred twenty-three spectral features from 19 molecules (not counting isotopic species of some of them) were observed, including the rotational spectra of TiO, TiO 2 , and AlCl for the first time in this source. The parameters and an atlas of all spectral features are presented. Observations of each line with a synthesized beam of ∼0.''9, reveal the complex kinematics and morphology of the nebula surrounding VY CMa. Many of the molecules are observed in high-lying rotational levels or in excited vibrational levels. From these, it was established that the main source of the submillimeter-wave continuum (dust) and the high-excitation molecular gas (the star) are separated by about 0.''15. Apparent coincidences between the molecular gas observed with the SMA, and some of the arcs and knots observed at infrared wavelengths and in the optical scattered light by the Hubble Space Telescope are identified. The observations presented here provide important constraints on the molecular chemistry in oxygen-dominated circumstellar environments and a deeper picture of the complex circumstellar environment of VY CMa

  7. Molecular Classification of Lobular Carcinoma of the Breast

    Science.gov (United States)

    Fu, Denggang; Zuo, Qi; Huang, Qi; Su, Li; Ring, Huijun Z.; Ring, Brian Z.

    2017-01-01

    The morphology of breast tumors is complicated and diagnosis can be difficult. We present here a novel diagnostic model which we validate on both array-based and RNA sequencing platforms which reliably distinguishes this tumor type across multiple cohorts. We also examine how this molecular classification predicts sensitivity to common chemotherapeutics in cell-line based assays. A total of 1845 invasive breast cancer cases in six cohorts were collected, split into discovery and validation cohorts, and a classifier was created and compared to pathological diagnosis, grade and survival. In the validation cohorts the concordance of predicted diagnosis with a pathological diagnosis was 92%, and 97% when inconclusively classified cases were excluded. Tumor-derived cell lines were classified with the model as having predominantly ductal or lobular-like molecular physiologies, and sensitivity of these lines to relevant compounds was analyzed. A diagnostic tool can be created that reliably distinguishes lobular from ductal carcinoma and allows the classification of cell lines on the basis of molecular profiles associated with these tumor types. This tool may assist in improved diagnosis and aid in explorations of the response of lobular type breast tumor models to different compounds. PMID:28303886

  8. Identification of differentially expressed genes in the oviduct of two rabbit lines divergently selected for uterine capacity using suppression subtractive hybridization.

    Science.gov (United States)

    Ballester, M; Castelló, A; Peiró, R; Argente, M J; Santacreu, M A; Folch, J M

    2013-06-01

    Suppressive subtractive hybridization libraries from oviduct at 62 h post-mating of two lines of rabbits divergently selected for uterine capacity were generated to identify differentially expressed genes. A total of 438 singletons and 126 contigs were obtained by cluster assembly and sequence alignment of 704 expressed sequence tags (ESTs), of which 54% showed homology to known proteins of the non-redundant NCBI databases. Differential screening by dot blot validated 71 ESTs, of which 47 showed similarity to known genes. Transcripts of genes were functionally annotated in the molecular function and the biological process gene ontology categories using the BLAST2GO software and were assigned to reproductive developmental process, immune response, amino acid metabolism and degradation, response to stress and apoptosis terms. Finally, three interesting genes, PGR, HSD17B4 and ERO1L, were identified as overexpressed in the low line using RT-qPCR. Our study provides a list of candidate genes that can be useful to understanding the molecular mechanisms underlying the phenotypic differences observed in early embryo survival and development traits. © 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics.

  9. Status of biotechnology with emphasis on molecular techniques for mutation breeding in the Philippines

    Energy Technology Data Exchange (ETDEWEB)

    Lapade, A.G.; Nazarea, T.Y.; Veluz, A.M.S.; Marbella, L.J.; Nato, A.Q.; Coloma, C.B. Jr.; Asencion, A.B. [Philippine Nuclear Research Institute, Commonwealth Avenue, Quezon (Philippines)

    2002-02-01

    This paper summarizes the status of biotechnology with emphasis on molecular techniques for plant breeding in the Philippines. Several molecular and in-vitro culture techniques are integrated in plant breeding for crop improvement at PNRI, UPLB, IRRI and PhilRice. At IRRI, PCR techniques, RFLP and RAPD, PCR techniques, RFLP and RAPD were developed to establish high density molecular maps, determine breadth and diversity of germplasm and characterize alien introgression. The molecular maps have identified DNA sequence of resistance genes of HYVs and NPTs to abiotic and biotic stresses, the major achievement is the development of high density molecular maps in rice with at least 2000 markers. The biotechnology program at PhilRice for varietal improvement includes: (1) utilization of molecular marker technology such gene mapping of desired traits in rice, analysis of genetic relationships of germplasm materials and breeding lines through DNA fingerprinting and genetic diversity studies and development and application of marker aided selection for disease resistance (RTD and BLB); (2) application of in-vitro techniques in the development of lines with tolerance to adverse conditions; (3) molecular cloning of important genes for RTD resistance; (4) genetic transformation for male sterility and resistance to sheath blight and stem borers; and (5) transfer of disease resistance from wild species to cultivated varieties. In IPB, molecular markers:microsatellites or SSR, AFLP and RGA are being used for mapping and diversity studies in coconut, mango, banana, mungbean, corn and tomato. Mutation breeding at PNRI using gamma radiation has resulted in the development of crop varieties with desirable traits. The use of AFLP coupled to PCR is being used to study polymorphism in plant variants of radiation-induced mutants of rice, pineapple and ornamentals. (author)

  10. Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers.

    Science.gov (United States)

    Girardot, Charles; Scholtalbers, Jelle; Sauer, Sajoscha; Su, Shu-Yi; Furlong, Eileen E M

    2016-10-08

    The yield obtained from next generation sequencers has increased almost exponentially in recent years, making sample multiplexing common practice. While barcodes (known sequences of fixed length) primarily encode the sample identity of sequenced DNA fragments, barcodes made of random sequences (Unique Molecular Identifier or UMIs) are often used to distinguish between PCR duplicates and transcript abundance in, for example, single-cell RNA sequencing (scRNA-seq). In paired-end sequencing, different barcodes can be inserted at each fragment end to either increase the number of multiplexed samples in the library or to use one of the barcodes as UMI. Alternatively, UMIs can be combined with the sample barcodes into composite barcodes, or with standard Illumina® indexing. Subsequent analysis must take read duplicates and sample identity into account, by identifying UMIs. Existing tools do not support these complex barcoding configurations and custom code development is frequently required. Here, we present Je, a suite of tools that accommodates complex barcoding strategies, extracts UMIs and filters read duplicates taking UMIs into account. Using Je on publicly available scRNA-seq and iCLIP data containing UMIs, the number of unique reads increased by up to 36 %, compared to when UMIs are ignored. Je is implemented in JAVA and uses the Picard API. Code, executables and documentation are freely available at http://gbcs.embl.de/Je . Je can also be easily installed in Galaxy through the Galaxy toolshed.

  11. Spotting Separator Points at Line Terminals in Compressed Document Images for Text-line Segmentation

    OpenAIRE

    R, Amarnath; Nagabhushan, P.

    2017-01-01

    Line separators are used to segregate text-lines from one another in document image analysis. Finding the separator points at every line terminal in a document image would enable text-line segmentation. In particular, identifying the separators in handwritten text could be a thrilling exercise. Obviously it would be challenging to perform this in the compressed version of a document image and that is the proposed objective in this research. Such an effort would prevent the computational burde...

  12. Spitzer spectral line mapping of the HH211 outflow

    DEFF Research Database (Denmark)

    Dionatos, Odyssefs; Nisini, Brunella; Cabrit, Sylvie

    2010-01-01

    of emission line diagnostics and an existing grid of molecular shock models. The physical properties of the warm gas are compared against other molecular jet tracers and to the results of a similar study towards the L1448-C outflow. Results: We have detected and mapped the v=0-0 S(0) - S(7) H2 lines and fine...... compared to solar abundances by a factor ~10-50. Conclusions: Spitzer spectral mapping observations reveal for the first time a cool H$_2$ component towards the CO jet of HH211 consistent with the CO material being fully molecular and warm at ~ 300 K. The maps also reveal for the first time the existence...... uncertainties on jet speed and shock conditions are too large for a definite conclusion....

  13. Comparing human pancreatic cell secretomes by in vitro aptamer selection identifies cyclophilin B as a candidate pancreatic cancer biomarker.

    Science.gov (United States)

    Ray, Partha; Rialon-Guevara, Kristy L; Veras, Emanuela; Sullenger, Bruce A; White, Rebekah R

    2012-05-01

    Most cases of pancreatic cancer are not diagnosed until they are no longer curable with surgery. Therefore, it is critical to develop a sensitive, preferably noninvasive, method for detecting the disease at an earlier stage. In order to identify biomarkers for pancreatic cancer, we devised an in vitro positive/negative selection strategy to identify RNA ligands (aptamers) that could detect structural differences between the secretomes of pancreatic cancer and non-cancerous cells. Using this molecular recognition approach, we identified an aptamer (M9-5) that differentially bound conditioned media from cancerous and non-cancerous human pancreatic cell lines. This aptamer further discriminated between the sera of pancreatic cancer patients and healthy volunteers with high sensitivity and specificity. We utilized biochemical purification methods and mass-spectrometric analysis to identify the M9-5 target as cyclophilin B (CypB). This molecular recognition-based strategy simultaneously identified CypB as a serum biomarker and generated a new reagent to recognize it in body fluids. Moreover, this approach should be generalizable to other diseases and complementary to traditional approaches that focus on differences in expression level between samples. Finally, we suggest that the aptamer we identified has the potential to serve as a tool for the early detection of pancreatic cancer.

  14. On multiscale moving contact line theory.

    Science.gov (United States)

    Li, Shaofan; Fan, Houfu

    2015-07-08

    In this paper, a multiscale moving contact line (MMCL) theory is presented and employed to simulate liquid droplet spreading and capillary motion. The proposed MMCL theory combines a coarse-grained adhesive contact model with a fluid interface membrane theory, so that it can couple molecular scale adhesive interaction and surface tension with hydrodynamics of microscale flow. By doing so, the intermolecular force, the van der Waals or double layer force, separates and levitates the liquid droplet from the supporting solid substrate, which avoids the shear stress singularity caused by the no-slip condition in conventional hydrodynamics theory of moving contact line. Thus, the MMCL allows the difference of the surface energies and surface stresses to drive droplet spreading naturally. To validate the proposed MMCL theory, we have employed it to simulate droplet spreading over various elastic substrates. The numerical simulation results obtained by using MMCL are in good agreement with the molecular dynamics results reported in the literature.

  15. Teaching Braille Line Tracking Using Stimulus Fading

    Science.gov (United States)

    Scheithauer, Mindy C.; Tiger, Jeffrey H.

    2014-01-01

    Line tracking is a prerequisite skill for braille literacy that involves moving one's finger horizontally across a line of braille text and identifying when a line ends so the reader may reset his or her finger on the subsequent line. Current procedures for teaching line tracking are incomplete, because they focus on tracking lines with only…

  16. Interaction between the SNR Sagittarius A East and the 50-km s-1 Molecular Cloud

    International Nuclear Information System (INIS)

    Tsuboi, Masato; Okumura, Sachiko K; Miyazaki, Atsushi

    2006-01-01

    We performed high-resolution observations of the Galactic Center 50-km s -1 molecular cloud in the CS J = 1 - 0 line using the Nobeyama Millimeter Array. The 50-km s -1 molecular cloud corresponds to a break in the Sagittarius (Sgr) A east shell. A very broad and negative velocity wing feature is detected at an apparent contact spot between the molecular cloud and the Sgr A east shell. The velocity width of the wing feature is over 50-km s -1 . The width is three times wider than those of typical Galactic Center clouds. This strongly suggests that the shell is interacting physically with the molecular cloud. The asymmetric velocity profile of the wing feature indicates that the Sgr A east shell expands and crashes into the far side of the molecular cloud. About 50 clumps are identified in the cloud using CLUMPFIND. The velocity width-size relation and the mass spectrum of clumps in the cloud are similar to those in Central Molecular Zone (CMZ)

  17. Processing of high-molecular-weight form adrenocorticotropin in human adrenocorticotropin-secreting tumor cell line (DMS-79) after transfection of prohormone convertase 1/3 gene.

    Science.gov (United States)

    Tateno, T; Kato, M; Tani, Y; Yoshimoto, T; Oki, Y; Hirata, Y

    2010-02-01

    Ectopic ACTH-producing tumors preferentially secrete biologically inactive ACTH precursors and ACTH-related fragments. DMS-79 is known to secrete unprocessed high-molecular-weight (HMW) form ACTH. To determine whether prohormone convertase (PC) 1/3 is involved in the abnormal processing of proopiomelanocortin (POMC), we studied whether PC1/3 and 2 genes are expressed in DMS-79, and whether overexpression of PC1/3 gene affects POMC processing pattern. Steady-state mRNA levels of PC1/3 and 2 were determined by real-time RT-PCR. Molecular weights of ACTH-related peptides were determined by chromatographical analyses coupled with ACTH and beta-endorphin (beta-END) radioimmunoassays. PC1/3 gene was transfected into DMS-79 by retrovirus transduction using pMX-IP vector encoding PC1/3 cDNA. The steady-state mRNA levels of PC1/3 and 2 in DMS-79 were lower than those in ACTH-secreting and nonfunctioning pituitary tumors. DMS-79 predominantly secreted HMW form with both ACTH and beta-END immunoreactivities by size-exclusion chromatography. After purification by immunoaffinity chromatography with anti-ACTH antibody, the apparent molecular weight of HMW form ACTH was estimated to be 16 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis with silver staining. After retroviral transfection of PC1/3 cDNA into DMS-79 and puromycin selection, PC1/3 stably-expressing cell line (DMS-79T) secreted two immunoreactive ACTH components, a major one coeluting with ACTH(1-39) and a minor one as a HMW form as well as two beta- END immunoreactive components coeluting with beta-lipotropic hormone and beta-END, respectively. Thus, we have established PC1/3 stably-expressing cell line (DMS-79T) capable of proteolytically processing ACTH precursor molecule(s) into mature ACTH and beta-END.

  18. Spectral Line Shapes in Plasmas and Gases

    International Nuclear Information System (INIS)

    Oks, E.; Dalimier, D.; Stamm, R.; Stehle, CH.; Gonzalez, M.A.

    2011-01-01

    The subject of spectral line shapes (SLS), a.k.a. spectral line broadening, which embraces both shapes and shifts of spectral lines, is of both fundamental and practical importance. On the fundamental side, the study of the spectral line profiles reveals the underlying atomic and molecular interactions. On the practical side, the spectral line profiles are employed as powerful diagnostic tools for various media, such as neutral gases, technological gas discharges, magnetically confined plasmas for fusion, laser- and Z-pinch-produced plasmas (for fusion and other purposes), astrophysical plasmas (most importantly, solar plasmas), and planetary atmospheres. The research area covered by this special issue includes both the SLS dominated by various electric fields (including electron and ion micro fields in strongly ionized plasmas) and the SLS controlled by neutral particles. In the physical slang, the former is called plasma broadening while the latter is called neutral broadening (of course, the results of neutral broadening apply also to the spectral line broadening in neutral gases)

  19. Molecular anthropology in the genomic era.

    Science.gov (United States)

    Destro-Bisol, Giovanni; Jobling, Mark A; Rocha, Jorge; Novembre, John; Richards, Martin B; Mulligan, Connie; Batini, Chiara; Manni, Franz

    2010-01-01

    Molecular Anthropology is a relatively young field of research. In fact, less than 50 years have passed since the symposium "Classification and Human Evolution" (1962, Burg Wartenstein, Austria), where the term was formally introduced by Emil Zuckerkandl. In this time, Molecular Anthropology has developed both methodologically and theoretically and extended its applications, so covering key aspects of human evolution such as the reconstruction of the history of human populations and peopling processes, the characterization of DNA in extinct humans and the role of adaptive processes in shaping the genetic diversity of our species. In the current scientific panorama, molecular anthropologists have to face a double challenge. As members of the anthropological community, we are strongly committed to the integration of biological findings and other lines of evidence (e.g. linguistic and archaeological), while keeping in line with methodological innovations which are moving the approach from the genetic to the genomic level. In this framework, the meeting "DNA Polymorphisms in Human Populations: Molecular Anthropology in the Genomic Era" (Rome, December 3-5, 2009) offered an opportunity for discussion among scholars from different disciplines, while paying attention to the impact of recent methodological innovations. Here we present an overview of the meeting and discuss perspectives and prospects of Molecular Anthropology in the genomic era.

  20. HASE - The Helsinki adaptive sample preparation line

    Energy Technology Data Exchange (ETDEWEB)

    Palonen, V., E-mail: vesa.palonen@helsinki.fi [Department of Physics, University of Helsinki, P.O. Box 43, FI-00014 (Finland); Pesonen, A. [Laboratory of Chronology, Finnish Museum of Natural History, P.O. Box 64, FI-00014 (Finland); Herranen, T.; Tikkanen, P. [Department of Physics, University of Helsinki, P.O. Box 43, FI-00014 (Finland); Oinonen, M. [Laboratory of Chronology, Finnish Museum of Natural History, P.O. Box 64, FI-00014 (Finland)

    2013-01-15

    We have designed and built an adaptive sample preparation line with separate modules for combustion, molecular sieve handling, CO{sub 2} gas cleaning, CO{sub 2} storage, and graphitization. The line is also connected to an elemental analyzer. Operation of the vacuum equipment, a flow controller, pressure sensors, ovens, and graphitization reactors are automated with a reliable NI-cRIO real-time system. Stepped combustion can be performed in two ovens at temperatures up to 900 Degree-Sign C. Depending on the application, CuO or O{sub 2}-flow combustion can be used. A flow controller is used to adjust the O{sub 2} flow and pressure during combustion. For environmental samples, a module for molecular sieve regeneration and sample desorption is attached to the line replacing the combustion module. In the storage module, CO{sub 2} samples can be stored behind a gas-tight diaphragm valve and either stored for later graphitization or taken for measurements with separate equipment (AMS gas ion source or a separate mass spectrometer). The graphitization module consists of four automated reactors, capable of graphitizing samples with masses from 3 mg down to 50 {mu}g.

  1. Establishment and characterization of 7 novel hepatocellular carcinoma cell lines from patient-derived tumor xenografts.

    Directory of Open Access Journals (Sweden)

    Hong Xin

    Full Text Available Hepatocellular carcinoma (HCC is a common cancer with poor prognosis worldwide and the molecular mechanism is not well understood. This study aimed to establish a collection of human HCC cell lines from patient-derived xenograft (PDX models. From the 20 surgical HCC sample collections, 7 tumors were successfully developed in immunodeficient mice and further established 7 novel HCC cell lines (LIXC002, LIXC003, LIXC004, LIXC006, LIXC011, LIXC012 and CPL0903 by primary culture. The characterization of cell lines was defined by morphology, growth kinetics, cell cycle, chromosome analysis, short tandem repeat (STR analysis, molecular profile, and tumorigenicity. Additionally, response to clinical chemotherapeutics was validated both in vitro and in vivo. STR analysis indicated that all cell lines were unique cells different from known cell lines and free of contamination by bacteria or mycoplasma. The other findings were quite heterogeneous between individual lines. Chromosome aberration could be found in all cell lines. Alpha-fetoprotein was overexpressed only in 3 out of 7 cell lines. 4 cell lines expressed high level of vimentin. Ki67 was strongly stained in all cell lines. mRNA level of retinoic acid induced protein 3 (RAI3 was decreased in all cell lines. The 7 novel cell lines showed variable sensitivity to 8 tested compounds. LIXC011 and CPL0903 possessed multiple drug resistance property. Sorafenib inhibited xenograft tumor growth of LIXC006, but not of LIXC012. Our results indicated that the 7 novel cell lines with low passage maintaining their clinical and pathological characters could be good tools for further exploring the molecular mechanism of HCC and anti-cancer drug screening.

  2. Diagnostic performance of automated liquid culture and molecular line probe assay in smear-negative pulmonary tuberculosis.

    Science.gov (United States)

    Kotwal, Aarti; Biswas, Debasis; Raghuvanshi, Shailendra; Sindhwani, Girish; Kakati, Barnali; Sharma, Shweta

    2017-04-01

    The diagnosis of smear-negative pulmonary tuberculosis (PTB) is particularly challenging, and automated liquid culture and molecular line probe assays (LPA) may prove particularly useful. The objective of our study was to evaluate the diagnostic potential of automated liquid culture (ALC) technology and commercial LPA in sputum smear-negative PTB suspects. Spot sputum samples were collected from 145 chest-symptomatic smear-negative patients and subjected to ALC, direct drug susceptibility test (DST) testing and LPA, as per manufacturers' instructions. A diagnostic yield of 26.2% was observed among sputum smear-negative TB suspects with 47.4% of the culture isolates being either INH- and/or rifampicin-resistant. Complete agreement was observed between the results of ALC assay and LPA except for two isolates which demonstrated sensitivity to INH and rifampicin at direct DST but were rifampicin-resistant in LPA. Two novel mutations were also detected among the multidrug isolates by LPA. In view of the diagnostic challenges associated with the diagnosis of TB in sputum smear-negative patients, our study demonstrates the applicability of ALC and LPA in establishing diagnostic evidence of TB.

  3. Retroviral insertions in the VISION database identify molecular pathways in mouse lymphoid leukemia and lymphoma.

    Science.gov (United States)

    Weiser, Keith C; Liu, Bin; Hansen, Gwenn M; Skapura, Darlene; Hentges, Kathryn E; Yarlagadda, Sujatha; Morse Iii, Herbert C; Justice, Monica J

    2007-10-01

    AKXD recombinant inbred (RI) strains develop a variety of leukemias and lymphomas due to somatically acquired insertions of retroviral DNA into the genome of hematopoetic cells that can mutate cellular proto-oncogenes and tumor suppressor genes. We generated a new set of tumors from nine AKXD RI strains selected for their propensity to develop B-cell tumors, the most common type of human hematopoietic cancers. We employed a PCR technique called viral insertion site amplification (VISA) to rapidly isolate genomic sequence at the site of provirus insertion. Here we describe 550 VISA sequence tags (VSTs) that identify 74 common insertion sites (CISs), of which 21 have not been identified previously. Several suspected proto-oncogenes and tumor suppressor genes lie near CISs, providing supportive evidence for their roles in cancer. Furthermore, numerous previously uncharacterized genes lie near CISs, providing a pool of candidate disease genes for future research. Pathway analysis of candidate genes identified several signaling pathways as common and powerful routes to blood cancer, including Notch, E-protein, NFkappaB, and Ras signaling. Misregulation of several Notch signaling genes was confirmed by quantitative RT-PCR. Our data suggest that analyses of insertional mutagenesis on a single genetic background are biased toward the identification of cooperating mutations. This tumor collection represents the most comprehensive study of the genetics of B-cell leukemia and lymphoma development in mice. We have deposited the VST sequences, CISs in a genome viewer, histopathology, and molecular tumor typing data in a public web database called VISION (Viral Insertion Sites Identifying Oncogenes), which is located at http://www.mouse-genome.bcm.tmc.edu/vision .

  4. Meta-Analysis of Placental Transcriptome Data Identifies a Novel Molecular Pathway Related to Preeclampsia.

    Science.gov (United States)

    van Uitert, Miranda; Moerland, Perry D; Enquobahrie, Daniel A; Laivuori, Hannele; van der Post, Joris A M; Ris-Stalpers, Carrie; Afink, Gijs B

    2015-01-01

    Studies using the placental transcriptome to identify key molecules relevant for preeclampsia are hampered by a relatively small sample size. In addition, they use a variety of bioinformatics and statistical methods, making comparison of findings challenging. To generate a more robust preeclampsia gene expression signature, we performed a meta-analysis on the original data of 11 placenta RNA microarray experiments, representing 139 normotensive and 116 preeclamptic pregnancies. Microarray data were pre-processed and analyzed using standardized bioinformatics and statistical procedures and the effect sizes were combined using an inverse-variance random-effects model. Interactions between genes in the resulting gene expression signature were identified by pathway analysis (Ingenuity Pathway Analysis, Gene Set Enrichment Analysis, Graphite) and protein-protein associations (STRING). This approach has resulted in a comprehensive list of differentially expressed genes that led to a 388-gene meta-signature of preeclamptic placenta. Pathway analysis highlights the involvement of the previously identified hypoxia/HIF1A pathway in the establishment of the preeclamptic gene expression profile, while analysis of protein interaction networks indicates CREBBP/EP300 as a novel element central to the preeclamptic placental transcriptome. In addition, there is an apparent high incidence of preeclampsia in women carrying a child with a mutation in CREBBP/EP300 (Rubinstein-Taybi Syndrome). The 388-gene preeclampsia meta-signature offers a vital starting point for further studies into the relevance of these genes (in particular CREBBP/EP300) and their concomitant pathways as biomarkers or functional molecules in preeclampsia. This will result in a better understanding of the molecular basis of this disease and opens up the opportunity to develop rational therapies targeting the placental dysfunction causal to preeclampsia.

  5. Species identification refined by molecular scatology in a community of sympatric carnivores in Xinjiang, China

    OpenAIRE

    LAGUARDIA, Alice; WANG, Jun; SHI, Fang-Lei; SHI, Kun; RIORDAN, Philip

    2015-01-01

    Many ecological studies and conservation management plans employ noninvasive scat sampling based on the assumption that species’ scats can be correctly identified in the field. However, in habitats with sympatric similarly sized carnivores, misidentification of scats is frequent and can lead to bias in research results. To address the scat identification dilemma, molecular scatology techniques have been developed to extract DNA from the donor cells present on the outer lining of the scat samp...

  6. Conventional and molecular cytogenetics of human non-medullary thyroid carcinoma: characterization of eight cell line models and review of the literature on clinical samples

    International Nuclear Information System (INIS)

    Ribeiro, Franclim Ricardo; Meireles, Ana Margarida; Rocha, Ana Sofia; Teixeira, Manuel Rodrigues

    2008-01-01

    Cell lines are often poorly characterized from a genetic point of view, reducing their usefulness as tumor models. Our purpose was to assess the genetic background of eight commonly used human thyroid carcinoma models and to compare the findings with those reported for primary tumors of the gland. We used chromosome banding analysis and comparative genomic hybridization to profile eight non-medullary thyroid carcinoma cell lines of papillary (TPC-1, FB2, K1 and B-CPAP), follicular (XTC-1) or anaplastic origin (8505C, C643 and HTH74). To assess the representativeness of the findings, we additionally performed a thorough review of cytogenetic (n = 125) and DNA copy number information (n = 270) available in the literature on clinical samples of thyroid carcinoma. The detailed characterization of chromosomal markers specific for each cell line revealed two cases of mistaken identities: FB2 was shown to derive from TPC-1 cells, whereas K1 cells have their origin in cell line GLAG-66. All cellular models displayed genomic aberrations of varying complexity, and recurrent gains at 5p, 5q, 8q, and 20q (6/7 cell lines) and losses at 8p, 13q, 18q, and Xp (4/7 cell lines) were seen. Importantly, the genomic profiles were compatible with those of the respective primary tumors, as seen in the meta-analysis of the existing literature data. We provide the genomic background of seven independent thyroid carcinoma models representative of the clinical tumors of the corresponding histotypes, and highlight regions of recurrent aberrations that may guide future studies aimed at identifying target genes. Our findings further support the importance of routinely performing cytogenetic studies on cell lines, to detect cross-contamination mishaps such as those identified here

  7. Cellular and Phenotypic Characterization of Canine Osteosarcoma Cell Lines

    Directory of Open Access Journals (Sweden)

    Marie E. Legare, Jamie Bush, Amanda K. Ashley, Taka Kato, William H. Hanneman

    2011-01-01

    Full Text Available Canine and human osteosarcoma (OSA have many similarities, with the majority of reported cases occurring in the appendicular skeleton, gender predominance noted, high rate of metastasis at the time of presentation, and a lack of known etiology for this devastating disease. Due to poor understanding of the molecular mechanisms underlying OSA, we have characterized seven different OSA canine cell lines: Abrams, D17, Grey, Hughes, Ingles, Jarques, and Marisco and compared them to U2, a human OSA cell line, for the following parameters: morphology, growth, contact inhibition, migrational tendencies, alkaline phosphatase staining, heterologous tumor growth, double-strand DNA breaks, and oxidative damage. All results demonstrated the positive characteristics of the Abrams cell line for use in future studies of OSA. Of particular interest, the robust growth of a subcutaneous tumor and rapid pulmonary metastasis of the Abrams cell line in an immunocompromised mouse shows incredible potential for the future use of Abrams as a canine OSA model. Further investigations utilizing a canine cell model of OSA, such as Abrams, will be invaluable to understanding the molecular events underlying OSA, pharmaceutical inhibition of metastasis, and eventual prevention of this devastating disease.

  8. The molecular chemistry of diffuse and translucent clouds in the line-of-sight to Sgr B2: Absorption by simple organic and inorganic molecules in the GBT PRIMOS survey

    Science.gov (United States)

    Corby, J. F.; McGuire, B. A.; Herbst, E.; Remijan, A. J.

    2018-02-01

    The 1-50 GHz PRebiotic Interstellar MOlecular Survey (PRIMOS) contains 50 molecular absorption lines observed in clouds located in the line-of-sight to Sgr B2(N). The line-of-sight material is associated with diffuse and translucent clouds located in the Galactic center, bar, and spiral arms in the disk. We measured the column densities and estimate abundances, relative to H2, of 11 molecules and additional isotopologues observed in this material. We used absorption by optically thin transitions of c-C3H2 to estimate the molecular hydrogen columns, and argue that this method is preferable to more commonly used methods. We discuss the kinematic structure and abundance patterns of small molecules including the sulfur-bearing species CS, SO, CCS, H2CS, and HCS+; oxygen-bearing molecules OH, SiO, and H2CO; and simple hydrocarbon molecules c-C3H2, l-C3H, and l-C3H+. Finally, we discuss the implications of the observed chemistry for the structure of the gas and dust in the ISM. Highlighted results include the following. First, whereas gas in the disk has a molecular hydrogen fraction of 0.65, clouds on the outer edge of the Galactic bar and in or near the Galactic center have molecular fractions of 0.85 and >0.9, respectively. Second, we observe trends in isotope ratios with Galactocentric distance; while carbon and silicon show enhancement of the rare isotopes at low Galactocentric distances, sulfur exhibits no trend with Galactocentric distance. We also determine that the ratio of c-C3H2/c-H13CCCH provides a good estimate of the 12C/13C ratio, whereas H2CO/H213CO exhibits fractionation. Third, we report the presence of l-C3H+ in diffuse clouds for the first time. Finally, we suggest that CS has an enhanced abundance within higher density clumps of material in the disk, and therefore may be diagnostic of cloud conditions. If this holds, the diffuse clouds in the Galactic disk contain multiple embedded hyperdensities in a clumpy structure, and the density profile is not

  9. Characterization and classification of one new cytoplasmic male sterility (CMS) line based on morphological, cytological and molecular markers in non-heading Chinese cabbage (Brassica rapa L.).

    Science.gov (United States)

    Heng, Shuangping; Shi, Dianyi; Hu, Zhenhua; Huang, Tao; Li, Jinping; Liu, Liyan; Xia, Chunxiu; Yuan, Zhenzhen; Xu, Yuejin; Fu, Tingdong; Wan, Zhengjie

    2015-09-01

    A new non-heading Chinese cabbage CMS line M119A was characterized and specific molecular markers were developed to classify different CMS types. One new non-heading Chinese cabbage (Brassica rapa L.) cytoplasmic male sterile (CMS) line M119A was obtained by interspecific crosses between the recently discovered hau CMS line of Brassica juncea and B. rapa. Furthermore, the line was characterized and compared with other five isonuclear-alloplasmic CMS lines. The M119A line produced six stamens without pollen and only two stamen fused together in fewer flowers. Tissue section indicated that anther abortion in M119A may have occurred during differentiation of the archesporial cells without pollen sac. All the six CMS lines were grouped into three types based on the presence of three PCR fragments of 825, 465 and 772 bp amplified with different mitochondrial genes specific primers. The 825-bp fragment was amplified both in 09-10A and H201A using the specific primer pair P-orf224-atp6, and showed 100 % identity with the mitochondrial gene of pol CMS. The 465-bp fragment was amplified in 30A and 105A using the primer pair P-orf138 and shared 100 % identity with the mitochondrial gene of ogu CMS. The 772-bp fragment was amplified in M119A and H203A using the primer pair P-orf288 and showed 100 % identity with the mitochondrial gene of hau CMS. Therefore, these markers could efficiently distinguish different types of isonuclear-alloplasmic CMS lines of non-heading Chinese cabbage, which were useful for improving the efficiency of cross-breeding and heterosis utilization in cruciferous vegetables.

  10. VizieR Online Data Catalog: Molecular clouds with GLIMPSE/MIPSGAL data (Retes-Romero+, 2017)

    Science.gov (United States)

    Retes-Romero, R.; Mayya, Y. D.; Luna, A.; Carrasco, L.

    2017-11-01

    All of the 12 selected molecular clouds have GLIMPSE and MIPSGAL public data available. Typical Spitzer RGB images (3.6um, 8.0um, and 24um) of the resulting sample of clouds are shown in Figure 1, where the position of the IRAS source is identified. In order to define the parent molecular cloud that harbors the high-mass star-forming regions, we used 13CO(J=1-0) emission data from the Galactic Ring Survey (GRS) database (Jackson+ 2006ApJS..163..145J). The survey data have a velocity resolution of 0.21km/s, a typical (1σ) rms sensitivity of ~0.13K, a main beam efficiency of {eta}mb=0.48, and a beam of 46". The 13CO emission spectra for the line of sight (LOS) to the selected IRAS sources are shown in Figure 2, where the observed velocity of the CS(J=2-1) emission line (Bronfman+ 1996, J/A+AS/115/81) is also marked. (3 data files).

  11. Identifying yield-optimizing environments for two cowpea breeding lines by manipulating photoperiod and harvest scenario

    Science.gov (United States)

    Ohler, T. A.; Mitchell, C. A.

    1996-01-01

    Photoperiod and harvest scenario of cowpea (Vigna unguiculata L. Walp) canopies were manipulated to optimize productivity for use in future controlled ecological life-support systems. Productivity was measured by edible yield rate (EYR:g m-2 day-1), shoot harvest index (SHI: g edible biomass [g total shoot dry weight]), and yield-efficiency rate (YER:g edible biomass m-2 day-1 per[g nonedible shoot dry weight]). Breeding lines 'IT84S-2246' (S-2246) and "IT82D-889' (D-889) were grown in a greenhouse under 8-, 12-, or 24-h photoperiods. S-2246 was short-day and D-889 was day-neutral for flowering. Under each photoperiod, cowpeas were harvested either for leaves only, seeds only, or leaves plus seeds (mixed harvest). Photoperiod did not affect EYR of either breeding line for any harvest scenario tested. Averaged over both breeding lines, seed harvest gave the highest EYR at 6.7 g m-2 day-1. The highest SHI (65%) and YER (94 mg m-2 day-1 g-1) were achieved for leaf-only harvest of D-889 under an 8-h photoperiod. For leaf-only harvest of S-2246, both SHI and YER increased with increasing photoperiod, but declined for seed-only and mixed harvests. However, photoperiod had no effect on SHI or YER for D-889 for any harvest scenario. A second experiment utilized the short-day cowpea breeding line 'IT89KD-288' (D-288) and the day-neutral breeding line 'IT87D-941-1' (D-941) to compare yield parameters using photoperiod extension under differing lamp types. This experiment confirmed the photoperiod responses of D-889 and S-2246 to a mixed-harvest scenario and indicated that daylength extension with higher irradiance from high pressure sodium lamps further suppressed EYR, SHI, and YER of the short-day breeding line D-288.

  12. Parallel mRNA, proteomics and miRNA expression analysis in cell line models of the intestine.

    Science.gov (United States)

    O'Sullivan, Finbarr; Keenan, Joanne; Aherne, Sinead; O'Neill, Fiona; Clarke, Colin; Henry, Michael; Meleady, Paula; Breen, Laura; Barron, Niall; Clynes, Martin; Horgan, Karina; Doolan, Padraig; Murphy, Richard

    2017-11-07

    To identify miRNA-regulated proteins differentially expressed between Caco2 and HT-29: two principal cell line models of the intestine. Exponentially growing Caco-2 and HT-29 cells were harvested and prepared for mRNA, miRNA and proteomic profiling. mRNA microarray profiling analysis was carried out using the Affymetrix GeneChip Human Gene 1.0 ST array. miRNA microarray profiling analysis was carried out using the Affymetrix Genechip miRNA 3.0 array. Quantitative Label-free LC-MS/MS proteomic analysis was performed using a Dionex Ultimate 3000 RSLCnano system coupled to a hybrid linear ion trap/Orbitrap mass spectrometer. Peptide identities were validated in Proteome Discoverer 2.1 and were subsequently imported into Progenesis QI software for further analysis. Hierarchical cluster analysis for all three parallel datasets (miRNA, proteomics, mRNA) was conducted in the R software environment using the Euclidean distance measure and Ward's clustering algorithm. The prediction of miRNA and oppositely correlated protein/mRNA interactions was performed using TargetScan 6.1. GO biological process, molecular function and cellular component enrichment analysis was carried out for the DE miRNA, protein and mRNA lists via the Pathway Studio 11.3 Web interface using their Mammalian database. Differential expression (DE) profiling comparing the intestinal cell lines HT-29 and Caco-2 identified 1795 Genes, 168 Proteins and 160 miRNAs as DE between the two cell lines. At the gene level, 1084 genes were upregulated and 711 were downregulated in the Caco-2 cell line relative to the HT-29 cell line. At the protein level, 57 proteins were found to be upregulated and 111 downregulated in the Caco-2 cell line relative to the HT-29 cell line. Finally, at the miRNAs level, 104 were upregulated and 56 downregulated in the Caco-2 cell line relative to the HT-29 cell line. Gene ontology (GO) analysis of the DE mRNA identified cell adhesion, migration and ECM organization, cellular lipid

  13. Identification of genes associated with cisplatin resistance in human oral squamous cell carcinoma cell line

    International Nuclear Information System (INIS)

    Zhang, Ping; Zhang, Zhiyuan; Zhou, Xiaojian; Qiu, Weiliu; Chen, Fangan; Chen, Wantao

    2006-01-01

    Cisplatin is widely used for chemotherapy of head and neck squamous cell carcinoma. However, details of the molecular mechanism responsible for cisplatin resistance are still unclear. The aim of this study was to identify the expression of genes related to cisplatin resistance in oral squamous cell carcinoma cells. A cisplatin-resistant cell line, Tca/cisplatin, was established from a cisplatin-sensitive cell line, Tca8113, which was derived from moderately-differentiated tongue squamous cell carcinoma. Global gene expression in this resistant cell line and its sensitive parent cell line was analyzed using Affymetrix HG-U95Av2 microarrays. Candidate genes involved in DNA repair, the MAP pathway and cell cycle regulation were chosen to validate the microarray analysis results. Cell cycle distribution and apoptosis following cisplatin exposure were also investigated. Cisplatin resistance in Tca/cisplatin cells was stable for two years in cisplatin-free culture medium. The IC50 for cisplatin in Tca/cisplatin was 6.5-fold higher than that in Tca8113. Microarray analysis identified 38 genes that were up-regulated and 25 that were down-regulated in this cell line. Some were novel candidates, while others are involved in well-characterized mechanisms that could be relevant to cisplatin resistance, such as RECQL for DNA repair and MAP2K6 in the MAP pathway; all the genes were further validated by Real-time PCR. The cell cycle-regulated genes CCND1 and CCND3 were involved in cisplatin resistance; 24-hour exposure to 10 μM cisplatin induced a marked S phase block in Tca/cisplatin cells but not in Tca8113 cells. The Tca8113 cell line and its stable drug-resistant variant Tca/cisplatin provided a useful model for identifying candidate genes responsible for the mechanism of cisplatin resistance in oral squamous cell carcinoma. Our data provide a useful basis for screening candidate targets for early diagnosis and further intervention in cisplatin resistance

  14. Identification of genes associated with cisplatin resistance in human oral squamous cell carcinoma cell line

    Directory of Open Access Journals (Sweden)

    Zhang Ping

    2006-09-01

    Full Text Available Abstract Background Cisplatin is widely used for chemotherapy of head and neck squamous cell carcinoma. However, details of the molecular mechanism responsible for cisplatin resistance are still unclear. The aim of this study was to identify the expression of genes related to cisplatin resistance in oral squamous cell carcinoma cells. Methods A cisplatin-resistant cell line, Tca/cisplatin, was established from a cisplatin-sensitive cell line, Tca8113, which was derived from moderately-differentiated tongue squamous cell carcinoma. Global gene expression in this resistant cell line and its sensitive parent cell line was analyzed using Affymetrix HG-U95Av2 microarrays. Candidate genes involved in DNA repair, the MAP pathway and cell cycle regulation were chosen to validate the microarray analysis results. Cell cycle distribution and apoptosis following cisplatin exposure were also investigated. Results Cisplatin resistance in Tca/cisplatin cells was stable for two years in cisplatin-free culture medium. The IC50 for cisplatin in Tca/cisplatin was 6.5-fold higher than that in Tca8113. Microarray analysis identified 38 genes that were up-regulated and 25 that were down-regulated in this cell line. Some were novel candidates, while others are involved in well-characterized mechanisms that could be relevant to cisplatin resistance, such as RECQL for DNA repair and MAP2K6 in the MAP pathway; all the genes were further validated by Real-time PCR. The cell cycle-regulated genes CCND1 and CCND3 were involved in cisplatin resistance; 24-hour exposure to 10 μM cisplatin induced a marked S phase block in Tca/cisplatin cells but not in Tca8113 cells. Conclusion The Tca8113 cell line and its stable drug-resistant variant Tca/cisplatin provided a useful model for identifying candidate genes responsible for the mechanism of cisplatin resistance in oral squamous cell carcinoma. Our data provide a useful basis for screening candidate targets for early diagnosis

  15. In Vivo Detection of HSP90 Identifies Breast Cancers with Aggressive Behavior.

    Science.gov (United States)

    Osada, Takuya; Kaneko, Kensuke; Gwin, William R; Morse, Michael A; Hobeika, Amy; Pogue, Brian W; Hartman, Zachary C; Hughes, Philip F; Haystead, Timothy; Lyerly, H Kim

    2017-12-15

    Purpose: Hsp90, a chaperone to numerous molecular pathways in malignant cells, is elevated in aggressive breast cancers. We hypothesized that identifying breast cells with elevated Hsp90 activity in situ could result in early detection of aggressive breast cancers. Experimental Design: We exploited the uptake of an Hsp90 inhibitor by malignant cells to create an imaging probe (HS131) of Hsp90 activity by linking it to a near-infrared (nIR) dye. HS131 uptake into cells correlated with cell membrane expression of Hsp90 and was used to image molecular subtypes of murine and human breast cancers in vitro and in murine models. Results: HS131 imaging was both sensitive and specific in detecting the murine 4T1 breast cancer cell line, as well as subclones with differing metastatic potential. Highly metastatic subclones (4T07) had high HS131 uptake, but subclones with lower metastatic potential (67NR, 168FARN) had low HS131 uptake. We generated isogenic cell lines to demonstrate that overexpression of a variety of specific oncogenes resulted in high HS131 uptake and retention. Finally, we demonstrated that HS131 could be used to detect spontaneous tumors in MMTV-neu mice, as well as primary and metastatic human breast cancer xenografts. HS131 could image invasive lobular breast cancer, a histologic subtype of breast cancer which is often undetectable by mammography. Conclusions: An HSP90-targeting nIR probe is sensitive and specific in imaging all molecular subtypes of murine and human breast cancer, with higher uptake in aggressive and highly metastatic clones. Clinical studies with Hsp90-targeting nIR probes will be initiated shortly. Clin Cancer Res; 23(24); 7531-42. ©2017 AACR . ©2017 American Association for Cancer Research.

  16. Antiproliferative/cytotoxic effects of molecular iodine, povidone-iodine and Lugol's solution in different human carcinoma cell lines.

    Science.gov (United States)

    Rösner, Harald; Möller, Wolfgang; Groebner, Sabine; Torremante, Pompilio

    2016-09-01

    Clinical trials have revealed that molecular iodine (I 2 ) has beneficial effects in fibrocystic breast disease and in cyclic mastalgia. Likewise, povidone-iodine (PVP-I), which is widely used in clinical practice as an antiseptic agent following tumour surgery, has been demonstrated to have cytotoxic effects on colon cancer and ascites tumour cells. Our previous study indicated that the growth of breast cancer and seven other human malignant cell lines was variably diminished by I 2 and iodolactones. With the intention of developing an iodine-based anticancer therapy, the present investigations extended these studies by comparing the cytotoxic capacities of I 2 , potassium iodide (KJ), PVP-I and Lugol's solution on various human carcinoma cell lines. Upon staining the cell nuclei with Hoechst 33342, the cell densities were determined microscopically. While KJ alone did not affect cell proliferation, it enhanced the antiproliferative activity of I 2 . In addition, PVP-I significantly inhibited the proliferation of human MCF-7 breast carcinoma, IPC melanoma, and A549 and H1299 lung carcinoma cells in a concentration corresponding to 20 µM I 2 . Likewise, Lugol's solution in concentrations corresponding to 20-80 µM I 2 were observed to reduce the growth of MCF-7 cells. Experiments with fresh human blood samples revealed that the antiproliferative activity of PVP-I and I 2 is preserved in blood plasma to a high degree. These findings suggest that PVP-I, Lugol's solution, and a combination of iodide and I 2 may be potent agents for use in the development of antitumour strategies.

  17. Molecular profiling of appendiceal epithelial tumors using massively parallel sequencing to identify somatic mutations.

    Science.gov (United States)

    Liu, Xiaoying; Mody, Kabir; de Abreu, Francine B; Pipas, J Marc; Peterson, Jason D; Gallagher, Torrey L; Suriawinata, Arief A; Ripple, Gregory H; Hourdequin, Kathryn C; Smith, Kerrington D; Barth, Richard J; Colacchio, Thomas A; Tsapakos, Michael J; Zaki, Bassem I; Gardner, Timothy B; Gordon, Stuart R; Amos, Christopher I; Wells, Wendy A; Tsongalis, Gregory J

    2014-07-01

    Some epithelial neoplasms of the appendix, including low-grade appendiceal mucinous neoplasm and adenocarcinoma, can result in pseudomyxoma peritonei (PMP). Little is known about the mutational spectra of these tumor types and whether mutations may be of clinical significance with respect to therapeutic selection. In this study, we identified somatic mutations using the Ion Torrent AmpliSeq Cancer Hotspot Panel v2. Specimens consisted of 3 nonneoplastic retention cysts/mucocele, 15 low-grade mucinous neoplasms (LAMNs), 8 low-grade/well-differentiated mucinous adenocarcinomas with pseudomyxoma peritonei, and 12 adenocarcinomas with/without goblet cell/signet ring cell features. Barcoded libraries were prepared from up to 10 ng of extracted DNA and multiplexed on single 318 chips for sequencing. Data analysis was performed using Golden Helix SVS. Variants that remained after the analysis pipeline were individually interrogated using the Integrative Genomics Viewer. A single Janus kinase 3 (JAK3) mutation was detected in the mucocele group. Eight mutations were identified in the V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) and GNAS complex locus (GNAS) genes among LAMN samples. Additional gene mutations were identified in the AKT1 (v-akt murine thymoma viral oncogene homolog 1), APC (adenomatous polyposis coli), JAK3, MET (met proto-oncogene), phosphatidylinositol-4,5-bisphosphate 3-kinase (PIK3CA), RB1 (retinoblastoma 1), STK11 (serine/threonine kinase 11), and tumor protein p53 (TP53) genes. Among the PMPs, 6 mutations were detected in the KRAS gene and also in the GNAS, TP53, and RB1 genes. Appendiceal cancers showed mutations in the APC, ATM (ataxia telangiectasia mutated), KRAS, IDH1 [isocitrate dehydrogenase 1 (NADP+)], NRAS [neuroblastoma RAS viral (v-ras) oncogene homolog], PIK3CA, SMAD4 (SMAD family member 4), and TP53 genes. Our results suggest molecular heterogeneity among epithelial tumors of the appendix. Next generation sequencing efforts

  18. Genetic inactivation of the Fanconi anemia gene FANCC identified in the hepatocellular carcinoma cell line HuH-7 confers sensitivity towards DNA-interstrand crosslinking agents

    Directory of Open Access Journals (Sweden)

    Bassermann Florian

    2010-05-01

    Full Text Available Abstract Background Inactivation of the Fanconi anemia (FA pathway through defects in one of 13 FA genes occurs at low frequency in various solid cancer entities among the general population. As FA pathway inactivation confers a distinct hypersensitivity towards DNA interstrand-crosslinking (ICL-agents, FA defects represent rational targets for individualized therapeutic strategies. Except for pancreatic cancer, however, the prevalence of FA defects in gastrointestinal (GI tumors has not yet been systematically explored. Results A panel of GI cancer cell lines was screened for FA pathway inactivation applying FANCD2 monoubiquitination and FANCD2/RAD51 nuclear focus formation and a newly identified FA pathway-deficient cell line was functionally characterized. The hepatocellular carcinoma (HCC line HuH-7 was defective in FANCD2 monoubiquitination and FANCD2 nuclear focus formation but proficient in RAD51 focus formation. Gene complementation studies revealed that this proximal FA pathway inactivation was attributable to defective FANCC function in HuH-7 cells. Accordingly, a homozygous inactivating FANCC nonsense mutation (c.553C > T, p.R185X was identified in HuH-7, resulting in partial transcriptional skipping of exon 6 and leading to the classic cellular FA hypersensitivity phenotype; HuH-7 cells exhibited a strongly reduced proliferation rate and a pronounced G2 cell cycle arrest at distinctly lower concentrations of ICL-agents than a panel of non-isogenic, FA pathway-proficient HCC cell lines. Upon retroviral transduction of HuH-7 cells with FANCC cDNA, FA pathway functions were restored and ICL-hypersensitivity abrogated. Analyses of 18 surgical HCC specimens yielded no further examples for genetic or epigenetic inactivation of FANCC, FANCF, or FANCG in HCC, suggesting a low prevalence of proximal FA pathway inactivation in this tumor type. Conclusions As the majority of HCC are chemoresistant, assessment of FA pathway function in HCC could

  19. Antimycobacterial drug discovery using Mycobacteria-infected amoebae identifies anti-infectives and new molecular targets.

    Science.gov (United States)

    Trofimov, Valentin; Kicka, Sébastien; Mucaria, Sabrina; Hanna, Nabil; Ramon-Olayo, Fernando; Del Peral, Laura Vela-Gonzalez; Lelièvre, Joël; Ballell, Lluís; Scapozza, Leonardo; Besra, Gurdyal S; Cox, Jonathan A G; Soldati, Thierry

    2018-03-02

    Tuberculosis remains a serious threat to human health world-wide, and improved efficiency of medical treatment requires a better understanding of the pathogenesis and the discovery of new drugs. In the present study, we performed a whole-cell based screen in order to complete the characterization of 168 compounds from the GlaxoSmithKline TB-set. We have established and utilized novel previously unexplored host-model systems to characterize the GSK compounds, i.e. the amoeboid organisms D. discoideum and A. castellanii, as well as a microglial phagocytic cell line, BV2. We infected these host cells with Mycobacterium marinum to monitor and characterize the anti-infective activity of the compounds with quantitative fluorescence measurements and high-content microscopy. In summary, 88.1% of the compounds were confirmed as antibiotics against M. marinum, 11.3% and 4.8% displayed strong anti-infective activity in, respectively, the mammalian and protozoan infection models. Additionally, in the two systems, 13-14% of the compounds displayed pro-infective activity. Our studies underline the relevance of using evolutionarily distant pathogen and host models in order to reveal conserved mechanisms of virulence and defence, respectively, which are potential "universal" targets for intervention. Subsequent mechanism of action studies based on generation of over-expresser M. bovis BCG strains, generation of spontaneous resistant mutants and whole genome sequencing revealed four new molecular targets, including FbpA, MurC, MmpL3 and GlpK.

  20. Contact Line Dynamics

    Science.gov (United States)

    Kreiss, Gunilla; Holmgren, Hanna; Kronbichler, Martin; Ge, Anthony; Brant, Luca

    2017-11-01

    The conventional no-slip boundary condition leads to a non-integrable stress singularity at a moving contact line. This makes numerical simulations of two-phase flow challenging, especially when capillarity of the contact point is essential for the dynamics of the flow. We will describe a modeling methodology, which is suitable for numerical simulations, and present results from numerical computations. The methodology is based on combining a relation between the apparent contact angle and the contact line velocity, with the similarity solution for Stokes flow at a planar interface. The relation between angle and velocity can be determined by theoretical arguments, or from simulations using a more detailed model. In our approach we have used results from phase field simulations in a small domain, but using a molecular dynamics model should also be possible. In both cases more physics is included and the stress singularity is removed.

  1. Observation of visible emission from the molecular helium ion in the afterglow of a dense helium Z-pinch plasma

    International Nuclear Information System (INIS)

    Tucker, J.E.; Brake, M.L.; Gilgenbach, R.M.

    1986-01-01

    The authors present the results of axial and radial time resolved visible emission spectroscopy from the afterglow of a dense helium Z-pinch. These results show that the visible emissions in the pinch afterglow are dominated by line emissions from molecular helium and He II. Axial spectroscopy measurements show the occurrence of several absorption bands which cannot be identified as molecular or atomic helium nor impurities from the discharge chamber materials. The authors believe that these absorption bands are attributable to the molecular helium ion which is present in the discharge. The molecular ion has been observed by others in low pressure and temperature helium discharges directly by means of mass spectrometry and indirectly by the presence of helium atoms in the 2/sup 3/S state, (the He 2/sup 3/S state is believed to result from molecular helium ion recombination). However, the molecular helium ion has not previously been observed spectroscopically

  2. New sources of soybean seed meal and oil composition traits identified through TILLING

    Directory of Open Access Journals (Sweden)

    Bilyeu Kristin D

    2009-07-01

    Full Text Available Abstract Background Several techniques are available to study gene function, but many are less than ideal for soybean. Reverse genetics, a relatively new approach, can be utilized to identify novel mutations in candidate genes; this technique has not produced an allelic variant with a confirmed phenotype in soybean. Soybean raffinose synthase genes and microsomal omega-6 fatty acid desaturase genes were screened for novel alleles in mutagenized soybean populations. Results Four mutations in independent lines were identified in the raffinose synthase gene RS2; two mutations resulted in amino acid mutations and one resulted in an altered seed oligosaccharide phenotype. The resulting phenotype was an increase in seed sucrose levels as well as a decrease in both raffinose and stachyose seed oligosaccharide levels. Three mutations in independent lines were identified in the omega-6 fatty acid desaturase gene FAD2-1A; all three mutations resulted in missense amino acid mutations and one resulted in an altered seed fatty acid profile that led to an increase in oleic acid and a decrease in linoleic acid in the seed oil. Conclusion The oligosaccharide phenotype controlled by the novel RS2 allele is similar to previously observed seed oligosaccharide phenotypes in RS2 mutant (PI 200508 allele-containing lines. Due to the anti-nutritional characteristics of raffinose and stachyose, this represents a positive change in seed composition. The fatty acid phenotype controlled by the novel FAD2-1A allele controls an increase in oleic acid in the seed oil, a phenotype also observed in a line previously characterized to have a null allele of the FAD2-1A gene. Molecular marker assays were developed to reliably detect the inheritance of the mutant alleles and can be used in efficient breeding for these desired seed phenotypes. Our results serve as the first demonstration of the identification of soybean mutants controlling seed phenotypes discovered through the

  3. Molecular transitions as probes of the physical conditions of extragalactic environments

    Science.gov (United States)

    Viti, Serena

    2017-11-01

    Aims: We present a method to interpret molecular observations and molecular line ratios in nearby extragalactic regions. Methods: Ab initio grids of time dependent chemical models, varying in gas density, temperature, cosmic ray ionization rate, and radiation field, are used as inputs into RADEX calculations. Tables of abundances, column densities, theoretical line intensities, and line ratios for some of the most used dense gas tracers are provided. The degree of correlation as well as degeneracy inherent in molecular ratios is discussed. Comparisons of the theoretical intensities with example observations are also provided. Results: We find that, within the parameters space explored, chemical abundances can be constrained by a well-defined set of gas density, gas temperature, and cosmic ray ionization rates for the species we investigate here. However, line intensities, and more importantly line ratios, from different chemical models can be very similar, thereby leading to a clear degeneracy. We also find that the gas subjected to a galactic cosmic ray ionization rate will not necessarily have reached steady state in 1 million years. The species most affected by time dependency effects are HCN and CS, which are both high density tracers. We use our ab initio method to fit an example set of data from two galaxies, I.e. M 82 and NGC 253. We find that (I) molecular line ratios can be easily matched even with erroneous individual line intensities; (II) no set of species can be matched by a one-component interstellar medium (ISM); and (III) a species may be a good tracer of an energetic process but only under specific density and temperature conditions. Conclusions: We provide tables of chemical abundances and line intensities ratios for some of the most commonly observed extragalactic tracers of dense gas for a grid of models. We show that by taking the chemistry behind each species and the individual line intensities into consideration, many degeneracies that arise

  4. Molecular line study of massive star-forming regions from the Red MSX Source survey

    Science.gov (United States)

    Yu, Naiping; Wang, Jun-Jie

    2014-05-01

    In this paper, we have selected a sample of massive star-forming regions from the Red MSX Source survey, in order to study star formation activities (mainly outflow and inflow signatures). We have focused on three molecular lines from the Millimeter Astronomy Legacy Team Survey at 90 GHz: HCO+(1-0), H13CO+(1-0) and SiO(2-1). According to previous observations, our sources can be divided into two groups: nine massive young stellar object candidates (radio-quiet) and 10 H II regions (which have spherical or unresolved radio emissions). Outflow activities have been found in 11 sources, while only three show inflow signatures in all. The high outflow detection rate means that outflows are common in massive star-forming regions. The inflow detection rate was relatively low. We suggest that this was because of the beam dilution of the telescope. All three inflow candidates have outflow(s). The outward radiation and thermal pressure from the central massive star(s) do not seem to be strong enough to halt accretion in G345.0034-00.2240. Our simple model of G318.9480-00.1969 shows that it has an infall velocity of about 1.8 km s-1. The spectral energy distribution analysis agrees our sources are massive and intermediate-massive star formation regions.

  5. MelanomaDB: a Web Tool for Integrative Analysis of Melanoma Genomic Information to Identify Disease-Associated Molecular Pathways

    Directory of Open Access Journals (Sweden)

    Alexander Joseph Trevarton

    2013-07-01

    Full Text Available Despite on-going research, metastatic melanoma survival rates remain low and treatment options are limited. Researchers can now access a rapidly growing amount of molecular and clinical information about melanoma. This information is becoming difficult to assemble and interpret due to its dispersed nature, yet as it grows it becomes increasingly valuable for understanding melanoma. Integration of this information into a comprehensive resource to aid rational experimental design and patient stratification is needed. As an initial step in this direction, we have assembled a web-accessible melanoma database, MelanomaDB, which incorporates clinical and molecular data from publically available sources, which will be regularly updated as new information becomes available. This database allows complex links to be drawn between many different aspects of melanoma biology: genetic changes (e.g. mutations in individual melanomas revealed by DNA sequencing, associations between gene expression and patient survival, data concerning drug targets, biomarkers, druggability and clinical trials, as well as our own statistical analysis of relationships between molecular pathways and clinical parameters that have been produced using these data sets. The database is freely available at http://genesetdb.auckland.ac.nz/melanomadb/about.html . A subset of the information in the database can also be accessed through a freely available web application in the Illumina genomic cloud computing platform BaseSpace at http://www.biomatters.com/apps/melanoma-profiler-for-research . This illustrates dysregulation of specific signalling pathways, both across 310 exome-sequenced melanomas and in individual tumours and identifies novel features about the distribution of somatic variants in melanoma. We suggest that this database can provide a context in which to interpret the tumour molecular profiles of individual melanoma patients relative to biological information and available

  6. High Temperature end of the socalled "Koga-line"

    DEFF Research Database (Denmark)

    Koga, Yoshikata; Westh, Peter; Atake, Tooru

    2009-01-01

    The so-called "Koga line" is a collection of the loci of anomalies in various third derivatives of the Gibbs function, G, in the temperature-mole fraction field for aqueous solutions of nonelectrolytes. This splits the H2O-rich region into two, in each of which the molecular organization and inte......The so-called "Koga line" is a collection of the loci of anomalies in various third derivatives of the Gibbs function, G, in the temperature-mole fraction field for aqueous solutions of nonelectrolytes. This splits the H2O-rich region into two, in each of which the molecular organization...... quantities from the former data showed step-type anomalies, while those from the latter negative peak-type anomalies. The loci of these anomalous points seem to point to about 70 degrees C at infinite dilution....

  7. Entrainment of Breast Cell Lines Results in Rhythmic Fluctuations of MicroRNAs

    Directory of Open Access Journals (Sweden)

    Rafael Chacolla-Huaringa

    2017-07-01

    Full Text Available Circadian rhythms are essential for temporal (~24 h regulation of molecular processes in diverse species. Dysregulation of circadian gene expression has been implicated in the pathogenesis of various disorders, including hypertension, diabetes, depression, and cancer. Recently, microRNAs (miRNAs have been identified as critical modulators of gene expression post-transcriptionally, and perhaps involved in circadian clock architecture or their output functions. The aim of the present study is to explore the temporal expression of miRNAs among entrained breast cell lines. For this purpose, we evaluated the temporal (28 h expression of 2006 miRNAs in MCF-10A, MCF-7, and MDA-MB-231 cells using microarrays after serum shock entrainment. We noted hundreds of miRNAs that exhibit rhythmic fluctuations in each breast cell line, and some of them across two or three cell lines. Afterwards, we validated the rhythmic profiles exhibited by miR-141-5p, miR-1225-5p, miR-17-5p, miR-222-5p, miR-769-3p, and miR-548ay-3p in the above cell lines, as well as in ZR-7530 and HCC-1954 using RT-qPCR. Our results show that serum shock entrainment in breast cells lines induces rhythmic fluctuations of distinct sets of miRNAs, which have the potential to be related to endogenous circadian clock, but extensive investigation is required to elucidate that connection.

  8. Cellular and molecular studies on ataxia-telangiectasia lymphoblastoid cell lines

    International Nuclear Information System (INIS)

    Fiorilli, M.; Crescenzi, M.; Carbonari, M.; Russo, G.; Businco, L.; Aiuti, F.

    1985-01-01

    We have examined several AT-related lesions in lymphoblastoid cell lines (LCLs) derived from AT patients. Diminished sensitivity to gamma-irradiation was found in six of seven AT-LCLs. A seventh line, from a patient with apparently normal T-cell immunity, responded normally following radiation. Constitutive proteins from exponentially growing AT-LCLs were assessed by SDS-PAGE analysis and did not differ significantly from normals. IgM synthesis was also normal except for one AT-LCL that contained native IgM molecules of different sizes, corresponding to the presence of pentamers and oligomers. Analysis under reducing conditions showed normal-sized secretory mu-chains. Finally, we examined mRNAs corresponding to two oncogenes, c-myc and c-myb, in AT and normal LCLs and found marked overproduction of c-myc in one AT-LCL (i.e., ATL6). The latter findings suggest that AT cells might be prone to aberrantly express cellular oncogenes as a result of chromosomal instability and consequent transposition of oncogenes

  9. Meta-Analysis of Placental Transcriptome Data Identifies a Novel Molecular Pathway Related to Preeclampsia.

    Directory of Open Access Journals (Sweden)

    Miranda van Uitert

    Full Text Available Studies using the placental transcriptome to identify key molecules relevant for preeclampsia are hampered by a relatively small sample size. In addition, they use a variety of bioinformatics and statistical methods, making comparison of findings challenging. To generate a more robust preeclampsia gene expression signature, we performed a meta-analysis on the original data of 11 placenta RNA microarray experiments, representing 139 normotensive and 116 preeclamptic pregnancies. Microarray data were pre-processed and analyzed using standardized bioinformatics and statistical procedures and the effect sizes were combined using an inverse-variance random-effects model. Interactions between genes in the resulting gene expression signature were identified by pathway analysis (Ingenuity Pathway Analysis, Gene Set Enrichment Analysis, Graphite and protein-protein associations (STRING. This approach has resulted in a comprehensive list of differentially expressed genes that led to a 388-gene meta-signature of preeclamptic placenta. Pathway analysis highlights the involvement of the previously identified hypoxia/HIF1A pathway in the establishment of the preeclamptic gene expression profile, while analysis of protein interaction networks indicates CREBBP/EP300 as a novel element central to the preeclamptic placental transcriptome. In addition, there is an apparent high incidence of preeclampsia in women carrying a child with a mutation in CREBBP/EP300 (Rubinstein-Taybi Syndrome. The 388-gene preeclampsia meta-signature offers a vital starting point for further studies into the relevance of these genes (in particular CREBBP/EP300 and their concomitant pathways as biomarkers or functional molecules in preeclampsia. This will result in a better understanding of the molecular basis of this disease and opens up the opportunity to develop rational therapies targeting the placental dysfunction causal to preeclampsia.

  10. Gone with the heat: a fundamental constraint on the imaging of dust and molecular gas in the early Universe.

    Science.gov (United States)

    Zhang, Zhi-Yu; Papadopoulos, Padelis P; Ivison, R J; Galametz, Maud; Smith, M W L; Xilouris, Emmanuel M

    2016-06-01

    Images of dust continuum and carbon monoxide (CO) line emission are powerful tools for deducing structural characteristics of galaxies, such as disc sizes, H2 gas velocity fields and enclosed H2 and dynamical masses. We report on a fundamental constraint set by the cosmic microwave background (CMB) on the observed structural and dynamical characteristics of galaxies, as deduced from dust continuum and CO-line imaging at high redshifts. As the CMB temperature rises in the distant Universe, the ensuing thermal equilibrium between the CMB and the cold dust and H2 gas progressively erases all spatial and spectral contrasts between their brightness distributions and the CMB. For high-redshift galaxies, this strongly biases the recoverable H2 gas and dust mass distributions, scale lengths, gas velocity fields and dynamical mass estimates. This limitation is unique to millimetre/submillimetre wavelengths and unlike its known effect on the global dust continuum and molecular line emission of galaxies, it cannot be addressed simply. We nevertheless identify a unique signature of CMB-affected continuum brightness distributions, namely an increasing rather than diminishing contrast between such brightness distributions and the CMB when the cold dust in distant galaxies is imaged at frequencies beyond the Raleigh-Jeans limit. For the molecular gas tracers, the same effect makes the atomic carbon lines maintain a larger contrast than the CO lines against the CMB.

  11. Atomic emission lines in the near ultraviolet; hydrogen through krypton, section 2

    Science.gov (United States)

    Kelly, R. L.

    1979-01-01

    A compilation of spectra from the first 36 elements was prepared from published literature available through October 1977. In most cases, only those lines which were actually observed in emission or absorption are listed. The wavelengths included range from 2000 Angstroms to 3200 Angstroms with some additional lines up to 3500 Angstroms. Only lines of stripped atoms are reported; no molecular bands are included.

  12. Atomic emission lines in the near ultraviolet; hydrogen through krypton, section 1

    Science.gov (United States)

    Kelly, R. L.

    1979-01-01

    A compilation of spectra from the first 36 elements was prepared from published literature available through October 1977. In most cases, only those lines which were actually observed in emission or absorption are listed. The wavelengths included range from 2000 Angstroms to 3200 Angstroms with some additional lines up to 3500 Angstroms. Only lines of stripped atoms are reported; no molecular bands are included.

  13. Molecular hydrogen emission from cold condensations in NGC 2440

    International Nuclear Information System (INIS)

    Reay, N.K.; Walton, N.A.

    1988-01-01

    Observations are reported of the ν = 1-0 S(1) line of molecular hydrogen in the high-excitation planetary nebula NGC 2440. The emission is particularly strong at the positions of the two bright condensations which lie well within the H II region and close to the position of the very hot T ≅ 350 000 K central star. The emission is consistent with an excited molecular hydrogen mass of ≅ 2-4 x 10 -5 solar mass in the condensations, and the total mass of excited molecular hydrogen associated with the H II region is estimated to be ≅ 6.1 x 10 -3 solar mass. We show that radiation pressure from the central star is insufficient to excite the S(1) line emission. (author)

  14. A transgenic mouse line for molecular genetic analysis of excitatory glutamatergic neurons

    DEFF Research Database (Denmark)

    Borgius, Lotta; Restrepo, C. Ernesto; Leao, Richardson N.

    2010-01-01

    Excitatory glutamatergic neurons are part of most of the neuronal circuits in the mammalian nervous system. We have used BAC-technology to generate a BAC-Vglut2::Cre mouse line where Cre expression is driven by the vesicular glutamate transporter 2 (Vglut2) promotor. This BAC-Vglut2::Cre mouse line...... showed specific expression of Cre in Vglut2 positive cells in the spinal cord with no ectopic expression in GABAergic or glycinergic neurons. This mouse line also showed specific Cre expression in Vglut2 positive structures in the brain such as thalamus, hypothalamus, superior colliculi, inferior...... colliculi and deep cerebellar nuclei together with nuclei in the midbrain and hindbrain. Cre-mediated recombination was restricted to Cre expressing cells in the spinal cord and brain and occurred as early as E 12.5. Known Vglut2 positive neurons showed normal electrophysiological properties in the BAC...

  15. Integration of molecular biology tools for identifying promoters and genes abundantly expressed in flowers of Oncidium Gower Ramsey

    Directory of Open Access Journals (Sweden)

    Tung Shu-Yun

    2011-04-01

    Full Text Available Abstract Background Orchids comprise one of the largest families of flowering plants and generate commercially important flowers. However, model plants, such as Arabidopsis thaliana do not contain all plant genes, and agronomic and horticulturally important genera and species must be individually studied. Results Several molecular biology tools were used to isolate flower-specific gene promoters from Oncidium 'Gower Ramsey' (Onc. GR. A cDNA library of reproductive tissues was used to construct a microarray in order to compare gene expression in flowers and leaves. Five genes were highly expressed in flower tissues, and the subcellular locations of the corresponding proteins were identified using lip transient transformation with fluorescent protein-fusion constructs. BAC clones of the 5 genes, together with 7 previously published flower- and reproductive growth-specific genes in Onc. GR, were identified for cloning of their promoter regions. Interestingly, 3 of the 5 novel flower-abundant genes were putative trypsin inhibitor (TI genes (OnTI1, OnTI2 and OnTI3, which were tandemly duplicated in the same BAC clone. Their promoters were identified using transient GUS reporter gene transformation and stable A. thaliana transformation analyses. Conclusions By combining cDNA microarray, BAC library, and bombardment assay techniques, we successfully identified flower-directed orchid genes and promoters.

  16. GARLIC - A general purpose atmospheric radiative transfer line-by-line infrared-microwave code: Implementation and evaluation

    Science.gov (United States)

    Schreier, Franz; Gimeno García, Sebastián; Hedelt, Pascal; Hess, Michael; Mendrok, Jana; Vasquez, Mayte; Xu, Jian

    2014-04-01

    A suite of programs for high resolution infrared-microwave atmospheric radiative transfer modeling has been developed with emphasis on efficient and reliable numerical algorithms and a modular approach appropriate for simulation and/or retrieval in a variety of applications. The Generic Atmospheric Radiation Line-by-line Infrared Code - GARLIC - is suitable for arbitrary observation geometry, instrumental field-of-view, and line shape. The core of GARLIC's subroutines constitutes the basis of forward models used to implement inversion codes to retrieve atmospheric state parameters from limb and nadir sounding instruments. This paper briefly introduces the physical and mathematical basics of GARLIC and its descendants and continues with an in-depth presentation of various implementation aspects: An optimized Voigt function algorithm combined with a two-grid approach is used to accelerate the line-by-line modeling of molecular cross sections; various quadrature methods are implemented to evaluate the Schwarzschild and Beer integrals; and Jacobians, i.e. derivatives with respect to the unknowns of the atmospheric inverse problem, are implemented by means of automatic differentiation. For an assessment of GARLIC's performance, a comparison of the quadrature methods for solution of the path integral is provided. Verification and validation are demonstrated using intercomparisons with other line-by-line codes and comparisons of synthetic spectra with spectra observed on Earth and from Venus.

  17. SPITZER MAPPING OF MOLECULAR HYDROGEN PURE ROTATIONAL LINES IN NGC 1333: A DETAILED STUDY OF FEEDBACK IN STAR FORMATION

    International Nuclear Information System (INIS)

    Maret, Sebastien; Bergin, Edwin A.; Neufeld, David A.; Sonnentrucker, Paule; Yuan Yuan; Green, Joel D.; Watson, Dan M.; Harwit, Martin O.; Kristensen, Lars E.; Melnick, Gary J.; Tolls, Volker; Werner, Michael W.; Willacy, Karen

    2009-01-01

    We present mid-infrared spectral maps of the NGC 1333 star-forming region, obtained with the infrared spectrometer on board the Spitzer Space Telescope. Eight pure H 2 rotational lines, from S(0) to S(7), are detected and mapped. The H 2 emission appears to be associated with the warm gas shocked by the multiple outflows present in the region. A comparison between the observed intensities and the predictions of detailed shock models indicates that the emission arises in both slow (12-24 km s -1 ) and fast (36-53 km s -1 ) C-type shocks with an initial ortho-to-para ratio (opr) ∼ 2 opr exhibits a large degree of spatial variations. In the postshocked gas, it is usually about 2, i.e., close to the equilibrium value (∼3). However, around at least two outflows, we observe a region with a much lower (∼0.5) opr. This region probably corresponds to gas which has been heated up recently by the passage of a shock front, but whose ortho-to-para has not reached equilibrium yet. This, together with the low initial opr needed to reproduce the observed emission, provide strong evidence that H 2 is mostly in para form in cold molecular clouds. The H 2 lines are found to contribute to 25%-50% of the total outflow luminosity, and thus can be used to ascertain the importance of star formation feedback on the natal cloud. From these lines, we determine the outflow mass loss rate and, indirectly, the stellar infall rate, the outflow momentum and the kinetic energy injected into the cloud over the embedded phase. The latter is found to exceed the binding energy of individual cores, suggesting that outflows could be the main mechanism for core disruption.

  18. Photoelectron photoion molecular beam spectroscopy

    International Nuclear Information System (INIS)

    Trevor, D.J.

    1980-12-01

    The use of supersonic molecular beams in photoionization mass spectroscopy and photoelectron spectroscopy to assist in the understanding of photoexcitation in the vacuum ultraviolet is described. Rotational relaxation and condensation due to supersonic expansion were shown to offer new possibilities for molecular photoionization studies. Molecular beam photoionization mass spectroscopy has been extended above 21 eV photon energy by the use of Stanford Synchrotron Radiation Laboratory (SSRL) facilities. Design considerations are discussed that have advanced the state-of-the-art in high resolution vuv photoelectron spectroscopy. To extend gas-phase studies to 160 eV photon energy, a windowless vuv-xuv beam line design is proposed

  19. Analysis and functional annotation of expressed sequence tags from in vitro cell lines of elasmobranchs: Spiny dogfish shark (Squalus acanthias) and little skate (Leucoraja erinacea).

    Science.gov (United States)

    Parton, Angela; Bayne, Christopher J; Barnes, David W

    2010-09-01

    Elasmobranchs are the most commonly used experimental models among the jawed, cartilaginous fish (Chondrichthyes). Previously we developed cell lines from embryos of two elasmobranchs, Squalus acanthias the spiny dogfish shark (SAE line), and Leucoraja erinacea the little skate (LEE-1 line). From these lines cDNA libraries were derived and expressed sequence tags (ESTs) generated. From the SAE cell line 4303 unique transcripts were identified, with 1848 of these representing unknown sequences (showing no BLASTX identification). From the LEE-1 cell line, 3660 unique transcripts were identified, and unknown, unique sequences totaled 1333. Gene Ontology (GO) annotation showed that GO assignments for the two cell lines were in general similar. These results suggest that the procedures used to derive the cell lines led to isolation of cell types of the same general embryonic origin from both species. The LEE-1 transcripts included GO categories "envelope" and "oxidoreductase activity" but the SAE transcripts did not. GO analysis of SAE transcripts identified the category "anatomical structure formation" that was not present in LEE-1 cells. Increased organelle compartments may exist within LEE-1 cells compared to SAE cells, and the higher oxidoreductase activity in LEE-1 cells may indicate a role for these cells in responses associated with innate immunity or in steroidogenesis. These EST libraries from elasmobranch cell lines provide information for assembly of genomic sequences and are useful in revealing gene diversity, new genes and molecular markers, as well as in providing means for elucidation of full-length cDNAs and probes for gene array analyses. This is the first study of this type with members of the Chondrichthyes. Copyright 2010 Elsevier Inc. All rights reserved.

  20. Molecular Population Genetics.

    Science.gov (United States)

    Casillas, Sònia; Barbadilla, Antonio

    2017-03-01

    Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular population genetics has been revolutionized by progress in data acquisition and theoretical developments. The conceptual elegance of the neutral theory of molecular evolution or the footprint carved by natural selection on the patterns of genetic variation are two examples of the vast number of inspiring findings of population genetics research. Since the inception of the field, Drosophila has been the prominent model species: molecular variation in populations was first described in Drosophila and most of the population genetics hypotheses were tested in Drosophila species. In this review, we describe the main concepts, methods, and landmarks of molecular population genetics, using the Drosophila model as a reference. We describe the different genetic data sets made available by advances in molecular technologies, and the theoretical developments fostered by these data. Finally, we review the results and new insights provided by the population genomics approach, and conclude by enumerating challenges and new lines of inquiry posed by increasingly large population scale sequence data. Copyright © 2017 Casillas and Barbadilla.

  1. The Influence of LINE-1 and SINE Retrotransposons on Mammalian Genomes.

    Science.gov (United States)

    Richardson, Sandra R; Doucet, Aurélien J; Kopera, Huira C; Moldovan, John B; Garcia-Perez, José Luis; Moran, John V

    2015-04-01

    Transposable elements have had a profound impact on the structure and function of mammalian genomes. The retrotransposon Long INterspersed Element-1 (LINE-1 or L1), by virtue of its replicative mobilization mechanism, comprises ∼17% of the human genome. Although the vast majority of human LINE-1 sequences are inactive molecular fossils, an estimated 80-100 copies per individual retain the ability to mobilize by a process termed retrotransposition. Indeed, LINE-1 is the only active, autonomous retrotransposon in humans and its retrotransposition continues to generate both intra-individual and inter-individual genetic diversity. Here, we briefly review the types of transposable elements that reside in mammalian genomes. We will focus our discussion on LINE-1 retrotransposons and the non-autonomous Short INterspersed Elements (SINEs) that rely on the proteins encoded by LINE-1 for their mobilization. We review cases where LINE-1-mediated retrotransposition events have resulted in genetic disease and discuss how the characterization of these mutagenic insertions led to the identification of retrotransposition-competent LINE-1s in the human and mouse genomes. We then discuss how the integration of molecular genetic, biochemical, and modern genomic technologies have yielded insight into the mechanism of LINE-1 retrotransposition, the impact of LINE-1-mediated retrotransposition events on mammalian genomes, and the host cellular mechanisms that protect the genome from unabated LINE-1-mediated retrotransposition events. Throughout this review, we highlight unanswered questions in LINE-1 biology that provide exciting opportunities for future research. Clearly, much has been learned about LINE-1 and SINE biology since the publication of Mobile DNA II thirteen years ago. Future studies should continue to yield exciting discoveries about how these retrotransposons contribute to genetic diversity in mammalian genomes.

  2. Development of T. aestivum L.-H. californicum alien chromosome lines and assignment of homoeologous groups of Hordeum californicum chromosomes.

    Science.gov (United States)

    Fang, Yuhui; Yuan, Jingya; Wang, Zhangjun; Wang, Haiyan; Xiao, Jin; Yang, Zhixi; Zhang, Ruiqi; Qi, Zengjun; Xu, Weigang; Hu, Lin; Wang, Xiu-E

    2014-08-20

    Hordeum californicum (2n = 2x = 14, HH) is resistant to several wheat diseases and tolerant to lower nitrogen. In this study, a molecular karyotype of H. californicum chromosomes in the Triticum aestivum L. cv. Chinese Spring (CS)-H. californicum amphidiploid (2n = 6x = 56, AABBDDHH) was established. By genomic in situ hybridization (GISH) and multicolor fluorescent in situ hybridization (FISH) using repetitive DNA clones (pTa71, pTa794 and pSc119.2) as probes, the H. californicum chromosomes could be differentiated from each other and from the wheat chromosomes unequivocally. Based on molecular karyotype and marker analyses, 12 wheat-alien chromosome lines, including four disomic addition lines (DAH1, DAH3, DAH5 and DAH6), five telosomic addition lines (MtH7L, MtH1S, MtH1L, DtH6S and DtH6L), one multiple addition line involving H. californicum chromosome H2, one disomic substitution line (DSH4) and one translocation line (TH7S/1BL), were identified from the progenies derived from the crosses of CS-H. californicum amphidiploid with common wheat varieties. A total of 482 EST (expressed sequence tag) or SSR (simple sequence repeat) markers specific for individual H. californicum chromosomes were identified, and 47, 50, 45, 49, 21, 51 and 40 markers were assigned to chromosomes H1, H2, H3, H4, H5, H6 and H7, respectively. According to the chromosome allocation of these markers, chromosomes H2, H3, H4, H5, and H7 of H. californicum have relationship with wheat homoeologous groups 5, 2, 6, 3, and 1, and hence could be designated as 5H(c), 2H(c), 6H(c), 3H(c) and 1H(c), respectively. The chromosomes H1 and H6 were designated as 7H(c) and 4H(c), respectively, by referring to SSR markers located on rye chromosomes. Copyright © 2014 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved.

  3. Transcriptomic Profiling Reveals Complex Molecular Regulation in Cotton Genic Male Sterile Mutant Yu98-8A.

    Directory of Open Access Journals (Sweden)

    Weiping Fang

    Full Text Available Although cotton genic male sterility (GMS plays an important role in the utilization of hybrid vigor, its precise molecular mechanism remains unclear. To characterize the molecular events of pollen abortion, transcriptome analysis, combined with histological observations, was conducted in the cotton GMS line, Yu98-8A. A total of 2,412 genes were identified as significant differentially expressed genes (DEGs before and during the critical pollen abortion stages. Bioinformatics and biochemical analysis showed that the DEGs mainly associated with sugars and starch metabolism, oxidative phosphorylation, and plant endogenous hormones play a critical and complicated role in pollen abortion. These findings extend a better understanding of the molecular events involved in the regulation of pollen abortion in genic male sterile cotton, which may provide a foundation for further research studies on cotton heterosis breeding.

  4. Workshop on Radio Recombination Lines

    CERN Document Server

    1980-01-01

    Since their first detection 15 years ago, radio recombination lines from several elements have been observed in a wide variety of objects including HII regions, planetary nebulae, molecular clouds, the diffuse interstellar medium, and recently, other galaxies. The observations span almost the entire range from 0.1 to 100 GHz, and employ both single­ djsh and aperture synthesis techniques. The theory of radio recombination lines has also advanced strongly, to the point where it is perhaps one of the best-understood in astro­ physics. In a parallel development, it has become possible over the last decade to study these same highly-excited atoms in the laboratory; this work provides further confirmation of the theoretical framework. However there has been continuing controversy over the astrophysical interpre­ tation of radio recombination line observations, especially regarding the role of stimulated emission. A workshop was held in Ottawa on 24-25 August, 1979, bringing together many of the active scientist...

  5. The Curious Molecular Gas Conditions in a z=2.6 Radio-loud Quasar

    Science.gov (United States)

    Sharon, Chelsea; Riechers, Dominik A.; Kuk Leung, Tsz; Weiss, Axel; Walter, Fabian; Carilli, Chris; Kraiburg Knudsen, Kirsten; Hodge, Jacqueline

    2018-01-01

    Theoretical work suggests that AGN play an important role in quenching star formation in massive galaxies. In addition to molecular outflows observed in the local universe, emission from very high-J CO rotational transitions has been one of the key pieces of evidence for AGN directly affecting the molecular gas reservoirs that fuel star formation. However, very few observations of Jupper>9 transitions exist for galaxies in the early universe. Here we will present the peculiar molecular gas conditions in MG 0414+0534 (MG 0414 hereafter), one of the few high-z galaxies with very high-J CO detections. MG 0414 is a strongly lensed IR-bright radio-loud quasar with broad Hα emission at z=2.6390. We recently confirmed the CO(3–2) detection from Barvainis et al. (1998), but were unable to detect the CO(1–0) line. The 3σ lower limit on the 3–2/1–0 line ratio (in units of brightness temperature) is r3,1>5.72, which is significantly higher than the r3,1≤1 typical for thermalized optically thick emission in other z˜2–3 AGN host galaxies. In addition, the CO(11–10) line was detected to high significance using the Atacama Large Millimeter/submillimeter Array, and the CO(11–10) line FWHM is nearly double that of the CO(3–2) line. We will discuss possible explanations for the peculiar line ratios in MG 0414 (such as optically thin emission, molecular outflows, and differential lensing) and what the origin of these ratios imply for molecular gas observations of other high-z AGN host galaxies.

  6. Molecular diagnostics of Galactic star-formation regions

    Science.gov (United States)

    Loenen, Edo; Baan, Willem; Spaans, Marco

    2007-10-01

    We propose a sensitive spectral survey of Galactic star-formation regions. Using the broadband correlator at two different frequencies, we expect to detect the (1-0) transition of CO, CN, HNC, HCN, HCO+, and HCO and various of their isotopes lines, as well as the (12-11) and (10-9) transitions of HC3N. The purpose of these observations is to create a consistent (public) database of molecular emission from galactic star-formation regions. The data will be interpreted using extensive physical and chemical modeling of the whole ensemble of lines, in order to get an accurate description of the molecular environment of these regions. In particular, this diagnostic approach will describe the optical depths, the densities, and the radiation fields in the medium and will allow the establishment of dominant temperature gradients. These observations are part of a program to study molecular emission on all scales, going from individual Galactic star-formation regions, through resolved nearby galaxies, to unresolved extra-galactic emission.

  7. The carbon inventory in a quiescent, filamentary molecular cloud in G328

    International Nuclear Information System (INIS)

    Burton, Michael G.; Ashley, Michael C. B.; Braiding, Catherine; Storey, John W. V.; Kulesa, Craig; Hollenbach, David J.; Wolfire, Mark; Glück, Christian; Rowell, Gavin

    2014-01-01

    We present spectral line images of [C I] 809 GHz, CO J = 1-0 115 GHz and H I 1.4 GHz line emission, and calculate the corresponding C, CO and H column densities, for a sinuous, quiescent giant molecular cloud about 5 kpc distant along the l = 328° sightline (hereafter G328) in our Galaxy. The [C I] data comes from the High Elevation Antarctic Terahertz telescope, a new facility on the summit of the Antarctic plateau where the precipitable water vapor falls to the lowest values found on the surface of the Earth. The CO and H I data sets come from the Mopra and Parkes/ATCA telescopes, respectively. We identify a filamentary molecular cloud, ∼75 × 5 pc long with mass ∼4 × 10 4 M ☉ and a narrow velocity emission range of just 4 km s –1 . The morphology and kinematics of this filament are similar in CO, [C I], and H I, though in the latter appears as self-absorption. We calculate line fluxes and column densities for the three emitting species, which are broadly consistent with a photodissociation region model for a GMC exposed to the average interstellar radiation field. The [C/CO] abundance ratio averaged through the filament is found to be approximately unity. The G328 filament is constrained to be cold (T Dust < 20 K) by the lack of far-IR emission, to show no clear signs of star formation, and to only be mildly turbulent from the narrow line width. We suggest that it may represent a GMC shortly after formation, or perhaps still in the process of formation.

  8. The carbon inventory in a quiescent, filamentary molecular cloud in G328

    Energy Technology Data Exchange (ETDEWEB)

    Burton, Michael G.; Ashley, Michael C. B.; Braiding, Catherine; Storey, John W. V. [School of Physics, University of New South Wales, Sydney, NSW 2052 (Australia); Kulesa, Craig [Steward Observatory, The University of Arizona, 933 North Cherry Avenue, Tucson, AZ 85721 (United States); Hollenbach, David J. [Carl Sagan Center, SETI Institute, 189 Bernado Avenue, Mountain View, CA 94043-5203 (United States); Wolfire, Mark [Astronomy Department, University of Maryland, College Park, MD 20742 (United States); Glück, Christian [KOSMA, I. Physikalisches Institut, Universität zu Köln, Zülpicher Str. 77, D-50937 Köln (Germany); Rowell, Gavin, E-mail: m.burton@unsw.edu.au [School of Chemistry and Physics, University of Adelaide, Adelaide, SA 5005 (Australia)

    2014-02-20

    We present spectral line images of [C I] 809 GHz, CO J = 1-0 115 GHz and H I 1.4 GHz line emission, and calculate the corresponding C, CO and H column densities, for a sinuous, quiescent giant molecular cloud about 5 kpc distant along the l = 328° sightline (hereafter G328) in our Galaxy. The [C I] data comes from the High Elevation Antarctic Terahertz telescope, a new facility on the summit of the Antarctic plateau where the precipitable water vapor falls to the lowest values found on the surface of the Earth. The CO and H I data sets come from the Mopra and Parkes/ATCA telescopes, respectively. We identify a filamentary molecular cloud, ∼75 × 5 pc long with mass ∼4 × 10{sup 4} M {sub ☉} and a narrow velocity emission range of just 4 km s{sup –1}. The morphology and kinematics of this filament are similar in CO, [C I], and H I, though in the latter appears as self-absorption. We calculate line fluxes and column densities for the three emitting species, which are broadly consistent with a photodissociation region model for a GMC exposed to the average interstellar radiation field. The [C/CO] abundance ratio averaged through the filament is found to be approximately unity. The G328 filament is constrained to be cold (T {sub Dust} < 20 K) by the lack of far-IR emission, to show no clear signs of star formation, and to only be mildly turbulent from the narrow line width. We suggest that it may represent a GMC shortly after formation, or perhaps still in the process of formation.

  9. Stability of arsenic peptides in plant extracts: off-line versus on-line parallel elemental and molecular mass spectrometric detection for liquid chromatographic separation.

    Science.gov (United States)

    Bluemlein, Katharina; Raab, Andrea; Feldmann, Jörg

    2009-01-01

    The instability of metal and metalloid complexes during analytical processes has always been an issue of an uncertainty regarding their speciation in plant extracts. Two different speciation protocols were compared regarding the analysis of arsenic phytochelatin (As(III)PC) complexes in fresh plant material. As the final step for separation/detection both methods used RP-HPLC simultaneously coupled to ICP-MS and ES-MS. However, one method was the often used off-line approach using two-dimensional separation, i.e. a pre-cleaning step using size-exclusion chromatography with subsequent fraction collection and freeze-drying prior to the analysis using RP-HPLC-ICP-MS and/or ES-MS. This approach revealed that less than 2% of the total arsenic was bound to peptides such as phytochelatins in the root extract of an arsenate exposed Thunbergia alata, whereas the direct on-line method showed that 83% of arsenic was bound to peptides, mainly as As(III)PC(3) and (GS)As(III)PC(2). Key analytical factors were identified which destabilise the As(III)PCs. The low pH of the mobile phase (0.1% formic acid) using RP-HPLC-ICP-MS/ES-MS stabilises the arsenic peptide complexes in the plant extract as well as the free peptide concentration, as shown by the kinetic disintegration study of the model compound As(III)(GS)(3) at pH 2.2 and 3.8. But only short half-lives of only a few hours were determined for the arsenic glutathione complex. Although As(III)PC(3) showed a ten times higher half-life (23 h) in a plant extract, the pre-cleaning step with subsequent fractionation in a mobile phase of pH 5.6 contributes to the destabilisation of the arsenic peptides in the off-line method. Furthermore, it was found that during a freeze-drying process more than 90% of an As(III)PC(3) complex and smaller free peptides such as PC(2) and PC(3) can be lost. Although the two-dimensional off-line method has been used successfully for other metal complexes, it is concluded here that the fractionation and

  10. Molecular diagnosis of Rickettsia infection in patients from Tunisia.

    Science.gov (United States)

    Khrouf, Fatma; Sellami, Hanene; Elleuch, Emna; Hattab, Zouhour; Ammari, Lamia; Khalfaoui, Moncef; Souissi, Jihed; Harrabi, Hejer; M'ghirbi, Youmna; Tiouiri, Hanene; Ben Jemaa, Mounir; Hammami, Adnene; Letaief, Amel; Bouattour, Ali; Znazen, Abir

    2016-07-01

    Diagnosis of rickettsioses had largely benefited from the development of molecular techniques. Unfortunately, in Tunisia, despite the large number of rickettsial cases registered every year, the Rickettsia species remain unidentified. In this study, we aimed to detect the Rickettsia species in clinical samples using molecular tests. A study was established to analyze skin biopsies, cutaneous swabs, and cerebrospinal fluid samples taken from clinically suspected patients to have rickettsial infection. Two molecular techniques were used to detect Rickettsia DNA: quantitative real time PCR (qPCR) and reverse line blot test (RLB). An analysis of the RLB hybridization assay results revealed the presence of Rickettsia DNA in skin biopsies (40.6%) and swabs (46.7%). Rickettsia conorii was the most prevalent identified species among tested samples. Other species of interest include Rickettsia typhi and Rickettsia massiliae. Using qPCR positivity rates in skin biopsies was 63.7% against 80% in swabs. R. conorii was the most frequently detected species, followed by R. typhi. The agreement between the two techniques was 68.6% (kappa=0.33). Molecular tests, especially using specific probes qPCR, allow for a rapid, better and confident diagnosis in clinical practice. They improve the survey of Mediterranean spotted fever which is considered to be the most important rickettsial infection in humans in Tunisia. Copyright © 2016 Elsevier GmbH. All rights reserved.

  11. Effect of alkylglycerone phosphate synthase on the expression profile of circRNAs in the human thyroid cancer cell line FRO.

    Science.gov (United States)

    Hou, Shasha; Tan, Jian; Yang, Bing; He, Lu; Zhu, Yu

    2018-05-01

    Thyroid cancer is a common primary tumor in China. Therefore, it is important to investigate the underlying molecular mechanism of thyroid cancer in order to achieve effective individualized treatments. In our previous study, a positive correlation between the expression of alkylglycerone phosphate synthase (AGPS) and the malignant phenotype of thyroid cancer cell lines was identified. The inactivation of AGPS was able to decrease the malignancy of cancer, and inhibit tumor growth and invasion. However, the function of AGPS on thyroid cancer was unclear. In the present study, it was revealed that AGPS was able to regulate the expression of circular RNAs (circRNAs), which may be the mechanism of its anticancer activity. Therefore, the effects of AGPS silencing and knockout on circRNA expression in the thyroid cancer cell line FRO were investigated using circRNAs microarray, and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed in order to investigate the underlying molecular mechanism of AGPS for the regulation of thyroid cancer through circRNAs.

  12. ENU Mutagenesis in Mice Identifies Candidate Genes For Hypogonadism

    Science.gov (United States)

    Weiss, Jeffrey; Hurley, Lisa A.; Harris, Rebecca M.; Finlayson, Courtney; Tong, Minghan; Fisher, Lisa A.; Moran, Jennifer L.; Beier, David R.; Mason, Christopher; Jameson, J. Larry

    2012-01-01

    Genome-wide mutagenesis was performed in mice to identify candidate genes for male infertility, for which the predominant causes remain idiopathic. Mice were mutagenized using N-ethyl-N-nitrosourea (ENU), bred, and screened for phenotypes associated with the male urogenital system. Fifteen heritable lines were isolated and chromosomal loci were assigned using low density genome-wide SNP arrays. Ten of the fifteen lines were pursued further using higher resolution SNP analysis to narrow the candidate gene regions. Exon sequencing of candidate genes identified mutations in mice with cystic kidneys (Bicc1), cryptorchidism (Rxfp2), restricted germ cell deficiency (Plk4), and severe germ cell deficiency (Prdm9). In two other lines with severe hypogonadism candidate sequencing failed to identify mutations, suggesting defects in genes with previously undocumented roles in gonadal function. These genomic intervals were sequenced in their entirety and a candidate mutation was identified in SnrpE in one of the two lines. The line harboring the SnrpE variant retains substantial spermatogenesis despite small testis size, an unusual phenotype. In addition to the reproductive defects, heritable phenotypes were observed in mice with ataxia (Myo5a), tremors (Pmp22), growth retardation (unknown gene), and hydrocephalus (unknown gene). These results demonstrate that the ENU screen is an effective tool for identifying potential causes of male infertility. PMID:22258617

  13. Isolation and molecular cytogenetic characterization of a wheat - Leymus mollis double monosomic addition line and its progenies with resistance to stripe rust.

    Science.gov (United States)

    Yang, Xiaofei; Li, Xin; Wang, Changyou; Chen, Chunhuan; Tian, Zengrong; Ji, Wanquan

    2017-12-01

    A common wheat - Leymus mollis (2n = 4x = 28, NsNsXmXm) double monosomic addition line, M11003-4-3-8/13/15 (2n = 44 = 42T.a + L.m2 + L.m3), with stripe rust resistance was developed (where T.a represents Triticum aestivum chromosome, L.m represents L. mollis chromosome, and L.m2/3 represents L. mollis chromosome of homoeologous groups 2 and 3). The progenies of line M11003-4-3-8/13/15 were characterized by cytological observation, specific molecular markers, fluorescence in situ hybridization (FISH), and genomic in situ hybridization (GISH). Among the progenies, there existed five different types (I, II, III, IV, and V) of chromosome constitution, the formulas of which were 2n = 44 = 42T.a + 1L.m2 + 1L.m3, 2n = 43 = 42T.a + 1L.m2, 2n = 43 = 42T.a + 1L.m3, 2n = 42 = 42T.a, and 2n = 44 = 42T.a + 2L.m2, respectively. Field disease screening showed that types I and III showed high resistance to stripe rust, while types II, IV, and V were susceptible. Leymus mollis was almost immune to stripe rust, whereas the wheat parent, cultivar 7182, was susceptible. Therefore, we concluded that the stripe rust resistance originated from L. mollis. These various lines could be further fully exploited as important disease resistance materials to enrich wheat genetic resources.

  14. Lifetime broadening of atomic lines produced upon ultrafast dissociation of HCl and HBr

    Energy Technology Data Exchange (ETDEWEB)

    Lablanquie, P., E-mail: pascal.lablanquie@upmc.fr [Sorbonne Universités, UPMC Univ Paris 06, LCPMR, 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05 (France); CNRS, LCPMR (UMR 7614), 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05 (France); Iwayama, H. [UVSOR Facility, Institute for Molecular Science, Okazaki 444-8585 (Japan); Penent, F. [Sorbonne Universités, UPMC Univ Paris 06, LCPMR, 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05 (France); CNRS, LCPMR (UMR 7614), 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05 (France); Soejima, K. [Department of Environmental Science, Niigata University, Niigata 950-2181 (Japan); Shigemasa, E. [UVSOR Facility, Institute for Molecular Science, Okazaki 444-8585 (Japan)

    2014-08-15

    Highlights: • Ultrafast dissociation of HCl is triggered by 2p{sub 3/2} → σ* excitation. • Ultrafast dissociation of HBr is triggered by 3d{sub 5/2} → σ* excitation. • Photoelectron spectroscopy reveals sharp vibrational molecular lines and broad atomic lines. • The profiles of the atomic lines are analyzed in detail. • We extract the lifetime of the inner shell hole in the neutral atomic fragment. - Abstract: Ultrafast dissociation of the HCl and HBr molecules excited respectively to the 2p{sub 3/2} → σ* and 3d{sub 5/2} → σ* resonances are studied with high resolution photoelectron spectroscopy. Sharp vibrational molecular lines and broad atomic lines are observed. The analysis of the profile of the atomic lines gives access to the lifetimes of the inner shell 2p{sub 3/2} hole in the Cl* (2p{sub 3/2}){sup −1} 3s{sup 2}3p{sup 6} configuration, and the inner shell 3d{sub 5/2} hole in the Br* (3d{sub 5/2}){sup −1} 4s{sup 2}4p{sup 6} configuration.

  15. Application of a Reverse Line Blot hybridisation assay for the species-specific identification of cyathostomins (Nematoda, Strongylida) from benzimidazole-treated horses in the Slovak Republic.

    Science.gov (United States)

    Cernanská, Dana; Paoletti, Barbara; Králová-Hromadová, Ivica; Iorio, Raffaella; Cudeková, Patrícia; Milillo, Piermarino; Traversa, Donato

    2009-03-09

    Five horse farms located in eastern Slovakia were investigated for the presence of benzimidazole-resistant strongyles by faecal egg count reduction test and egg hatch assay. Coprocultures were prepared for each farm from faecal samples taken pre- and post-treatment and harvested larvae were molecularly examined with a Reverse Line Blot assay. Faecal egg count reduction values ranged from 0 to 52.5% and all farms were positive for benzimidazole-resistant cyathostomins. Seven benzimidazole-resistant cyathostomin species were molecularly identified on farms before and also after treatment. These data demonstrate that resistance to benzimidazoles is well established in cyathostomin populations from horse farms in the Slovak Republic and that the molecular assay was able to determine the species-specific distribution of resistant cyathostomins under field conditions.

  16. Novel human multiple myeloma cell line UHKT-893

    Czech Academy of Sciences Publication Activity Database

    Uherková, L.; Vančurová, I.; Vyhlídalová, I.; Pleschnerová, M.; Špička, I.; Mihalová, R.; Březinová, J.; Hodný, Zdeněk; Čermáková, K.; Polanská, V.; Marinov, I.; Jedelský, P.L.; Kuželová, K.; Stöckbauer, P.

    2013-01-01

    Roč. 37, č. 3 (2013), s. 320-326 ISSN 0145-2126 Institutional support: RVO:68378050 Keywords : human myeloma cell line * human multiple myeloma * plasma cell * IL-6 dependence * immunoglobulin * free light chain Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.692, year: 2013

  17. Survey of transmission line corridors. [Data on delays in transmission line construction

    Energy Technology Data Exchange (ETDEWEB)

    1979-01-05

    The intent of this study is to determine the extent of delays experienced in planning and constructing transmission lines in the continental United States. The reasons for the delays are identified for each line studied and their effect on the total electrical system is sought. Data was collected for 136 different lines either recently built or currently under study. Statistics were developed for each line in several categories and comparisons of lines delayed were made by company, area served and generation capacity. From the study presented here it was found that: right-of-way acquisition procedures including condemnation and easement negotiation practices delay more projects than local, state and federal regulatory requirements combined; load growth reductions particularly in the east have reduced the impact of regulatory delays; the south, southeast and southwestern areas of the country experience fewer delays in constructing transmission lines than the more populated states, and the cost for corridor delays was responded to for only 17 of the 142 projects surveyed. By far the most costly delay is the expense of condemning land for transmission right-of-way.

  18. Mechanisms to medicines: elucidating neural and molecular substrates of fear extinction to identify novel treatments for anxiety disorders.

    Science.gov (United States)

    Bukalo, Olena; Pinard, Courtney R; Holmes, Andrew

    2014-10-01

    The burden of anxiety disorders is growing, but the efficacy of available anxiolytic treatments remains inadequate. Cognitive behavioural therapy for anxiety disorders focuses on identifying and modifying maladaptive patterns of thinking and behaving, and has a testable analogue in rodents in the form of fear extinction. A large preclinical literature has amassed in recent years describing the neural and molecular basis of fear extinction in rodents. In this review, we discuss how this work is being harnessed to foster translational research on anxiety disorders and facilitate the search for new anxiolytic treatments. We begin by summarizing the anatomical and functional connectivity of a medial prefrontal cortex (mPFC)-amygdala circuit that subserves fear extinction, including new insights from optogenetics. We then cover some of the approaches that have been taken to model impaired fear extinction and associated impairments with mPFC-amygdala dysfunction. The principal goal of the review is to evaluate evidence that various neurotransmitter and neuromodulator systems mediate fear extinction by modulating the mPFC-amygdala circuitry. To that end, we describe studies that have tested how fear extinction is impaired or facilitated by pharmacological manipulations of dopamine, noradrenaline, 5-HT, GABA, glutamate, neuropeptides, endocannabinoids and various other systems, which either directly target the mPFC-amygdala circuit, or produce behavioural effects that are coincident with functional changes in the circuit. We conclude that there are good grounds to be optimistic that the progress in defining the molecular substrates of mPFC-amygdala circuit function can be effectively leveraged to identify plausible candidates for extinction-promoting therapies for anxiety disorders. © 2014 The British Pharmacological Society.

  19. Recent progress on the genetics and molecular breeding of brown planthopper resistance in rice.

    Science.gov (United States)

    Hu, Jie; Xiao, Cong; He, Yuqing

    2016-12-01

    Brown planthopper (BPH) is the most devastating pest of rice. Host-plant resistance is the most desirable and economic strategy in the management of BPH. To date, 29 major BPH resistance genes have been identified from indica cultivars and wild rice species, and more than ten genes have been fine mapped to chromosome regions of less than 200 kb. Four genes (Bph14, Bph26, Bph17 and bph29) have been cloned. The increasing number of fine-mapped and cloned genes provide a solid foundation for development of functional markers for use in breeding. Several BPH resistant introgression lines (ILs), near-isogenic lines (NILs) and pyramided lines (PLs) carrying single or multiple resistance genes were developed by marker assisted backcross breeding (MABC). Here we review recent progress on the genetics and molecular breeding of BPH resistance in rice. Prospect for developing cultivars with durable, broad-spectrum BPH resistance are discussed.

  20. Global Proteome Analysis of the NCI-60 Cell Line Panel

    Directory of Open Access Journals (Sweden)

    Amin Moghaddas Gholami

    2013-08-01

    Full Text Available The NCI-60 cell line collection is a very widely used panel for the study of cellular mechanisms of cancer in general and in vitro drug action in particular. It is a model system for the tissue types and genetic diversity of human cancers and has been extensively molecularly characterized. Here, we present a quantitative proteome and kinome profile of the NCI-60 panel covering, in total, 10,350 proteins (including 375 protein kinases and including a core cancer proteome of 5,578 proteins that were consistently quantified across all tissue types. Bioinformatic analysis revealed strong cell line clusters according to tissue type and disclosed hundreds of differentially regulated proteins representing potential biomarkers for numerous tumor properties. Integration with public transcriptome data showed considerable similarity between mRNA and protein expression. Modeling of proteome and drug-response profiles for 108 FDA-approved drugs identified known and potential protein markers for drug sensitivity and resistance. To enable community access to this unique resource, we incorporated it into a public database for comparative and integrative analysis (http://wzw.tum.de/proteomics/nci60.

  1. Genomic, Epigenomic, and Transcriptomic Profiling towards Identifying Omics Features and Specific Biomarkers That Distinguish Uterine Leiomyosarcoma and Leiomyoma at Molecular Levels

    Directory of Open Access Journals (Sweden)

    Tomoko Miyata

    2015-01-01

    Full Text Available Uterine leiomyosarcoma (LMS is the worst malignancy among the gynecologic cancers. Uterine leiomyoma (LM, a benign tumor of myometrial origin, is the most common among women of childbearing age. Because of their similar symptoms, it is difficult to preoperatively distinguish the two conditions only by ultrasound and pelvic MRI. While histopathological diagnosis is currently the main approach used to distinguish them postoperatively, unusual histologic variants of LM tend to be misdiagnosed as LMS. Therefore, development of molecular diagnosis as an alternative or confirmatory means will help to diagnose LMS more accurately. We adopted omics-based technologies to identify genome-wide features to distinguish LMS from LM and revealed that copy number, gene expression, and DNA methylation profiles successfully distinguished these tumors. LMS was found to possess features typically observed in malignant solid tumors, such as extensive chromosomal abnormalities, overexpression of cell cycle-related genes, hypomethylation spreading through large genomic regions, and frequent hypermethylation at the polycomb group target genes and protocadherin genes. We also identified candidate expression and DNA methylation markers, which will facilitate establishing postoperative molecular diagnostic tests based on conventional quantitative assays. Our results demonstrate the feasibility of establishing such tests and the possibility of developing preoperative and noninvasive methods.

  2. Molecular markers for identifying a new selected variety of Pacific white shrimp Litopenaeus vannamei

    Science.gov (United States)

    Yu, Yang; Zhang, Xiaojun; Liu, Jingwen; Li, Fuhua; Huang, Hao; Li, Yijun; Liu, Xiaolin; Xiang, Jianhai

    2015-01-01

    Selective breeding of the Pacific white shrimp Litopenaeus vannamei during the last decade has produced new varieties exhibiting high growth rates and disease resistance. However, the identification of new varieties of shrimps from their phenotypic characters is difficult. This study introduces a new approach for identifying varieties of shrimps using molecular markers of microsatellites and mitochondrial control region sequences. The method was employed to identify a new selected variety, Kehai No. 1 (KH-1), from three representative stocks (control group): Zhengda; Tongwei; and a stock collected from Fujian Province, which is now cultured in mainland China. By pooled genotyping of KH-1 and the control group, five microsatellites showing differences between KH-1 and the control group were screened out. Individual genotyping data confirmed the results from pooled genotyping. The genotyping data for the five microsatellites were applied to the assignment analysis of the KH-1 group and the control group using the partial Bayesian assignment method in GENECLASS2. By sequencing the mitochondrial control regions of individuals from the KH-1 and control group, four haplotypes were observed in the KH-1 group, whereas 14 haplotypes were obtained in the control group. By combining the microsatellite assignment analysis with mitochondrial control region analysis, the average accuracy of identification of individuals in the KH-1 group and control group reached 89%. The five selected microsatellite loci and mitochondrial control region sequences were highly polymorphic and could be used to distinguish new selected varieties of L. vannamei from other populations cultured in China.

  3. Molecular profiling of short-term and long-term surviving patients identifies CD34 mRNA level as prognostic for glioblastoma survival

    DEFF Research Database (Denmark)

    Michaelsen, Signe Regner; Urup, Thomas; Olsen, Lars Rønn

    2018-01-01

    Despite extensive treatment, overall survival (OS) for glioblastoma (GBM) remains poor. A small proportion of patients present long survival over 3 years, but the underlying molecular background separating these long-term survivors (LTS) from short-term survivors (STS) are insufficiently understood....... Accordingly, study aim was to identify independent prognostic biomarkers for survival. Study cohort consisted of 93 primary GBM patients treated with radiation-, chemo- and bevacizumab therapy, among which 14 STS (OS ≤ 12 months) and 6 LTS (OS ≥ 36 months) were identified, all confirmed being IDH wild......-type. RNA expression levels in diagnostic tumor specimen for 792 genes were analyzed by NanoString technology. While no differences were found with regard to GBM subtype between LTS versus STS, comparative analysis of individual genes identified 14 significantly differently expressed candidate genes...

  4. Gene expression signature analysis identifies vorinostat as a candidate therapy for gastric cancer.

    Directory of Open Access Journals (Sweden)

    Sofie Claerhout

    Full Text Available Gastric cancer continues to be one of the deadliest cancers in the world and therefore identification of new drugs targeting this type of cancer is thus of significant importance. The purpose of this study was to identify and validate a therapeutic agent which might improve the outcomes for gastric cancer patients in the future.Using microarray technology, we generated a gene expression profile of human gastric cancer-specific genes from human gastric cancer tissue samples. We used this profile in the Broad Institute's Connectivity Map analysis to identify candidate therapeutic compounds for gastric cancer. We found the histone deacetylase inhibitor vorinostat as the lead compound and thus a potential therapeutic drug for gastric cancer. Vorinostat induced both apoptosis and autophagy in gastric cancer cell lines. Pharmacological and genetic inhibition of autophagy however, increased the therapeutic efficacy of vorinostat, indicating that a combination of vorinostat with autophagy inhibitors may therapeutically be more beneficial. Moreover, gene expression analysis of gastric cancer identified a collection of genes (ITGB5, TYMS, MYB, APOC1, CBX5, PLA2G2A, and KIF20A whose expression was elevated in gastric tumor tissue and downregulated more than 2-fold by vorinostat treatment in gastric cancer cell lines. In contrast, SCGB2A1, TCN1, CFD, APLP1, and NQO1 manifested a reversed pattern.We showed that analysis of gene expression signature may represent an emerging approach to discover therapeutic agents for gastric cancer, such as vorinostat. The observation of altered gene expression after vorinostat treatment may provide the clue to identify the molecular mechanism of vorinostat and those patients likely to benefit from vorinostat treatment.

  5. Identifying clinically relevant drug resistance genes in drug-induced resistant cancer cell lines and post-chemotherapy tissues.

    Science.gov (United States)

    Tong, Mengsha; Zheng, Weicheng; Lu, Xingrong; Ao, Lu; Li, Xiangyu; Guan, Qingzhou; Cai, Hao; Li, Mengyao; Yan, Haidan; Guo, You; Chi, Pan; Guo, Zheng

    2015-12-01

    Until recently, few molecular signatures of drug resistance identified in drug-induced resistant cancer cell models can be translated into clinical practice. Here, we defined differentially expressed genes (DEGs) between pre-chemotherapy colorectal cancer (CRC) tissue samples of non-responders and responders for 5-fluorouracil and oxaliplatin-based therapy as clinically relevant drug resistance genes (CRG5-FU/L-OHP). Taking CRG5-FU/L-OHP as reference, we evaluated the clinical relevance of several types of genes derived from HCT116 CRC cells with resistance to 5-fluorouracil and oxaliplatin, respectively. The results revealed that DEGs between parental and resistant cells, when both were treated with the corresponding drug for a certain time, were significantly consistent with the CRG5-FU/L-OHP as well as the DEGs between the post-chemotherapy CRC specimens of responders and non-responders. This study suggests a novel strategy to extract clinically relevant drug resistance genes from both drug-induced resistant cell models and post-chemotherapy cancer tissue specimens.

  6. Global transcriptomic profiling of aspen trees under elevated [CO2] to identify potential molecular mechanisms responsible for enhanced radial growth.

    Science.gov (United States)

    Wei, Hairong; Gou, Jiqing; Yordanov, Yordan; Zhang, Huaxin; Thakur, Ramesh; Jones, Wendy; Burton, Andrew

    2013-03-01

    Aspen (Populus tremuloides) trees growing under elevated [CO(2)] at a free-air CO(2) enrichment (FACE) site produced significantly more biomass than control trees. We investigated the molecular mechanisms underlying the observed increase in biomass by producing transcriptomic profiles of the vascular cambium zone (VCZ) and leaves, and then performed a comparative study to identify significantly changed genes and pathways after 12 years exposure to elevated [CO(2)]. In leaves, elevated [CO(2)] enhanced expression of genes related to Calvin cycle activity and linked pathways. In the VCZ, the pathways involved in cell growth, cell division, hormone metabolism, and secondary cell wall formation were altered while auxin conjugation, ABA synthesis, and cytokinin glucosylation and degradation were inhibited. Similarly, the genes involved in hemicellulose and pectin biosynthesis were enhanced, but some genes that catalyze important steps in lignin biosynthesis pathway were inhibited. Evidence from systemic analysis supported the functioning of multiple molecular mechanisms that underpin the enhanced radial growth in response to elevated [CO(2)].

  7. Research on Line Patrol Strategy of 110kV Transmission Line after Lightning Strike

    Directory of Open Access Journals (Sweden)

    Li Mingjun

    2016-01-01

    Full Text Available Lightning faults occupy in the majority of instantaneous fault and reclosing can usually be successful, so power supply can be restored without immediate patrol in many cases. Firstly, this paper introduces the lightning fault positioning and identifying method. Then test electrical performance of insulators after lightning strike from 110kV lines. Data shows that lightning strike has little effect on the electric performance of insulator. Finally, illustrating disposal process of the 110 kV transmission line after lightning fault, certifying that the power supply reliability be ensured without line patrol.

  8. THE DETECTION OF A HOT MOLECULAR CORE IN THE LARGE MAGELLANIC CLOUD WITH ALMA

    International Nuclear Information System (INIS)

    Shimonishi, Takashi; Onaka, Takashi; Kawamura, Akiko; Aikawa, Yuri

    2016-01-01

    We report the first detection of a hot molecular core outside our Galaxy based on radio observations with ALMA toward a high-mass young stellar object (YSO) in a nearby low metallicity galaxy, the Large Magellanic Cloud (LMC). Molecular emission lines of CO, C 17 O, HCO + , H 13 CO + , H 2 CO, NO, SiO, H 2 CS, 33 SO, 32 SO 2 , 34 SO 2 , and 33 SO 2 are detected from a compact region (∼0.1 pc) associated with a high-mass YSO, ST11. The temperature of molecular gas is estimated to be higher than 100 K based on rotation diagram analysis of SO 2 and 34 SO 2 lines. The compact source size, warm gas temperature, high density, and rich molecular lines around a high-mass protostar suggest that ST11 is associated with a hot molecular core. We find that the molecular abundances of the LMC hot core are significantly different from those of Galactic hot cores. The abundances of CH 3 OH, H 2 CO, and HNCO are remarkably lower compared to Galactic hot cores by at least 1–3 orders of magnitude. We suggest that these abundances are characterized by the deficiency of molecules whose formation requires the hydrogenation of CO on grain surfaces. In contrast, NO shows a high abundance in ST11 despite the notably low abundance of nitrogen in the LMC. A multitude of SO 2 and its isotopologue line detections in ST11 imply that SO 2 can be a key molecular tracer of hot core chemistry in metal-poor environments. Furthermore, we find molecular outflows around the hot core, which is the second detection of an extragalactic protostellar outflow. In this paper, we discuss the physical and chemical characteristics of a hot molecular core in the low metallicity environment.

  9. Cartography of Pathway Signal Perturbations Identifies Distinct Molecular Pathomechanisms in Malignant and Chronic Lung Diseases

    Science.gov (United States)

    Arakelyan, Arsen; Nersisyan, Lilit; Petrek, Martin; Löffler-Wirth, Henry; Binder, Hans

    2016-01-01

    Lung diseases are described by a wide variety of developmental mechanisms and clinical manifestations. Accurate classification and diagnosis of lung diseases are the bases for development of effective treatments. While extensive studies are conducted toward characterization of various lung diseases at molecular level, no systematic approach has been developed so far. Here we have applied a methodology for pathway-centered mining of high throughput gene expression data to describe a wide range of lung diseases in the light of shared and specific pathway activity profiles. We have applied an algorithm combining a Pathway Signal Flow (PSF) algorithm for estimation of pathway activity deregulation states in lung diseases and malignancies, and a Self Organizing Maps algorithm for classification and clustering of the pathway activity profiles. The analysis results allowed clearly distinguish between cancer and non-cancer lung diseases. Lung cancers were characterized by pathways implicated in cell proliferation, metabolism, while non-malignant lung diseases were characterized by deregulations in pathways involved in immune/inflammatory response and fibrotic tissue remodeling. In contrast to lung malignancies, chronic lung diseases had relatively heterogeneous pathway deregulation profiles. We identified three groups of interstitial lung diseases and showed that the development of characteristic pathological processes, such as fibrosis, can be initiated by deregulations in different signaling pathways. In conclusion, this paper describes the pathobiology of lung diseases from systems viewpoint using pathway centered high-dimensional data mining approach. Our results contribute largely to current understanding of pathological events in lung cancers and non-malignant lung diseases. Moreover, this paper provides new insight into molecular mechanisms of a number of interstitial lung diseases that have been studied to a lesser extent. PMID:27200087

  10. Molecular genetic studies in Saudi population; identified variants from GWAS and meta-analysis in stroke.

    Science.gov (United States)

    Alharbi, Khalid Khalaf; Ali Khan, Imran; Alotaibi, Mohammad Abdullah; Saud Aloyaid, Abdullah; Al-Basheer, Haifa Abdulaziz; Alghamdi, Naelah Abdullah; Al-Baradie, Raid Saleem; Al-Sulaiman, A M

    2018-01-01

    Stroke is a multifactorial and heterogeneous disorder, correlates with heritability and considered as one of the major diseases. The prior reports performed the variable models such as genome-wide association studies (GWAS), replication, case-control, cross-sectional and meta-analysis studies and still, we lack diagnostic marker in the global world. There are limited studies were carried out in Saudi population, and we aim to investigate the molecular association of single nucleotide polymorphisms (SNPs) identified through GWAS and meta-analysis studies in stroke patients in the Saudi population. In this case-control study, we have opted gender equality of 207 cases and 207 controls from the capital city of Saudi Arabia in King Saud University Hospital. The peripheral blood (5 ml) sample will be collected in two different vacutainers, and three mL of the coagulated blood will be used for lipid analysis (biochemical tests) and two mL will be used for DNA analysis (molecular tests). Genomic DNA will be extracted with the collected blood samples, and specific primers will be designed for the opted SNPs ( SORT1 -rs646218 and OLR1 -rs11053646 polymorphisms) and PCR-RFLP will be performed and randomly DNA sequencing will be carried out to cross check the results. The rs646218 and rs11053646 polymorphisms were significantly associated with allele, genotype and dominant models with and without crude odds ratios (OR's) and Multiple logistic regression analysis (p Saudi population. The current results were in the association with the prior study results documented through GWAS and meta-analysis association. However, other ethnic population studies should be performed to rule out in the human hereditary diseases.

  11. Molecular clouds and galactic spiral structure

    International Nuclear Information System (INIS)

    Dame, T.M.

    1984-02-01

    Galactic CO line emission at 115 GHz was surveyed in order to study the distribution of molecular clouds in the inner galaxy. Comparison of this survey with similar H1 data reveals a detailed correlation with the most intense 21 cm features. To each of the classical 21 cm H1 spiral arms of the inner galaxy there corresponds a CO molecular arm which is generally more clearly defined and of higher contrast. A simple model is devised for the galactic distribution of molecular clouds. The modeling results suggest that molecular clouds are essentially transient objects, existing for 15 to 40 million years after their formation in a spiral arm, and are largely confined to spiral features about 300 pc wide

  12. Quantitative trait loci underlying resistance to sudden death syndrome (SDS) in MD96-5722 by 'Spencer' recombinant inbred line population of soybean.

    Science.gov (United States)

    Anderson, J; Akond, M; Kassem, M A; Meksem, K; Kantartzi, S K

    2015-04-01

    The best way to protect yield loss of soybean [Glycine max (L.) Merr.] due to sudden death syndrome (SDS), caused by Fusarium virguliforme (Aoki, O'Donnel, Homma & Lattanzi), is the development and use of resistant lines. Mapping quantitative trait loci (QTL) linked to SDS help developing resistant soybean germplasm through molecular marker-assisted selection strategy. QTL for SDS presented herein are from a high-density SNP-based genetic linkage map of MD 96-5722 (a.k.a 'Monocacy') by 'Spencer' recombinant inbred line using SoySNP6K Illumina Infinium BeadChip genotyping array. Ninety-four F 5:7 lines were evaluated for 2 years (2010 and 2011) at two locations (Carbondale and Valmeyer) in southern Illinois, USA to identify QTL controlling SDS resistance using disease index (DX). Composite interval mapping identified 19 SDS controlling QTL which were mapped on 11 separate linkage group (LG) or chromosomes (Chr) out of 20 LG or Chr of soybean genome. Many of these significant QTL identified in one environment/year were confirmed in another year or environment, which suggests a common genetic effects and modes of the pathogen. These new QTL are useful sources for SDS resistance studies in soybean breeding, complementing previously reported loci.

  13. A Study of Scientometric Methods to Identify Emerging Technologies

    Energy Technology Data Exchange (ETDEWEB)

    Abercrombie, Robert K [ORNL; Udoeyop, Akaninyene W [ORNL

    2011-01-01

    This work examines a scientometric model that tracks the emergence of an identified technology from initial discovery (via original scientific and conference literature), through critical discoveries (via original scientific, conference literature and patents), transitioning through Technology Readiness Levels (TRLs) and ultimately on to commercial application. During the period of innovation and technology transfer, the impact of scholarly works, patents and on-line web news sources are identified. As trends develop, currency of citations, collaboration indicators, and on-line news patterns are identified. The combinations of four distinct and separate searchable on-line networked sources (i.e., scholarly publications and citation, worldwide patents, news archives, and on-line mapping networks) are assembled to become one collective network (a dataset for analysis of relations). This established network becomes the basis from which to quickly analyze the temporal flow of activity (searchable events) for the example subject domain we investigated.

  14. The HITRAN 2008 molecular spectroscopic database

    International Nuclear Information System (INIS)

    Rothman, L.S.; Gordon, I.E.; Barbe, A.; Benner, D.Chris; Bernath, P.F.; Birk, M.; Boudon, V.; Brown, L.R.; Campargue, A.; Champion, J.-P.; Chance, K.; Coudert, L.H.; Dana, V.; Devi, V.M.; Fally, S.; Flaud, J.-M.

    2009-01-01

    This paper describes the status of the 2008 edition of the HITRAN molecular spectroscopic database. The new edition is the first official public release since the 2004 edition, although a number of crucial updates had been made available online since 2004. The HITRAN compilation consists of several components that serve as input for radiative-transfer calculation codes: individual line parameters for the microwave through visible spectra of molecules in the gas phase; absorption cross-sections for molecules having dense spectral features, i.e. spectra in which the individual lines are not resolved; individual line parameters and absorption cross-sections for bands in the ultraviolet; refractive indices of aerosols, tables and files of general properties associated with the database; and database management software. The line-by-line portion of the database contains spectroscopic parameters for 42 molecules including many of their isotopologues.

  15. Molecular forensics in avian conservation: a DNA-based approach for identifying mammalian predators of ground-nesting birds and eggs.

    Science.gov (United States)

    Hopken, Matthew W; Orning, Elizabeth K; Young, Julie K; Piaggio, Antoinette J

    2016-01-07

    The greater sage-grouse (Centrocercus urophasianus) is a ground-nesting bird from the Northern Rocky Mountains and a species at risk of extinction in in multiple U.S. states and Canada. Herein we report results from a proof of concept that mitochondrial and nuclear DNAs from mammalian predator saliva could be non-invasively collected from depredated greater sage-grouse eggshells and carcasses and used for predator species identification. Molecular forensic approaches have been applied to identify predators from depredated remains as one strategy to better understand predator-prey dynamics and guide management strategies. This can aid conservation efforts by correctly identifying predators most likely to impact threatened and endangered species. DNA isolated from non-invasive samples around nesting sites (e.g. fecal or hair samples) is one method that can increase the success and accuracy of predator species identification when compared to relying on nest remains alone. Predator saliva DNA was collected from depredated eggshells and carcasses using swabs. We sequenced two partial fragments of two mitochondrial genes and obtained microsatellite genotypes using canid specific primers for species and individual identification, respectively. Using this multilocus approach we were able to identify predators, at least down to family, from 11 out of 14 nests (79%) and three out of seven carcasses (47%). Predators detected most frequently were canids (86%), while other taxa included rodents, a striped skunk, and cattle. We attempted to match the genotypes of individual coyotes obtained from eggshells and carcasses with those obtained from fecal samples and coyotes collected in the areas, but no genotype matches were found. Predation is a main cause of nest failure in ground-nesting birds and can impact reproduction and recruitment. To inform predator management for ground-nesting bird conservation, accurate identification of predator species is necessary. Considering

  16. Ability of Rf5 and Rf6 to Restore Fertility of Chinsurah Boro II-type Cytoplasmic Male Sterile Oryza Sativa (ssp. Japonica) Lines.

    Science.gov (United States)

    Zhang, Honggen; Che, Jianlan; Ge, Yongshen; Pei, Yan; Zhang, Lijia; Liu, Qiaoquan; Gu, Minghong; Tang, Shuzhu

    2017-12-01

    Three-line Oryza sativa (ssp. japonica) hybrids have been developed mainly using Chinsurah Boro II (BT)-type cytoplasmic male sterility (CMS). The Rf1 gene restores the fertility of BT-type CMS lines, and is the only fertility restorer gene (Rf) that has been used to produce three-line japonica hybrids. Using more Rf genes to breed BT-type restorer lines may broaden the genetic diversity of the restorer lines, and represents a viable approach to improve the heterosis level of BT-type japonica hybrids. We identified two major Rf genes from '93-11' that are involved in restoring the fertility of BT-type CMS plants. These genes were identified from resequenced chromosome segment substitution lines derived from a cross between the japonica variety 'Nipponbare' and the indica variety '93-11'. Molecular mapping results revealed that these genes were Rf5 and Rf6, which are the Rf genes that restore fertility to Honglian-type CMS lines. The BT-type F 1 hybrids with either Rf5 or Rf6 exhibited normal seed setting rates, but F 1 plants carrying Rf6 showed more stable seed setting rates than those of plants carrying Rf5 under heat-stress conditions. Furthermore, the seed setting rates of F 1 hybrids carrying both Rf5 and Rf6 were more stable than that of F 1 plants carrying only one Rf gene. Rf6 is an important genetic resource for the breeding of BT-type japonica restorer lines. Our findings may be useful for breeders interested in developing BT-type japonica hybrids.

  17. Identification and characterization of contrasting sunflower genotypes to early leaf senescence process combining molecular and physiological studies (Helianthus annuus L.).

    Science.gov (United States)

    López Gialdi, A I; Moschen, S; Villán, C S; López Fernández, M P; Maldonado, S; Paniego, N; Heinz, R A; Fernandez, P

    2016-09-01

    Leaf senescence is a complex mechanism ruled by multiple genetic and environmental variables that affect crop yields. It is the last stage in leaf development, is characterized by an active decline in photosynthetic rate, nutrients recycling and cell death. The aim of this work was to identify contrasting sunflower inbred lines differing in leaf senescence and to deepen the study of this process in sunflower. Ten sunflower genotypes, previously selected by physiological analysis from 150 inbred genotypes, were evaluated under field conditions through physiological, cytological and molecular analysis. The physiological measurement allowed the identification of two contrasting senescence inbred lines, R453 and B481-6, with an increase in yield in the senescence delayed genotype. These findings were confirmed by cytological and molecular analysis using TUNEL, genomic DNA gel electrophoresis, flow sorting and gene expression analysis by qPCR. These results allowed the selection of the two most promising contrasting genotypes, which enables future studies and the identification of new biomarkers associated to early senescence in sunflower. In addition, they allowed the tuning of cytological techniques for a non-model species and its integration with molecular variables. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  18. Deep, Broadband Spectral Line Surveys of Molecule-rich Interstellar Clouds

    Energy Technology Data Exchange (ETDEWEB)

    Widicus Weaver, Susanna L.; Laas, Jacob C.; Zou, Luyao; Kroll, Jay A.; Rad, Mary L.; Hays, Brian M.; Sanders, James L.; Cross, Trevor N.; Wehres, Nadine; McGuire, Brett A. [Department of Chemistry, Emory University, Atlanta, GA 30322 (United States); Lis, Dariusz C.; Sumner, Matthew C., E-mail: susanna.widicus.weaver@emory.edu [California Institute of Technology, Cahill Center for Astronomy and Astrophysics 301-17, Pasadena, CA 91125 (United States)

    2017-09-01

    Spectral line surveys are an indispensable tool for exploring the physical and chemical evolution of astrophysical environments due to the vast amount of data that can be obtained in a relatively short amount of time. We present deep, broadband spectral line surveys of 30 interstellar clouds using two broadband λ  = 1.3 mm receivers at the Caltech Submillimeter Observatory. This information can be used to probe the influence of physical environment on molecular complexity. We observed a wide variety of sources to examine the relative abundances of organic molecules as they relate to the physical properties of the source (i.e., temperature, density, dynamics, etc.). The spectra are highly sensitive, with noise levels ≤25 mK at a velocity resolution of ∼0.35 km s{sup −1}. In the initial analysis presented here, column densities and rotational temperatures have been determined for the molecular species that contribute significantly to the spectral line density in this wavelength regime. We present these results and discuss their implications for complex molecule formation in the interstellar medium.

  19. A needle extraction utilizing a molecularly imprinted-sol-gel xerogel for on-line microextraction of the lung cancer biomarker bilirubin from plasma and urine samples.

    Science.gov (United States)

    Moein, Mohammad Mahdi; Jabbar, Dunia; Colmsjö, Anders; Abdel-Rehim, Mohamed

    2014-10-31

    In the present work, a needle trap utilizing a molecularly imprinted sol-gel xerogel was prepared for the on-line microextraction of bilirubin from plasma and urine samples. Each prepared needle could be used for approximately one hundred extractions before it was discarded. Imprinted and non-imprinted sol-gel xerogel were applied for the extraction of bilirubin from plasma and urine samples. The produced molecularly imprinted sol-gel xerogel polymer showed high binding capacity and fast adsorption/desorption kinetics for bilirubin in plasma and urine samples. The adsorption capacity of molecularly imprinted sol-gel xerogel polymer was approximately 60% higher than that of non-imprinted polymer. The effect of the conditioning, washing and elution solvents, pH, extraction time, adsorption capacity and imprinting factor were investigated. The limit of detection and the lower limit of quantification were set to 1.6 and 5nmolL(-1), respectively using plasma or urine samples. The standard calibration curves were obtained within the concentration range of 5-1000nmolL(-1) in both plasma and urine samples. The coefficients of determination values (R(2)) were ≥0.998 for all runs. The extraction recovery was approximately 80% for BR in the human plasma and urine samples. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Design of block copolymer membranes using segregation strength trend lines

    KAUST Repository

    Sutisna, Burhannudin; Polymeropoulos, Georgios; Musteata, Valentina-Elena; Peinemann, Klaus-Viktor; Avgeropoulos, Apostolos; Smilgies, Detlef-M.; Hadjichristidis, Nikolaos; Nunes, Suzana Pereira

    2016-01-01

    composition, polymer molecular weights, casting solution concentration, and evaporation time. We propose here an effective method for designing new block copolymer membranes. The method consists of predetermining a trend line for the preparation of isoporous

  1. Establishment of a new human pleomorphic malignant fibrous histiocytoma cell line, FU-MFH-2: molecular cytogenetic characterization by multicolor fluorescence in situ hybridization and comparative genomic hybridization

    Directory of Open Access Journals (Sweden)

    Isayama Teruto

    2010-11-01

    Full Text Available Abstract Background Pleomorphic malignant fibrous histiocytoma (MFH is one of the most frequent malignant soft tissue tumors in adults. Despite the considerable amount of research on MFH cell lines, their characterization at a molecular cytogenetic level has not been extensively analyzed. Methods and results We established a new permanent human cell line, FU-MFH-2, from a metastatic pleomorphic MFH of a 72-year-old Japanese man, and applied multicolor fluorescence in situ hybridization (M-FISH, Urovysion™ FISH, and comparative genomic hybridization (CGH for the characterization of chromosomal aberrations. FU-MFH-2 cells were spindle or polygonal in shape with oval nuclei, and were successfully maintained in vitro for over 80 passages. The histological features of heterotransplanted tumors in severe combined immunodeficiency mice were essentially the same as those of the original tumor. Cytogenetic and M-FISH analyses displayed a hypotriploid karyotype with numerous structural aberrations. Urovysion™ FISH revealed a homozygous deletion of the p16INK4A locus on chromosome band 9p21. CGH analysis showed a high-level amplification of 9q31-q34, gains of 1p12-p34.3, 2p21, 2q11.2-q21, 3p, 4p, 6q22-qter, 8p11.2, 8q11.2-q21.1, 9q21-qter, 11q13, 12q24, 15q21-qter, 16p13, 17, 20, and X, and losses of 1q43-qter, 4q32-qter, 5q14-q23, 7q32-qter, 8p21-pter, 8q23, 9p21-pter, 10p11.2-p13, and 10q11.2-q22. Conclusion The FU-MFH-2 cell line will be a particularly useful model for studying molecular pathogenesis of human pleomorphic MFH.

  2. Identification of flowering-related genes responsible for differences in bolting time between two radish inbred lines

    Directory of Open Access Journals (Sweden)

    Hye Sun Cho

    2016-12-01

    Full Text Available Late bolting after cold exposure is an economically important characteristic of radish (Raphanus sativus L., an important Brassicaceae root vegetable crop. However, little information is available regarding the genes and pathways that govern flowering time in this species. We performed high-throughput RNA sequencing analysis to elucidate the molecular mechanisms that determine the differences in flowering times between two radish lines, NH-JS1 (late bolting and NH-JS2 (early bolting. In total, 71,188 unigenes were identified by reference-guided assembly, of which 309, 788, and 980 genes were differentially expressed between the two inbred lines after 0, 15, and 35 days of vernalization, respectively. Among these genes, 218 homologs of Arabidopsis flowering-time (Ft genes were identified in the radish, and 49 of these genes were differentially expressed between the two radish lines in the presence or absence of vernalization treatment. Most of the Ft genes up-regulated in NH-JS1 vs NH-JS2 were repressors of flowering, such as RsFLC, consistent with the late-bolting phenotype of NH-JS1. Although the functions of genes down-regulated in NH-JS1 were less consistent with late-bolting characteristics than the up-regulated Ft genes, several Ft enhancer genes, including RsSOC1, a key floral integrator, showed an appropriate expression to the late-bolting phenotype. In addition, the patterns of gene expression related to the vernalization pathway closely corresponded with the different bolting times of the two inbred lines. These results suggest that the vernalization pathway is conserved between radish and Arabidopsis.

  3. Toward precise potential energy curves for diatomic molecules, derived from experimental line positions

    International Nuclear Information System (INIS)

    Helm, H.

    1984-01-01

    An inverted, first-order perturbation approach is used to derive potential energy curves for diatomic molecules from experimental line positions of molecular bands. The concept adopted here is based on the inverted perturbation analysis (IPA) proposed by Kozman and Hinze, but uses radial eigenfunctions of the trial potential energy curves as basis sets for the perturbation correction. Using molecular linepositions rather than molecular energy levels we circumvent the necessity of defining molecular constants for the molecule prior to the derivation of the potential energy curves. (Author)

  4. Genes associated with thermosensitive genic male sterility in rice identified by comparative expression profiling.

    Science.gov (United States)

    Pan, Yufang; Li, Qiaofeng; Wang, Zhizheng; Wang, Yang; Ma, Rui; Zhu, Lili; He, Guangcun; Chen, Rongzhi

    2014-12-16

    Thermosensitive genic male sterile (TGMS) lines and photoperiod-sensitive genic male sterile (PGMS) lines have been successfully used in hybridization to improve rice yields. However, the molecular mechanisms underlying male sterility transitions in most PGMS/TGMS rice lines are unclear. In the recently developed TGMS-Co27 line, the male sterility is based on co-suppression of a UDP-glucose pyrophosphorylase gene (Ugp1), but further study is needed to fully elucidate the molecular mechanisms involved. Microarray-based transcriptome profiling of TGMS-Co27 and wild-type Hejiang 19 (H1493) plants grown at high and low temperatures revealed that 15462 probe sets representing 8303 genes were differentially expressed in the two lines, under the two conditions, or both. Environmental factors strongly affected global gene expression. Some genes important for pollen development were strongly repressed in TGMS-Co27 at high temperature. More significantly, series-cluster analysis of differentially expressed genes (DEGs) between TGMS-Co27 plants grown under the two conditions showed that low temperature induced the expression of a gene cluster. This cluster was found to be essential for sterility transition. It includes many meiosis stage-related genes that are probably important for thermosensitive male sterility in TGMS-Co27, inter alia: Arg/Ser-rich domain (RS)-containing zinc finger proteins, polypyrimidine tract-binding proteins (PTBs), DEAD/DEAH box RNA helicases, ZOS (C2H2 zinc finger proteins of Oryza sativa), at least one polyadenylate-binding protein and some other RNA recognition motif (RRM) domain-containing proteins involved in post-transcriptional processes, eukaryotic initiation factor 5B (eIF5B), ribosomal proteins (L37, L1p/L10e, L27 and L24), aminoacyl-tRNA synthetases (ARSs), eukaryotic elongation factor Tu (eEF-Tu) and a peptide chain release factor protein involved in translation. The differential expression of 12 DEGs that are important for pollen

  5. Molecular tagging of a novel rust resistance gene R(12) in sunflower (Helianthus annuus L.).

    Science.gov (United States)

    Gong, L; Hulke, B S; Gulya, T J; Markell, S G; Qi, L L

    2013-01-01

    Sunflower production in North America has recently suffered economic losses in yield and seed quality from sunflower rust (Puccinia helianthi Schwein.) because of the increasing incidence and lack of resistance to new rust races. RHA 464, a newly released sunflower male fertility restorer line, is resistant to both of the most predominant and most virulent rust races identified in the Northern Great Plains of the USA. The gene conditioning rust resistance in RHA 464 originated from wild Helianthus annuus L., but has not been molecularly marked or determined to be independent from other rust loci. The objectives of this study are to identify molecular markers linked to the rust resistance gene and to investigate the allelism of this gene with the unmapped rust resistance genes present in HA-R6, HA-R8 and RHA 397. Virulence phenotypes of seedlings for the F(2) population and F(2:3) families suggested that a single dominant gene confers rust resistance in RHA 464, and this gene was designated as R(12). Bulked segregant analysis identified ten markers polymorphic between resistant and susceptible bulks. In subsequent genetic mapping, the ten markers covered 33.4 cM of genetic distance on linkage group 11 of sunflower. A co-dominant marker CRT275-11 is the closest marker distal to R(12) with a genetic distance of 1.0 cM, while ZVG53, a dominant marker linked in the repulsion phase, is proximal to R(12) with a genetic distance of 9.6 cM. The allelism test demonstrated that R(12) is not allelic to the rust resistance genes in HA-R6, HA-R8 and RHA 397, and it is also not linked to any previously mapped rust resistance genes. Discovery of the R(12) novel rust resistance locus in sunflower and associated markers will potentially support the molecular marker-assisted introgression and pyramiding of R(12) into sunflower breeding lines.

  6. The Adhesion of Lactobacillus salivarius REN to a Human Intestinal Epithelial Cell Line Requires S-layer Proteins.

    Science.gov (United States)

    Wang, Ran; Jiang, Lun; Zhang, Ming; Zhao, Liang; Hao, Yanling; Guo, Huiyuan; Sang, Yue; Zhang, Hao; Ren, Fazheng

    2017-03-10

    Lactobacillus salivarius REN, a novel probiotic isolated from Chinese centenarians, can adhere to intestinal epithelial cells and subsequently colonize the host. We show here that the surface-layer protein choline-binding protein A (CbpA) of L. salivarius REN was involved in adherence to the human colorectal adenocarcinoma cell line HT-29. Adhesion of a cbpA deletion mutant was significantly reduced compared with that of wild-type, suggesting that CbpA acts as an adhesin that mediates the interaction between the bacterium and its host. To identify the molecular mechanism of adhesion, we determined the crystal structure of a truncated form of CbpA that is likely involved in binding to its cell-surface receptor. The crystal structure identified CbpA as a peptidase of the M23 family whose members harbor a zinc-dependent catalytic site. Therefore, we propose that CbpA acts as a multifunctional surface protein that cleaves the host extracellular matrix and participates in adherence. Moreover, we identified enolase as the CbpA receptor on the surface of HT-29 cells. The present study reveals a new class of surface-layer proteins as well as the molecular mechanism that may contribute to the ability of L. salivarius REN to colonize the human gut.

  7. Chemistry of the High-mass Protostellar Molecular Clump IRAS 16562–3959

    Science.gov (United States)

    Guzmán, Andrés E.; Guzmán, Viviana V.; Garay, Guido; Bronfman, Leonardo; Hechenleitner, Federico

    2018-06-01

    We present molecular line observations of the high-mass molecular clump IRAS 16562‑3959 taken at 3 mm using the Atacama Large Millimeter/submillimeter Array at 1.″7 angular resolution (0.014 pc spatial resolution). This clump hosts the actively accreting high-mass young stellar object (HMYSO) G345.4938+01.4677, which is associated with a hypercompact H II region. We identify and analyze emission lines from 22 molecular species (encompassing 34 isomers) and classify them into two groups, depending on their spatial distribution within the clump. One of these groups gathers shock tracers (e.g., SiO, SO, HNCO) and species formed in dust grains like methanol (CH3OH), ethenone or ketene (H2CCO), and acetaldehyde (CH3CHO). The second group collects species closely resembling the dust continuum emission morphology and are formed mainly in the gas phase, like hydrocarbons (CCH, c-C3H2, CH3CCH), cyanopolyynes (HC3N and HC5N), and cyanides (HCN and CH3C3N). Emission from complex organic molecules (COMs) like CH3OH, propanenitrile (CH3CH2CN), and methoxymethane (CH3OCH3) arise from gas in the vicinity of a hot molecular core (T ≳ 100 K) associated with the HMYSO. Other COMs such as propyne (CH3CCH), acrylonitrile (CH2CHCN), and acetaldehyde seem to better trace warm (T ≲ 80 K) dense gas. In addition, deuterated ammonia (NH2D) is detected mostly in the outskirts of IRAS 16562‑3959 and associated with near-infrared dark globules, probably gaseous remnants of the clump’s prestellar phase. The spatial distribution of molecules in IRAS 16562‑3959 supports the view that in protostellar clumps, chemical tracers associated with different evolutionary stages—starless to hot cores/H II regions—exist coevally.

  8. Higher Levels of c-Met Expression and Phosphorylation Identify Cell Lines With Increased Sensitivity to AMG-458, a Novel Selective c-Met Inhibitor With Radiosensitizing Effects

    International Nuclear Information System (INIS)

    Li Bo; Torossian, Artour; Sun, Yunguang; Du, Ruihong; Dicker, Adam P.; Lu Bo

    2012-01-01

    Purpose: c-Met is overexpressed in some non-small cell lung cancer (NSCLC) cell lines and tissues. Cell lines with higher levels of c-Met expression and phosphorylation depend on this receptor for survival. We studied the effects of AMG-458 on 2 NSCLC cell lines. Methods and Materials: 3-(4,5-Dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl) -2H-tetrazolium assays assessed the sensitivities of the cells to AMG-458. Clonogenic survival assays illustrated the radiosensitizing effects of AMG-458. Western blot for cleaved caspase 3 measured apoptosis. Immunoblotting for c-Met, phospho-Met (p-Met), Akt/p-Akt, and Erk/p-Erk was performed to observe downstream signaling. Results: AMG-458 enhanced radiosensitivity in H441 but not in A549. H441 showed constitutive phosphorylation of c-Met. A549 expressed low levels of c-Met, which were phosphorylated only in the presence of exogenous hepatocyte growth factor. The combination of radiation therapy and AMG-458 treatment was found to synergistically increase apoptosis in the H441 cell line but not in A549. Radiation therapy, AMG-458, and combination treatment were found to reduce p-Akt and p-Erk levels in H441 but not in A549. H441 became less sensitive to AMG-458 after small interfering RNA knockdown of c-Met; there was no change in A549. After overexpression of c-Met, A549 became more sensitive, while H441 became less sensitive to AMG-458. Conclusions: AMG-458 was more effective in cells that expressed higher levels of c-Met/p-Met, suggesting that higher levels of c-Met and p-Met in NSCLC tissue may classify a subset of tumors that are more sensitive to molecular therapies against this receptor.

  9. Mechanisms to medicines: elucidating neural and molecular substrates of fear extinction to identify novel treatments for anxiety disorders

    Science.gov (United States)

    Bukalo, Olena; Pinard, Courtney R; Holmes, Andrew

    2014-01-01

    The burden of anxiety disorders is growing, but the efficacy of available anxiolytic treatments remains inadequate. Cognitive behavioural therapy for anxiety disorders focuses on identifying and modifying maladaptive patterns of thinking and behaving, and has a testable analogue in rodents in the form of fear extinction. A large preclinical literature has amassed in recent years describing the neural and molecular basis of fear extinction in rodents. In this review, we discuss how this work is being harnessed to foster translational research on anxiety disorders and facilitate the search for new anxiolytic treatments. We begin by summarizing the anatomical and functional connectivity of a medial prefrontal cortex (mPFC)–amygdala circuit that subserves fear extinction, including new insights from optogenetics. We then cover some of the approaches that have been taken to model impaired fear extinction and associated impairments with mPFC–amygdala dysfunction. The principal goal of the review is to evaluate evidence that various neurotransmitter and neuromodulator systems mediate fear extinction by modulating the mPFC–amygdala circuitry. To that end, we describe studies that have tested how fear extinction is impaired or facilitated by pharmacological manipulations of dopamine, noradrenaline, 5-HT, GABA, glutamate, neuropeptides, endocannabinoids and various other systems, which either directly target the mPFC–amygdala circuit, or produce behavioural effects that are coincident with functional changes in the circuit. We conclude that there are good grounds to be optimistic that the progress in defining the molecular substrates of mPFC–amygdala circuit function can be effectively leveraged to identify plausible candidates for extinction-promoting therapies for anxiety disorders. Linked Articles This article is part of a themed section on Animal Models in Psychiatry Research. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2014

  10. Molecular sieving through a graphene nanopore: non-equilibrium molecular dynamics simulation

    Institute of Scientific and Technical Information of China (English)

    Chengzhen Sun; Bofeng Bai

    2017-01-01

    Two-dimensional graphene nanopores have shown great promise as ultra-permeable molecular sieves based on their size-sieving effects.We design a nitrogen/hydrogen modified graphene nanopore and conduct a transient non-equilibrium molecular dynamics simulation on its molecular sieving effects.The distinct time-varying molecular crossing numbers show that this special nanopore can efficiently sieve CO2 and H2S molecules from CH4 molecules with high selectivity.By analyzing the molecular structure and pore functionalization-related molecular orientation and permeable zone in the nanopore,density distribution in the molecular adsorption layer on the graphene surface,as well as other features,the molecular sieving mechanisms of graphene nanopores are revealed.Finally,several implications on the design of highly-efficient graphene nanopores,especially for determining the porosity and chemical functionalization,as gas separation membranes are summarized based on the identified phenomena and mechanisms.

  11. DENSE CLUMPS AND CANDIDATES FOR MOLECULAR OUTFLOWS IN W40

    Energy Technology Data Exchange (ETDEWEB)

    Shimoikura, Tomomi; Dobashi, Kazuhito [Department of Astronomy and Earth Sciences, Tokyo Gakugei University, Koganei, Tokyo 184-8501 (Japan); Nakamura, Fumitaka; Hara, Chihomi; Kawabe, Ryohei [National Astronomical Observatory of Japan, Mitaka, Tokyo 181-8588 (Japan); Tanaka, Tomohiro [Department of Physical Science, Osaka Prefecture University, Sakai, Osaka 599-8531 (Japan); Shimajiri, Yoshito [Laboratoire AIM, CEA/DSM-CNRS-Université Paris Diderot, IRFU/Service d’Astrophysique, CEA Saclay, F-91191 Gif-sur-Yvette (France); Sugitani, Kouji, E-mail: ikura@u-gakugei.ac.jp [Graduate School of Natural Sciences, Nagoya City University, Mizuho-ku, Nagoya 467-8501 (Japan)

    2015-06-20

    We report the results of the {sup 12}CO (J = 3−2) and HCO{sup +} (J = 4−3) observations of the W40 H ii region with the Atacama Submillimeter Telescope Experiment (ASTE) 10 m telescope (HPBW ≃ 22″) to search for molecular outflows and dense clumps. We found that the velocity field in the region is highly complex, consisting of at least four distinct velocity components at V{sub LSR} ≃ 3, 5, 7, and 10 km s{sup −1}. The ∼7 km s{sup −1} component represents the systemic velocity of cold gas surrounding the entire region, and causes heavy absorption in the {sup 12}CO spectra over the velocity range 6 ≲ V{sub LSR} ≲ 9 km s{sup −1}. The ∼5 and ∼10 km s{sup −1} components exhibit high {sup 12}CO temperature (≳40 K) and are found mostly around the H ii region, suggesting that these components are likely to be tracing dense gas interacting with the expanding shell around the H ii region. Based on the {sup 12}CO data, we identified 13 regions of high velocity gas, which we interpret as candidate outflow lobes. Using the HCO{sup +} data, we also identified six clumps and estimated their physical parameters. On the basis of the ASTE data and near-infrared images from 2MASS, we present an updated three-dimensional model of this region. In order to investigate molecular outflows in W40, the SiO (J = 1−0, v = 0) emission line and some other emission lines at 40 GHz were also observed with the 45 m telescope at the Nobeyama Radio Observatory, but they were not detected at the present sensitivity.

  12. Characterization and evaluation of rice blast resistance of Chinese indica hybrid rice parental lines

    Directory of Open Access Journals (Sweden)

    Yunyu Wu

    2017-12-01

    Full Text Available The development of resistant varieties and hybrid combinations has been the most effective and economical strategy to control blast disease caused by Magnaporthe oryzae. However, the distribution of major R genes and blast resistance characterization in hybrid rice parents has not been well investigated, resulting in their limited use in hybrid rice blast-resistance breeding. In the present study, 88 elite indica hybrid rice parental lines were evaluated with 30 isolates of M. oryzae collected from the main planting area of indica hybrid rice in China and were characterized for the presence of 11 major resistance genes using molecular markers. The pathogenicity assays showed that four types of hybrid rice parent line showed some resistance to M. oryzae. However, the proportions of highly resistant lines and the mean resistance frequency (RF varied among the four types, with resistance in decreasing order shown by three-line restorer lines, three-line maintainer lines, two-line sterile lines, and two-line restorer lines. All 88 hybrid rice parental lines carried more than one R gene, but none carried the R genes Pi1 and Pi2. Although Pid3 and Pi9 were present only in three-line restorer lines and Pigm only in three-line maintainer lines, the remaining six R genes (Pib, Pid2, Pi5, Pia, Pi54, and Pita were present in the four types of hybrid rice parent with significantly different distribution frequencies. The correlation between R genes and resistance reactions was investigated. The results are expected to provide useful information for rational utilization of major R genes in hybrid rice breeding programs. Keywords: Hybrid rice parental lines, Magnaporthe oryzae, Pi genes, Resistance evaluation, Molecular markers

  13. Prevalence of the molecular marker of chloroquine resistance ( pfcrt ...

    African Journals Online (AJOL)

    In line with the World Health Organization (WHO) guideline on chloroquine (CQ) resistance, CQ was withdrawn as the first-line antimalarial drug in Nigeria in 2005 as a result of ... We monitored the resistance pattern 5 years after withdrawal of CQ, using the pfcrt K76T mutation as a molecular marker for CQ resistance.

  14. US line-ups outperform UK line-ups

    OpenAIRE

    Seale-Carlisle, Travis M.; Mickes, Laura

    2016-01-01

    In the USA and the UK, many thousands of police suspects are identified by eyewitnesses every year. Unfortunately, many of those suspects are innocent, which becomes evident when they are exonerated by DNA testing, often after having been imprisoned for years. It is, therefore, imperative to use identification procedures that best enable eyewitnesses to discriminate innocent from guilty suspects. Although police investigators in both countries often administer line-up procedures, the details ...

  15. Identifying cell and molecular stress after radiation in a three-dimensional (3-D) model of oral mucositis

    International Nuclear Information System (INIS)

    Lambros, Maria Polikandritou; Parsa, Cyrus; Mulamalla, HariChandana; Orlando, Robert; Lau, Bernard; Huang, Ying; Pon, Doreen; Chow, Moses

    2011-01-01

    Research highlights: → We irradiated a 3-D human oral cell culture of keratinocytes and fibroblasts with 12 and 2 Gy. → 6 h after irradiation the histopathology and apoptosis of the 3-D culture were evaluated. Microarrays were used to assess the gene expression in the irradiated 3-D tissue. → 12 Gy induced significant histopathologic changes and cellular apoptosis. → 12 Gy significantly affected genes of the NF-kB pathway, inflammatory cytokines and DAMPs. -- Abstract: Mucositis is a debilitating adverse effect of chemotherapy and radiation treatment. It is important to develop a simple and reliable in vitro model, which can routinely be used to screen new drugs for prevention and treatment of mucositis. Furthermore, identifying cell and molecular stresses especially in the initiation phase of mucositis in this model will help towards this end. We evaluated a three-dimensional (3-D) human oral cell culture that consisted of oral keratinocytes and fibroblasts as a model of oral mucositis. The 3-D cell culture model was irradiated with 12 or 2 Gy. Six hours after the irradiation we evaluated microscopic sections of the cell culture for evidence of morphologic changes including apoptosis. We used microarrays to compare the expression of several genes from the irradiated tissue with identical genes from tissue that was not irradiated. We found that irradiation with 12 Gy induced significant histopathologic effects including cellular apoptosis. Irradiation significantly affected the expression of several genes of the NF-kB pathway and several inflammatory cytokines, such as IL-1B, 1L-8, NF-kB1, and FOS compared to tissue that was not irradiated. We identified significant upregulation of several genes that belong to damage-associated molecular patterns (DAMPs) such as HMB1, S100A13, SA10014, and SA10016 in the 3-D tissues that received 12 Gy but not in tissues that received 2 Gy. In conclusion, this model quantifies radiation damage and this is an important first

  16. X-ray spectral line coincidences between fluorine VIII (and IX) and transition metal lines

    International Nuclear Information System (INIS)

    Charatis, G.; Rockett, P.D.; Burkhalter, P.G.

    1983-01-01

    X-ray spectroscopy was performed in the 12 to 15 A region, recording L-shell lines from selected laser-irradiated transition metals. Line coincidences and near coincidences were identified between Fe, Cr, Mn, and Ni L-spectra, and F VIII and F IX K-shell lines. Wavelengths were determined to accuracies of 1 to 3 mA and will be utilized in selecting potential pumping candidates in future x-ray lasing schemes. High-resolution x-ray spectra were collected under controlled illumination and target conditions using 1.05 μm and 0.527 μm laser excitation with the KMS CHROMA laser

  17. Development and Molecular Cytogenetic Identification of a Novel Wheat-Leymus mollis Lm#7Ns (7D Disomic Substitution Line with Stripe Rust Resistance.

    Directory of Open Access Journals (Sweden)

    Xiaofei Yang

    Full Text Available Leymus mollis (2n = 4x = 28, NsNsXmXm possesses novel and important genes for resistance against multi-fungal diseases. The development of new wheat-L. mollis introgression lines is of great significance for wheat disease resistance breeding. M11003-3-1-15-8, a novel disomic substitution line of common wheat cv. 7182 -L. mollis, developed and selected from the BC1F5 progeny between wheat cv. 7182 and octoploid Tritileymus M47 (2n = 8x = 56, AABBDDNsNs, was characterized by morphological and cytogenetic identification, analysis of functional molecular markers, genomic in situ hybridization (GISH, sequential fluorescence in situ hybridization (FISH-genomic in situ hybridization (GISH and disease resistance evaluation. Cytological observations suggested that M11003-3-1-15-8 contained 42 chromosomes and formed 21 bivalents at meiotic metaphase I. The GISH investigations showed that line contained 40 wheat chromosomes and a pair of L. mollis chromosomes. EST-STS multiple loci markers and PLUG (PCR-based Landmark Unique Gene markers confirmed that the introduced L. mollis chromosomes belonged to homoeologous group 7, it was designated as Lm#7Ns. While nulli-tetrasomic and sequential FISH-GISH analysis using the oligonucleotide Oligo-pSc119.2 and Oligo-pTa535 as probes revealed that the wheat 7D chromosomes were absent in M11003-3-1-15-8. Therefore, it was deduced that M11003-3-1-15-8 was a wheat-L. mollis Lm#7Ns (7D disomic substitution line. Field disease resistance demonstrated that the introduced L. mollis chromosomes Lm#7Ns were responsible for the stripe rust resistance at the adult stage. Moreover, M11003-3-1-15-8 had a superior numbers of florets. The novel disomic substitution line M11003-3-1-15-8, could be exploited as an important genetic material in wheat resistance breeding programs and genetic resources.

  18. Nanotribology investigations with classical molecular dynamics

    NARCIS (Netherlands)

    Solhjoo, Soheil

    2017-01-01

    This thesis presents a number of nanotribological problems investigated by means of classical molecular dynamics (MD) simulations, within the context of the applicability of continuum mechanics contact theories at the atomic scale. Along these lines, three different themes can be recognized herein:

  19. Galleria mellonella model identifies highly virulent strains among all major molecular types of Cryptococcus gattii.

    Directory of Open Access Journals (Sweden)

    Carolina Firacative

    Full Text Available Cryptococcosis is mainly caused by Cryptococcus neoformans. However, the number of cases due to C. gattii is increasing, affecting mainly immunocompetent hosts. C. gattii is divided into four major molecular types, VGI to VGIV, which differ in their host range, epidemiology, antifungal susceptibility and geographic distribution. Besides studies on the Vancouver Island outbreak strains, which showed that the subtype VGIIa is highly virulent compared to the subtype VGIIb, little is known about the virulence of the other major molecular types. To elucidate the virulence potential of the major molecular types of C. gattii, Galleria mellonella larvae were inoculated with ten globally selected strains per molecular type. Survival rates were recorded and known virulence factors were studied. One VGII, one VGIII and one VGIV strain were more virulent (p 0.05, 21 (five VGI, five VGII, four VGIII and seven VGIV were less virulent (p <0.05 while one strain of each molecular type were avirulent. Cell and capsule size of all strains increased markedly during larvae infection (p <0.001. No differences in growth rate at 37°C were observed. Melanin synthesis was directly related with the level of virulence: more virulent strains produced more melanin than less virulent strains (p <0.05. The results indicate that all C. gattii major molecular types exhibit a range of virulence, with some strains having the potential to be more virulent. The study highlights the necessity to further investigate the genetic background of more and less virulent strains in order to recognize critical features, other than the known virulence factors (capsule, melanin and growth at mammalian body temperature, that maybe crucial for the development and progression of cryptococcosis.

  20. O6-methylguanine-DNA methyltransferase in equine sarcoids: molecular and epigenetic analysis

    Directory of Open Access Journals (Sweden)

    Altamura Gennaro

    2012-11-01

    Full Text Available Abstract Background Bovine papillomaviruses (BPVs types 1 and 2 are the only known papillomaviruses able to jump the species. In fact, BPVs 1/2 induce neoplasia in their natural bovine host but infection is also associated to neoplastic skin lesions in equids termed sarcoids. The equine sarcoid is considered to be the most common equine cutaneous tumour worldwide for which no effective therapy is available. Very little is known about the molecular mechanisms underlying tumourigenesis, although genes contributing to sarcoid development have been identified. Several studies associate the development of cancer to the loss of function of a number of oncosuppressor genes. In this study the putative role of O6-methylguanine-DNA methyltrasferase (MGMT was investigated for sarcoids. The expression of the oncosuppressor protein was assessed in normal and sarcoid cells and tissues. In addition, the DNA methylation profile was analysed to assess the role of epigenetic mechanism in regulation of MGMT expression. Results A group of 15 equine sarcoids and two primary sarcoid cell lines (fibroblasts were analyzed for the expression of MGMT protein by immunohistochemistry, immunofluorescence and Western blotting techniques. The sarcoid cell line EqSO4b and the tumour samples showed a reduction or absence of MGMT expression. To investigate the causes of deregulated MGMT expression, ten samples were analyzed for the DNA methylation profile of the CpG island associated to the MGMT promoter. The analysis of 73 CpGs encompassing the region of interest showed in 1 out of 10 (10% sarcoids a pronouncedly altered methylation profile when compared to the control epidermal sample. Similarily the EqSO4b cell line showed an altered MGMT methylation pattern in comparison to normal fibroblasts. Conclusion As previously demonstrated for the oncosuppressor gene FHIT, analysis of MGMT expression in sarcoid tissues and a sarcoid-derived fibroblast cell line further suggests that

  1. Nuclear molecular halo: the ubiquitous occurrence of van der Waals molecular states near threshold in molecular, nuclear and particle physics

    International Nuclear Information System (INIS)

    Gai, Moshe

    1999-01-01

    The observation of large E1 strength near threshold in the electromagnetic dissociation of 11 Li poses a fundamental question: Is the large E1 strength due to the threshold or is it due to a low lying E1 state? Such molecular cluster states were observed in 18 O and in several nuclei near the drip line. We discuss the nature of the threshold effect as well as review the situation in Molecular (and Particle Physics) where such Molecular States are observed near the dissociation limit. We suggest that the situation in 11 Li is reminiscent of the argon-benzene molecule where the argon atom is loosely bound by a polarization (van der Waals) mechanism and thus leads to a very extended object lying near the dissociation limit. Such states are also suggested to dominate the structure of mesons [α 0 (980), f 0 (975)] and baryons [λ(1405)] with proposed Kaon molecular structure (Dalitz) near threshold. The inspection of such states throughout Physics allows us to gain insight into this phenomenon and suggest that a new collective Molecular Dipole Degree of Freedom plays a major role in the structure of hadrons (halo nuclei, mesons and baryons), and that quantitative tools such as the E1 Molecular Sum Rule are useful for elucidating the nature of the observed low lying E1 strength in halo nuclei. (author)

  2. Isotopic and molecular fractionation in combustion; three routes to molecular marker validation, including direct molecular 'dating' (GC/AMS)

    Science.gov (United States)

    Currie, L. A.; Klouda, G. A.; Benner, B. A.; Garrity, K.; Eglinton, T. I.

    The identification of unique isotopic, elemental, and molecular markers for sources of combustion aerosol has growing practical importance because of the potential effects of fine particle aerosol on health, visibility and global climate. It is urgent, therefore, that substantial efforts be directed toward the validation of assumptions involving the use of such tracers for source apportionment. We describe here three independent routes toward carbonaceous aerosol molecular marker identification and validation: (1) tracer regression and multivariate statistical techniques applied to field measurements of mixed source, carbonaceous aerosols; (2) a new development in aerosol 14C metrology: direct, pure compound accelerator mass spectrometry (AMS) by off-line GC/AMS ('molecular dating'); and (3) direct observation of isotopic and molecular source emissions during controlled laboratory combustion of specific fuels. Findings from the combined studies include: independent support for benzo( ghi)perylene as a motor vehicle tracer from the first (statistical) and second (direct 'dating') studies; a new indication, from the third (controlled combustion) study, of a relation between 13C isotopic fractionation and PAH molecular fractionation, also linked with fuel and stage of combustion; and quantitative data showing the influence of both fuel type and combustion conditions on the yields of such species as elemental carbon and PAH, reinforcing the importance of exercising caution when applying presumed conservative elemental or organic tracers to fossil or biomass burning field data as in the first study.

  3. Gene Expression Signature Analysis Identifies Vorinostat as a Candidate Therapy for Gastric Cancer

    Science.gov (United States)

    Choi, Woonyoung; Park, Yun-Yong; Kim, KyoungHyun; Kim, Sang-Bae; Lee, Ju-Seog; Mills, Gordon B.; Cho, Jae Yong

    2011-01-01

    Background Gastric cancer continues to be one of the deadliest cancers in the world and therefore identification of new drugs targeting this type of cancer is thus of significant importance. The purpose of this study was to identify and validate a therapeutic agent which might improve the outcomes for gastric cancer patients in the future. Methodology/Principal Findings Using microarray technology, we generated a gene expression profile of human gastric cancer–specific genes from human gastric cancer tissue samples. We used this profile in the Broad Institute's Connectivity Map analysis to identify candidate therapeutic compounds for gastric cancer. We found the histone deacetylase inhibitor vorinostat as the lead compound and thus a potential therapeutic drug for gastric cancer. Vorinostat induced both apoptosis and autophagy in gastric cancer cell lines. Pharmacological and genetic inhibition of autophagy however, increased the therapeutic efficacy of vorinostat, indicating that a combination of vorinostat with autophagy inhibitors may therapeutically be more beneficial. Moreover, gene expression analysis of gastric cancer identified a collection of genes (ITGB5, TYMS, MYB, APOC1, CBX5, PLA2G2A, and KIF20A) whose expression was elevated in gastric tumor tissue and downregulated more than 2-fold by vorinostat treatment in gastric cancer cell lines. In contrast, SCGB2A1, TCN1, CFD, APLP1, and NQO1 manifested a reversed pattern. Conclusions/Significance We showed that analysis of gene expression signature may represent an emerging approach to discover therapeutic agents for gastric cancer, such as vorinostat. The observation of altered gene expression after vorinostat treatment may provide the clue to identify the molecular mechanism of vorinostat and those patients likely to benefit from vorinostat treatment. PMID:21931799

  4. Simplified methodology for large scale isolation of homozygous transgenic lines of lettuce

    Directory of Open Access Journals (Sweden)

    Flavia S. Darqui

    2018-01-01

    Conclusions: This protocol allows a simplified scaling-up of the production of multiple homozygous transgenic progeny lines in the early generations avoiding expensive and time-consuming molecular assays.

  5. The HITRAN 2004 molecular spectroscopic database

    Energy Technology Data Exchange (ETDEWEB)

    Rothman, L.S. [Harvard-Smithsonian Center for Astrophysics, Atomic and Molecular Physics Division, Cambridge, MA 02138 (United States)]. E-mail: lrothman@cfa.harvard.edu; Jacquemart, D. [Harvard-Smithsonian Center for Astrophysics, Atomic and Molecular Physics Division, Cambridge, MA 02138 (United States); Barbe, A. [Universite de Reims-Champagne-Ardenne, Groupe de Spectrometrie Moleculaire et Atmospherique, 51062 Reims (France)] (and others)

    2005-12-01

    This paper describes the status of the 2004 edition of the HITRAN molecular spectroscopic database. The HITRAN compilation consists of several components that serve as input for radiative transfer calculation codes: individual line parameters for the microwave through visible spectra of molecules in the gas phase; absorption cross-sections for molecules having dense spectral features, i.e., spectra in which the individual lines are unresolvable; individual line parameters and absorption cross-sections for bands in the ultra-violet; refractive indices of aerosols; tables and files of general properties associated with the database; and database management software. The line-by-line portion of the database contains spectroscopic parameters for 39 molecules including many of their isotopologues. The format of the section of the database on individual line parameters of HITRAN has undergone the most extensive enhancement in almost two decades. It now lists the Einstein A-coefficients, statistical weights of the upper and lower levels of the transitions, a better system for the representation of quantum identifications, and enhanced referencing and uncertainty codes. In addition, there is a provision for making corrections to the broadening of line transitions due to line mixing.

  6. The HITRAN 2004 molecular spectroscopic database

    International Nuclear Information System (INIS)

    Rothman, L.S.; Jacquemart, D.; Barbe, A.

    2005-01-01

    This paper describes the status of the 2004 edition of the HITRAN molecular spectroscopic database. The HITRAN compilation consists of several components that serve as input for radiative transfer calculation codes: individual line parameters for the microwave through visible spectra of molecules in the gas phase; absorption cross-sections for molecules having dense spectral features, i.e., spectra in which the individual lines are unresolvable; individual line parameters and absorption cross-sections for bands in the ultra-violet; refractive indices of aerosols; tables and files of general properties associated with the database; and database management software. The line-by-line portion of the database contains spectroscopic parameters for 39 molecules including many of their isotopologues. The format of the section of the database on individual line parameters of HITRAN has undergone the most extensive enhancement in almost two decades. It now lists the Einstein A-coefficients, statistical weights of the upper and lower levels of the transitions, a better system for the representation of quantum identifications, and enhanced referencing and uncertainty codes. In addition, there is a provision for making corrections to the broadening of line transitions due to line mixing

  7. Identifying structural variants using linked-read sequencing data.

    Science.gov (United States)

    Elyanow, Rebecca; Wu, Hsin-Ta; Raphael, Benjamin J

    2017-11-03

    Structural variation, including large deletions, duplications, inversions, translocations, and other rearrangements, is common in human and cancer genomes. A number of methods have been developed to identify structural variants from Illumina short-read sequencing data. However, reliable identification of structural variants remains challenging because many variants have breakpoints in repetitive regions of the genome and thus are difficult to identify with short reads. The recently developed linked-read sequencing technology from 10X Genomics combines a novel barcoding strategy with Illumina sequencing. This technology labels all reads that originate from a small number (~5-10) DNA molecules ~50Kbp in length with the same molecular barcode. These barcoded reads contain long-range sequence information that is advantageous for identification of structural variants. We present Novel Adjacency Identification with Barcoded Reads (NAIBR), an algorithm to identify structural variants in linked-read sequencing data. NAIBR predicts novel adjacencies in a individual genome resulting from structural variants using a probabilistic model that combines multiple signals in barcoded reads. We show that NAIBR outperforms several existing methods for structural variant identification - including two recent methods that also analyze linked-reads - on simulated sequencing data and 10X whole-genome sequencing data from the NA12878 human genome and the HCC1954 breast cancer cell line. Several of the novel somatic structural variants identified in HCC1954 overlap known cancer genes. Software is available at compbio.cs.brown.edu/software. braphael@princeton.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  8. Functional capacity of XRCC1 protein variants identified in DNA repair-deficient Chinese hamster ovary cell lines and the human population

    DEFF Research Database (Denmark)

    Berquist, Brian R; Singh, Dharmendra Kumar; Fan, Jinshui

    2010-01-01

    XRCC1 operates as a scaffold protein in base excision repair, a pathway that copes with base and sugar damage in DNA. Studies using recombinant XRCC1 proteins revealed that: a C389Y substitution, responsible for the repair defects of the EM-C11 CHO cell line, caused protein instability; a V86R...... mutation abolished the interaction with POLbeta, but did not disrupt the interactions with PARP-1, LIG3alpha and PCNA; and an E98K substitution, identified in EM-C12, reduced protein integrity, marginally destabilized the POLbeta interaction, and slightly enhanced DNA binding. Two rare (P161L and Y576S...

  9. Identifying and validating a combined mRNA and microRNA signature in response to imatinib treatment in a chronic myeloid leukemia cell line.

    Directory of Open Access Journals (Sweden)

    Steven Bhutra

    Full Text Available Imatinib, a targeted tyrosine kinase inhibitor, is the gold standard for managing chronic myeloid leukemia (CML. Despite its wide application, imatinib resistance occurs in 20-30% of individuals with CML. Multiple potential biomarkers have been identified to predict imatinib response; however, the majority of them remain externally uncorroborated. In this study, we set out to systematically identify gene/microRNA (miRNA whose expression changes are related to imatinib response. Through a Gene Expression Omnibus search, we identified two genome-wide expression datasets that contain expression changes in response to imatinib treatment in a CML cell line (K562: one for mRNA and the other for miRNA. Significantly differentially expressed transcripts/miRNAs post imatinib treatment were identified from both datasets. Three additional filtering criteria were applied 1 miRbase/miRanda predictive algorithm; 2 opposite direction of imatinib effect for genes and miRNAs; and 3 literature support. These criteria narrowed our candidate gene-miRNA to a single pair: IL8 and miR-493-5p. Using PCR we confirmed the significant up-regulation and down-regulation of miR-493-5p and IL8 by imatinib treatment, respectively in K562 cells. In addition, IL8 expression was significantly down-regulated in K562 cells 24 hours after miR-493-5p mimic transfection (p = 0.002. Furthermore, we demonstrated significant cellular growth inhibition after IL8 inhibition through either gene silencing or by over-expression of miR-493-5p (p = 0.0005 and p = 0.001 respectively. The IL8 inhibition also further sensitized K562 cells to imatinib cytotoxicity (p < 0.0001. Our study combined expression changes in transcriptome and miRNA after imatinib exposure to identify a potential gene-miRNA pair that is a critical target in imatinib response. Experimental validation supports the relationships between IL8 and miR-493-5p and between this gene-miRNA pair and imatinib sensitivity in a CML cell

  10. Expression Profiling of Differentiating Emerin-Null Myogenic Progenitor Identifies Molecular Pathways Implicated in Their Impaired Differentiation

    Directory of Open Access Journals (Sweden)

    Ashvin Iyer

    2017-10-01

    Full Text Available Mutations in the gene encoding emerin cause Emery-Dreifuss muscular dystrophy (EDMD, a disorder causing progressive skeletal muscle wasting, irregular heart rhythms and contractures of major tendons. RNA sequencing was performed on differentiating wildtype and emerin-null myogenic progenitors to identify molecular pathways implicated in EDMD, 340 genes were uniquely differentially expressed during the transition from day 0 to day 1 in wildtype cells. 1605 genes were uniquely expressed in emerin-null cells; 1706 genes were shared among both wildtype and emerin-null cells. One thousand and forty-seven transcripts showed differential expression during the transition from day 1 to day 2. Four hundred and thirty-one transcripts showed altered expression in both wildtype and emerin-null cells. Two hundred and ninety-five transcripts were differentially expressed only in emerin-null cells and 321 transcripts were differentially expressed only in wildtype cells. DAVID, STRING and Ingenuity Pathway Analysis identified pathways implicated in impaired emerin-null differentiation, including cell signaling, cell cycle checkpoints, integrin signaling, YAP/TAZ signaling, stem cell differentiation, and multiple muscle development and myogenic differentiation pathways. Functional enrichment analysis showed biological functions associated with the growth of muscle tissue and myogenesis of skeletal muscle were inhibited. The large number of differentially expressed transcripts upon differentiation induction suggests emerin functions during transcriptional reprograming of progenitors to committed myoblasts.

  11. Current Molecular Targeted Therapy in Advanced Gastric Cancer: A Comprehensive Review of Therapeutic Mechanism, Clinical Trials, and Practical Application

    Directory of Open Access Journals (Sweden)

    Kaichun Li

    2016-01-01

    Full Text Available Despite the great progress in the treatment of gastric cancer, it is still the third leading cause of cancer death worldwide. Patients often miss the opportunity for a surgical cure, because the cancer has already developed into advanced cancer when identified. Compared to best supportive care, chemotherapy can improve quality of life and prolong survival time, but the overall survival is often short. Due to the molecular study of gastric cancer, new molecular targeted drugs have entered the clinical use. Trastuzumab, an antibody targeting human epidermal growth factor receptor 2 (HER2, can significantly improve survival in advanced gastric cancer patients with HER2 overexpression. Second-line treatment of advanced gastric cancer with ramucirumab, an antibody targeting VEGFR-2, alone or in combination with paclitaxel, has been proved to provide a beneficial effect. The VEGFR-2 tyrosine kinase inhibitor, apatinib, can improve the survival of advanced gastric cancer patients after second-line chemotherapy failure. Unfortunately, none of the EGFR targeting antibodies (cetuximab or panitumumab, VEGF targeting monoclonal antibodies (bevacizumab, mTOR inhibitor (everolimus, or HGF/MET pathway targeting drugs has a significant survival benefit. Many other clinical trials based on molecular markers are underway. This review will summarize targeted therapies for advanced gastric cancer.

  12. DOE-EPRI On-Line Monitoring Implementation Guidelines

    International Nuclear Information System (INIS)

    E. Davis, R. Bickford

    2003-01-01

    Industry and EPRI experience at several plants has shown on-line monitoring to be very effective in identifying out-of-calibration instrument channels or indications of equipment-degradation problems. The EPRI implementation project for on-line monitoring has demonstrated the feasibility of on-line monitoring at several participating nuclear plants. The results have been very encouraging, and substantial progress is anticipated in the coming years

  13. Composition and functional analysis of low-molecular-weight glutenin alleles with Aroona near-isogenic lines of bread wheat

    Directory of Open Access Journals (Sweden)

    Zhang Xiaofei

    2012-12-01

    Full Text Available Abstract Background Low-molecular-weight glutenin subunits (LMW-GS strongly influence the bread-making quality of bread wheat. These proteins are encoded by a multi-gene family located at the Glu-A3, Glu-B3 and Glu-D3 loci on the short arms of homoeologous group 1 chromosomes, and show high allelic variation. To characterize the genetic and protein compositions of LMW-GS alleles, we investigated 16 Aroona near-isogenic lines (NILs using SDS-PAGE, 2D-PAGE and the LMW-GS gene marker system. Moreover, the composition of glutenin macro-polymers, dough properties and pan bread quality parameters were determined for functional analysis of LMW-GS alleles in the NILs. Results Using the LMW-GS gene marker system, 14–20 LMW-GS genes were identified in individual NILs. At the Glu-A3 locus, two m-type and 2–4 i-type genes were identified and their allelic variants showed high polymorphisms in length and nucleotide sequences. The Glu-A3d allele possessed three active genes, the highest number among Glu-A3 alleles. At the Glu-B3 locus, 2–3 m-type and 1–3 s-type genes were identified from individual NILs. Based on the different compositions of s-type genes, Glu-B3 alleles were divided into two groups, one containing Glu-B3a, B3b, B3f and B3g, and the other comprising Glu-B3c, B3d, B3h and B3i. Eight conserved genes were identified among Glu-D3 alleles, except for Glu-D3f. The protein products of the unique active genes in each NIL were detected using protein electrophoresis. Among Glu-3 alleles, the Glu-A3e genotype without i-type LMW-GS performed worst in almost all quality properties. Glu-B3b, B3g and B3i showed better quality parameters than the other Glu-B3 alleles, whereas the Glu-B3c allele containing s-type genes with low expression levels had an inferior effect on bread-making quality. Due to the conserved genes at Glu-D3 locus, Glu-D3 alleles showed no significant differences in effects on all quality parameters. Conclusions This work

  14. Warm and cold molecular gas conditions modeled in 87 galaxies observed by the Herschel SPIRE FTS

    Science.gov (United States)

    Kamenetzky, Julia; Rangwala, Naseem; Glenn, Jason

    2018-01-01

    Molecular gas is the raw material for star formation, and like the interstellar medium (ISM) in general, it can exist in regions of higher and lower excitation. Rotational transitions of the CO molecule are bright and sensitive to cold molecular gas. While the majority of the molecular gas exists in the very cold component traced by CO J=1-0, the higher-J lines trace the highly excited gas that may be more indicative of star formation processes. The atmosphere is opaque to these lines, but the launch of the Herschel Space Observatory made them accessible for study of Galactic and extragalactic sources. We have conducted two-component, non-local thermodynamic equilibrium (non-LTE) modeling of the CO lines from J=1‑0 through J=13‑12 in 87 galaxies observed by the Herschel SPIRE Fourier Transform Spectrometer (FTS). We used the nested sampling algorithm Multinest to compare the measured CO spectral line energy distributions (SLEDs) to the ones produced by a custom version of the non-LTE code RADEX. This allowed us to fully examine the degeneracies in parameter space for kinetic temperature, molecular gas density, CO column density, and area filling factor.Here we discuss the major findings of our study, as well as the important implications of two-component molecular gas modeling. The average pressure of the warm gas is slightly correlated with galaxy LFIR, but that of the cold gas is not. A high-J (such as J=11-10) to J=1-0 line ratio is diagnostic of warm component pressure. We find a very large spread in our derived values of "alpha-CO," with no discernable trend with LFIR, and average molecular gas depletion times that decrease with LFIR. If only a few molecular lines are available in a galaxy's SLED, the limited ability to model only one component will change the results. A one-component fit often underestimates the flux of carbon monoxide (CO) J=1‑0 and the mass. If low-J lines are not included, mass is underestimated by an order of magnitude. Even when

  15. Cine: Line excitation by infrared fluorescence in cometary atmospheres

    Science.gov (United States)

    de Val-Borro, Miguel; Cordiner, Martin A.; Milam, Stefanie N.; Charnley, Steven B.

    2017-03-01

    CINE is a Python module for calculating infrared pumping efficiencies that can be applied to the most common molecules found in cometary comae such as water, hydrogen cyanide or methanol. Excitation by solar radiation of vibrational bands followed by radiative decay to the ground vibrational state is one of the main mechanisms for molecular excitation in comets. This code calculates the effective pumping rates for rotational levels in the ground vibrational state scaled by the heliocentric distance of the comet. Line transitions are queried from the latest version of the HITRAN spectroscopic repository using the astroquery affiliated package of astropy. Molecular data are obtained from the LAMDA database. These coefficients are useful for modeling rotational emission lines observed in cometary spectra at sub-millimeter wavelengths. Combined with computational methods to solve the radiative transfer equations based, e.g., on the Monte Carlo algorithm, this model can retrieve production rates and rotational temperatures from the observed emission spectrum.

  16. Suppression subtractive hybridization profiles of radial growth phase and metastatic melanoma cell lines reveal novel potential targets

    International Nuclear Information System (INIS)

    Sousa, Josane F; Espreafico, Enilza M

    2008-01-01

    Melanoma progression occurs through three major stages: radial growth phase (RGP), confined to the epidermis; vertical growth phase (VGP), when the tumor has invaded into the dermis; and metastasis. In this work, we used suppression subtractive hybridization (SSH) to investigate the molecular signature of melanoma progression, by comparing a group of metastatic cell lines with an RGP-like cell line showing characteristics of early neoplastic lesions including expression of the metastasis suppressor KISS1, lack of αvβ3-integrin and low levels of RHOC. Two subtracted cDNA collections were obtained, one (RGP library) by subtracting the RGP cell line (WM1552C) cDNA from a cDNA pool from four metastatic cell lines (WM9, WM852, 1205Lu and WM1617), and the other (Met library) by the reverse subtraction. Clones were sequenced and annotated, and expression validation was done by Northern blot and RT-PCR. Gene Ontology annotation and searches in large-scale melanoma expression studies were done for the genes identified. We identified 367 clones from the RGP library and 386 from the Met library, of which 351 and 368, respectively, match human mRNA sequences, representing 288 and 217 annotated genes. We confirmed the differential expression of all genes selected for validation. In the Met library, we found an enrichment of genes in the growth factors/receptor, adhesion and motility categories whereas in the RGP library, enriched categories were nucleotide biosynthesis, DNA packing/repair, and macromolecular/vesicular trafficking. Interestingly, 19% of the genes from the RGP library map to chromosome 1 against 4% of the ones from Met library. This study identifies two populations of genes differentially expressed between melanoma cell lines from two tumor stages and suggests that these sets of genes represent profiles of less aggressive versus metastatic melanomas. A search for expression profiles of melanoma in available expression study databases allowed us to point to a

  17. Characterization of stem-like cells in a new astroblastoma cell line

    Energy Technology Data Exchange (ETDEWEB)

    Coban, Esra Aydemir; Kasikci, Ezgi [Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Yeditepe University, Istanbul (Turkey); Karatas, Omer Faruk [Molecular Biology and Genetics Department, Erzurum Technical University, Erzurum (Turkey); Suakar, Oznur; Kuskucu, Aysegul [Department of Medical Genetics, Yeditepe University Medical School and Yeditepe University Hospital, Istanbul (Turkey); Altunbek, Mine [Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Yeditepe University, Istanbul (Turkey); Türe, Uğur [Department of Neurosurgery, Yeditepe University School of Medicine, Istanbul (Turkey); Sahin, Fikrettin [Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Yeditepe University, Istanbul (Turkey); Bayrak, Omer Faruk, E-mail: ofbayrak@yeditepe.edu.tr [Department of Medical Genetics, Yeditepe University Medical School and Yeditepe University Hospital, Istanbul (Turkey)

    2017-03-15

    Cell lines established from tumors are the most commonly used models in cancer research, and their use in recent years has enabled a greater understanding of the biology of cancer and the means to develop effective treatment strategies. Astroblastomas are uncommon neuroepithelial tumors of glial origin, predominantly affecting young people, mainly teenagers and children, predominantly females. To date, only a single study has reported that astroblastomas contain a large number of neural stem-like cells, which had only a partial proliferation capacity and differentiation. Our objective was to establish an astroblastoma cell line to investigate the presence of astroblastic cells and cancer stem-like cells. The migratory and invasion abilities of the cells were quantified with invasion and migration assays and compared to a glioblastoma cell line. The presence of stem cells was detected with surface-marker analysis by using flow cytometry, and measuring the differentiation ability with a differentiation assay and the self-renewal capacity with a sphere-forming assay. These characteristics may determine whether this novel cell line is a model for astroblastomas that may have stem-cell characteristics. With this novel cell line, scientists can investigate the molecular pathways underlying astroblastomas and develop new therapeutic strategies for patients with these tumors. - Highlights: • An establishment of a novel astroblastoma cell line was proposed. • The presence of astroblastic cells and cancer stem-like cells was investigated. • The molecular pathways underlying astroblastomas may be investigated. • New therapeutic strategies for patients with astroblastoma may be developed.

  18. GARLIC — A general purpose atmospheric radiative transfer line-by-line infrared-microwave code: Implementation and evaluation

    International Nuclear Information System (INIS)

    Schreier, Franz; Gimeno García, Sebastián; Hedelt, Pascal; Hess, Michael; Mendrok, Jana; Vasquez, Mayte; Xu, Jian

    2014-01-01

    A suite of programs for high resolution infrared-microwave atmospheric radiative transfer modeling has been developed with emphasis on efficient and reliable numerical algorithms and a modular approach appropriate for simulation and/or retrieval in a variety of applications. The Generic Atmospheric Radiation Line-by-line Infrared Code — GARLIC — is suitable for arbitrary observation geometry, instrumental field-of-view, and line shape. The core of GARLIC's subroutines constitutes the basis of forward models used to implement inversion codes to retrieve atmospheric state parameters from limb and nadir sounding instruments. This paper briefly introduces the physical and mathematical basics of GARLIC and its descendants and continues with an in-depth presentation of various implementation aspects: An optimized Voigt function algorithm combined with a two-grid approach is used to accelerate the line-by-line modeling of molecular cross sections; various quadrature methods are implemented to evaluate the Schwarzschild and Beer integrals; and Jacobians, i.e. derivatives with respect to the unknowns of the atmospheric inverse problem, are implemented by means of automatic differentiation. For an assessment of GARLIC's performance, a comparison of the quadrature methods for solution of the path integral is provided. Verification and validation are demonstrated using intercomparisons with other line-by-line codes and comparisons of synthetic spectra with spectra observed on Earth and from Venus. - Highlights: • High resolution infrared-microwave radiative transfer model. • Discussion of algorithmic and computational aspects. • Jacobians by automatic/algorithmic differentiation. • Performance evaluation by intercomparisons, verification, validation

  19. FLI-1 Flightless-1 and LET-60 Ras control germ line morphogenesis in C. elegans

    Directory of Open Access Journals (Sweden)

    Dentler William L

    2008-05-01

    Full Text Available Abstract Background In the C. elegans germ line, syncytial germ line nuclei are arranged at the cortex of the germ line as they exit mitosis and enter meiosis, forming a nucleus-free core of germ line cytoplasm called the rachis. Molecular mechanisms of rachis formation and germ line organization are not well understood. Results Mutations in the fli-1 gene disrupt rachis organization without affecting meiotic differentiation, a phenotype in C. elegans referred to here as the germ line morphogenesis (Glm phenotype. In fli-1 mutants, chains of meiotic germ nuclei spanned the rachis and were partially enveloped by invaginations of germ line plasma membrane, similar to nuclei at the cortex. Extensions of the somatic sheath cells that surround the germ line protruded deep inside the rachis and were associated with displaced nuclei in fli-1 mutants. fli-1 encodes a molecule with leucine-rich repeats and gelsolin repeats similar to Drosophila flightless 1 and human Fliih, which have been shown to act as cytoplasmic actin regulators as well as nuclear transcriptional regulators. Mutations in let-60 Ras, previously implicated in germ line development, were found to cause the Glm phenotype. Constitutively-active LET-60 partially rescued the fli-1 Glm phenotype, suggesting that LET-60 Ras and FLI-1 might act together to control germ line morphogenesis. Conclusion FLI-1 controls germ line morphogenesis and rachis organization, a process about which little is known at the molecular level. The LET-60 Ras GTPase might act with FLI-1 to control germ line morphogenesis.

  20. Molecular evolution of rbcL in three gymnosperm families: identifying adaptive and coevolutionary patterns

    LENUS (Irish Health Repository)

    Sen, Lin

    2011-06-03

    Abstract Background The chloroplast-localized ribulose-1, 5-biphosphate carboxylase\\/oxygenase (Rubisco), the primary enzyme responsible for autotrophy, is instrumental in the continual adaptation of plants to variations in the concentrations of CO2. The large subunit (LSU) of Rubisco is encoded by the chloroplast rbcL gene. Although adaptive processes have been previously identified at this gene, characterizing the relationships between the mutational dynamics at the protein level may yield clues on the biological meaning of such adaptive processes. The role of such coevolutionary dynamics in the continual fine-tuning of RbcL remains obscure. Results We used the timescale and phylogenetic analyses to investigate and search for processes of adaptive evolution in rbcL gene in three gymnosperm families, namely Podocarpaceae, Taxaceae and Cephalotaxaceae. To understand the relationships between regions identified as having evolved under adaptive evolution, we performed coevolutionary analyses using the software CAPS. Importantly, adaptive processes were identified at amino acid sites located on the contact regions among the Rubisco subunits and on the interface between Rubisco and its activase. Adaptive amino acid replacements at these regions may have optimized the holoenzyme activity. This hypothesis was pinpointed by evidence originated from our analysis of coevolution that supported the correlated evolution between Rubisco and its activase. Interestingly, the correlated adaptive processes between both these proteins have paralleled the geological variation history of the concentration of atmospheric CO2. Conclusions The gene rbcL has experienced bursts of adaptations in response to the changing concentration of CO2 in the atmosphere. These adaptations have emerged as a result of a continuous dynamic of mutations, many of which may have involved innovation of functional Rubisco features. Analysis of the protein structure and the functional implications of such

  1. The Association of Molecular Gas and Natal Super Star Clusters in Henize 2–10

    Science.gov (United States)

    Johnson, Kelsey E.; Brogan, Crystal L.; Indebetouw, Remy; Testi, Leonardo; Wilner, David J.; Reines, Amy E.; Chen, C.-H. Rosie; Vanzi, Leonardo

    2018-02-01

    We present ALMA observations of the dwarf starburst galaxy He 2–10 in combination with previous SMA CO observations to probe the molecular environments of natal super star clusters (SSCs). These observations include the HCO+(1-0), HCN(1-0), HNC(1-0), and CCH(1-0) molecular lines, as well as 88 GHz continuum with a spatial resolution of 1\\buildrel{\\prime\\prime}\\over{.} 7× 1\\buildrel{\\prime\\prime}\\over{.} 6. After correcting for the contribution from free–free emission to the 88 GHz continuum flux density (∼60% of the 88 GHz emission), we derive a total gas mass for He 2–10 of {M}{gas}=4{--}6× {10}8 M ⊙, roughly 5%–20% of the dynamical mass. Based on a principle component analysis, HCO+ is found to be the best “general” tracer of molecular emission. The line widths and luminosities of the CO emission suggests that the molecular clouds could either be as small as ∼8 pc, or alternately have enhanced line widths. The CO emission and 88 GHz continuum are anti-correlated, suggesting that either the dust and molecular gas are not cospatial, which could reflect that the 88 GHz continuum is dominated by free–free emission. The CO and CCH emission are also relatively anti-correlated, which is consistent with the CCH being photo-enhanced, and/or the CO being dissociated in the regions near the natal SSCs. The molecular line ratios of regions containing the natal star clusters are different from the line ratios observed for regions elsewhere in the galaxy. In particular, the regions with thermal radio emission all have {CO}(2{--}1)/{{HCO}}+(1-0)correlated with the evolutionary stage of the clusters.

  2. Multiplex flow cytometry barcoding and antibody arrays identify surface antigen profiles of primary and metastatic colon cancer cell lines.

    Directory of Open Access Journals (Sweden)

    Kumar Sukhdeo

    Full Text Available Colon cancer is a deadly disease affecting millions of people worldwide. Current treatment challenges include management of disease burden as well as improvements in detection and targeting of tumor cells. To identify disease state-specific surface antigen signatures, we combined fluorescent cell barcoding with high-throughput flow cytometric profiling of primary and metastatic colon cancer lines (SW480, SW620, and HCT116. Our multiplexed technique offers improvements over conventional methods by permitting the simultaneous and rapid screening of cancer cells with reduced effort and cost. The method uses a protein-level analysis with commercially available antibodies on live cells with intact epitopes to detect potential tumor-specific targets that can be further investigated for their clinical utility. Multiplexed antibody arrays can easily be applied to other tumor types or pathologies for discovery-based approaches to target identification.

  3. Advanced chordoma treated by first-line molecular targeted therapies: Outcomes and prognostic factors. A retrospective study of the French Sarcoma Group (GSF/GETO) and the Association des Neuro-Oncologues d'Expression Française (ANOCEF).

    Science.gov (United States)

    Lebellec, Loïc; Chauffert, Bruno; Blay, Jean-Yves; Le Cesne, Axel; Chevreau, Christine; Bompas, Emmanuelle; Bertucci, François; Cupissol, Didier; Fabbro, Michel; Saada-Bouzid, Esma; Duffaud, Florence; Feuvret, Loïc; Bonneville-Levard, Alice; Bay, Jacques-Olivier; Vauleon, Elodie; Vinceneux, Armelle; Noel, Georges; Penel, Nicolas; Mir, Olivier

    2017-07-01

    To assess the role of first-line Molecular Targeted Therapies (MTTs) in Advanced chordoma (AC) patients. Retrospective study of 80 patients treated between January 2004 and December 2015 at 15 major French Sarcoma or Neurooncology Centres. The sex ratio M/F was 46/34. The median age was 59 (6-86) years. The primary sites were the sacrum (50, 62.5%), mobile spine (12, 15.0%), and skull base (18, 22.5%). Metastases were present in 28 patients (36.0%). The first line of MTTs consisted of imatinib (62, 77.5%), sorafenib (11, 13.7%), erlotinib (5, 6.3%), sunitinib (1, 1.2%) and temsirolimus (1, 1.2%). The reported responses were: partial response (5, 6.3%), stable disease (58, 72.5%), or progressive disease (10, 12.5%). Symptomatic improvement was seen in 28/66 assessable patients (42.4%) and was associated with an objective response occurrence (p = 0.005), imatinib (p = 0.020) or erlotinib use (p = 0.028). The median progression-free survival (PFS) was 9.4°months (95% CI, [6.8-16.1]). Two independent factors of poor prognosis for PFS were identified: a skull-based primary location (HR = 2.5, p = 0.019), and the interval between diagnosis and MTT of guide treatment decisions and design further clinical trials. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Low density molecular cloud in the vicinity of the Pleiades

    International Nuclear Information System (INIS)

    Federman, S.R.; Wilson, R.F.

    1984-01-01

    The central region of a small, low density molecular cloud, which lies to the south of the Pleiades cluster, has been studied through the use of molecular line observations. Column densities for CH, OH, 12 CO, and 13 CO are derived from the radio data. The CH and OH data yield a visual extinction through the center of the cloud of about 3 mag. The ratio of the antenna temperatures for the OH main lines is consistent with optically thin emission; therefore, the OH results are a good indication of the total extinction through the optically thin emission; therefore, the OH results are a good indication of the total extinction through the cloud. The analysis of the carbon monoxide data produces a relatively high kinetic temperature of at least 20 K, a low total gas density of approx.300-500 cm -3 , and a column density of approx.4 x 10 17 cm -2 for 12 CO. Thus this small molecular cloud is not typical of the molecular material generally studied in Taurus

  5. CellMiner: a relational database and query tool for the NCI-60 cancer cell lines

    Directory of Open Access Journals (Sweden)

    Reinhold William C

    2009-06-01

    Full Text Available Abstract Background Advances in the high-throughput omic technologies have made it possible to profile cells in a large number of ways at the DNA, RNA, protein, chromosomal, functional, and pharmacological levels. A persistent problem is that some classes of molecular data are labeled with gene identifiers, others with transcript or protein identifiers, and still others with chromosomal locations. What has lagged behind is the ability to integrate the resulting data to uncover complex relationships and patterns. Those issues are reflected in full form by molecular profile data on the panel of 60 diverse human cancer cell lines (the NCI-60 used since 1990 by the U.S. National Cancer Institute to screen compounds for anticancer activity. To our knowledge, CellMiner is the first online database resource for integration of the diverse molecular types of NCI-60 and related meta data. Description CellMiner enables scientists to perform advanced querying of molecular information on NCI-60 (and additional types through a single web interface. CellMiner is a freely available tool that organizes and stores raw and normalized data that represent multiple types of molecular characterizations at the DNA, RNA, protein, and pharmacological levels. Annotations for each project, along with associated metadata on the samples and datasets, are stored in a MySQL database and linked to the molecular profile data. Data can be queried and downloaded along with comprehensive information on experimental and analytic methods for each data set. A Data Intersection tool allows selection of a list of genes (proteins in common between two or more data sets and outputs the data for those genes (proteins in the respective sets. In addition to its role as an integrative resource for the NCI-60, the CellMiner package also serves as a shell for incorporation of molecular profile data on other cell or tissue sample types. Conclusion CellMiner is a relational database tool for

  6. Determination of molecular markers associated with anthesis-silking interval in maize

    International Nuclear Information System (INIS)

    Simpson, J.

    1998-01-01

    Maize lines contrasting in anthesis-silking, interval (ASI), a trait strongly linked to drought tolerance, have been analyzed under different water stress conditions in the field and with molecular markers. Correlation of marker and field data has revealed molecular markers strongly associated with flowering and yield traits. (author)

  7. Ewald Electrostatics for Mixtures of Point and Continuous Line Charges.

    Science.gov (United States)

    Antila, Hanne S; Tassel, Paul R Van; Sammalkorpi, Maria

    2015-10-15

    Many charged macro- or supramolecular systems, such as DNA, are approximately rod-shaped and, to the lowest order, may be treated as continuous line charges. However, the standard method used to calculate electrostatics in molecular simulation, the Ewald summation, is designed to treat systems of point charges. We extend the Ewald concept to a hybrid system containing both point charges and continuous line charges. We find the calculated force between a point charge and (i) a continuous line charge and (ii) a discrete line charge consisting of uniformly spaced point charges to be numerically equivalent when the separation greatly exceeds the discretization length. At shorter separations, discretization induces deviations in the force and energy, and point charge-point charge correlation effects. Because significant computational savings are also possible, the continuous line charge Ewald method presented here offers the possibility of accurate and efficient electrostatic calculations.

  8. High-resolution Laboratory Measurements of Coronal Lines near the Fe IX Line at 171 Å

    Science.gov (United States)

    Beiersdorfer, Peter; Träbert, Elmar

    2018-02-01

    We present high-resolution laboratory measurements in the spectral region between 165 and 175 Å that focus on the emission from various ions of C, O, F, Ne, S, Ar, Fe, and Ni. This wavelength region is centered on the λ171 Fe IX channel of the Atmospheric Imaging Assembly on the Solar Dynamics Observatory, and we place special emphasis on the weaker emission lines of Fe IX predicted in this region. In general, our measurements show a multitude of weak lines missing in the current databases, where the emission lines of Ni are probably most in need of further identification and reclassification. We also find that the wavelengths of some of the known lines need updating. Using the multi-reference Møller–Plesset method for wavelength predictions and collisional-radiative modeling of the line intensities, we have made tentative assignments of more than a dozen lines to the spectrum of Fe IX, some of which have formerly been identified as Fe VII, Fe XIV, or Fe XVI lines. Several Fe features remain unassigned, although they appear to be either Fe VII or Fe X lines. Further work will be needed to complete and correct the spectral line lists in this wavelength region.

  9. Metabolic and molecular changes of the phenylpropanoid pathway in tomato (Solanum lycopersicum lines carrying different Solanum pennellii wild chromosomal regions

    Directory of Open Access Journals (Sweden)

    Maria Manuela Rigano

    2016-10-01

    Full Text Available Solanum lycopersicum represents an important dietary source of bioactive compounds including the antioxidants flavonoids and phenolic acids. We previously identified two genotypes (IL7-3 and IL12-4 carrying loci from the wild species Solanum pennellii, which increased antioxidants in the fruit. Successively, these lines were crossed and two genotypes carrying both introgressions at the homozygous condition (DHO88 and DHO88-SL were selected. The amount of total antioxidant compounds was increased in DHOs compared to both ILs and the control genotype M82. In order to understand the genetic mechanisms underlying the positive interaction between the two wild regions pyramided in DHO genotypes, detailed analyses of the metabolites accumulated in the fruit were carried out by colorimetric methods and LC/MS/MS. These analyses evidenced a lower content of flavonoids in DHOs and in ILs, compared to M82. By contrast, in the DHOs the relative content of phenolic acids increased, particularly the fraction of hexoses, thus evidencing a redirection of the phenylpropanoid flux towards the biosynthesis of phenolic acid glycosides in these genotypes. In addition, the line DHO88 exhibited a lower content of free phenolic acids compared to M82. Interestingly, the two DHOs analyzed differ in the size of the wild region on chromosome 12. Genes mapping in the introgression regions were further investigated. Several genes of the phenylpropanoid biosynthetic pathway were identified, such as one 4-coumarate:CoA ligase and two UDP-glycosyltransferases in the region 12-4 and one chalcone isomerase and one UDP-glycosyltransferase in the region 7-3. Transcriptomic analyses demonstrated a different expression of the detected genes in the ILs and in the DHOs compared to M82.These analyses, combined with biochemical analyses, suggested a central role of the 4-coumarate:CoA ligase in redirecting the phenylpropanoid pathways towards the biosynthesis of phenolic acids in the

  10. Molecular environmental science and synchrotron radiation sources

    Energy Technology Data Exchange (ETDEWEB)

    Brown, G.E. Jr. [Stanford Univ., CA (United States)

    1995-12-31

    Molecular environmental science is a relatively new field but focuses on the chemical and physical forms of toxic and/or radioactive contaminants in soils, sediments, man-made waste forms, natural waters, and the atmosphere; their possible reactions with inorganic and organic compounds, plants, and organisms in the environment; and the molecular-level factors that control their toxicity, bioavailability, and transport. The chemical speciation of a contaminant is a major factor in determining its behavior in the environment, and synchrotron-based X-ray absorption fine structure (XAFS) spectroscopy is one of the spectroscopies of choice to quantitatively determine speciation of heavy metal contaminants in situ without selective extraction or other sample treatment. The use of high-flux insertion device beam lines at synchrotron sources and multi-element array detectors has permitted XAFS studies of metals such as Se and As in natural soils at concentration levels as low as 50 ppm. The X-ray absorption near edge structure of these metals is particularly useful in determining their oxidation state. Examples of such studies will be presented, and new insertion device beam lines under development at SSRL and the Advanced Photon Source for molecular environmental science applications will be discussed.

  11. Three millimeter molecular line observations in Sagittarius B2. 1: Full synthesis mapping study of HNO, CCS, and HC(13)CCN

    Science.gov (United States)

    Kuan, Yi-Jehng; Snyder, Lewis E.

    1994-01-01

    We present the first full synthesis maps of the small molecules HNO, CCS, and HC(13)CCN in Sgr B2. We have observed the 3.8 mm continuum, the HNO J(sub K(sub -1)K(sub 1)) = 1(sub O1)-0(sub OO), the CCS J(sub N) = 7(sub 6)-6(sub 5), and the HC(13)CCN J = 9-8 transitions in the core of the Sgr B2 molecular cloud, using the Berkeley Illinois Maryland Association (BIMA) millimeter array and the NRAO 12 m telescope. We have found that HNO exists in five major gas clumps in the Sgr B2 region, which we have labeled HNO(N), HNO(NW), HNO(E), HNO(M), and HNO(S). Of particular interest is HNO(M), a major molecular gas concentration approximately 15 sec west of Sgr B2(M) in a region of young star formation. HNO is found to be closely associated with the ionized gas and might be depleted around bright H II complexes. In general, the peak intensity of the HNO emission is found to be offset from the peak of the continuum emission. We found evidence for some chemical differentiation among the three species, HNO, CCS, and HC(13)CCN, but the abundance ratios are in fair agreement with theoretical models. Two unidentified lines, U81420 and U81518, were observed, and a previously unknown compact dust source was detected. Our HNO data indicate the presence of a rotating approximately (2.2-4.4) x 10(exp 3)solar mass gas envelope surrounding Sgr B2(N), a possible bipolar gas outflow in HNO(M), and possibly a large (approximately 4.2 x 10(exp 4)solar mass) extended rotating disk associated with HNO(S). In addition, the CCS and HC(13)CCN data approximately outline the extended component of Sgr B2 and clearly show that the southern continuum source Sgr B2(S) is actually a major molecular source as well. Consequently, the kinematics of the Sgr B2 molecular cloud is quite complex, but in moving from the northwest to south, the LSR velocity generally changes from 79 to 46 km/s.

  12. An Algorithm to Compress Line-transition Data for Radiative-transfer Calculations

    Science.gov (United States)

    Cubillos, Patricio E.

    2017-11-01

    Molecular line-transition lists are an essential ingredient for radiative-transfer calculations. With recent databases now surpassing the billion-line mark, handling them has become computationally prohibitive, due to both the required processing power and memory. Here I present a temperature-dependent algorithm to separate strong from weak line transitions, reformatting the large majority of the weaker lines into a cross-section data file, and retaining the detailed line-by-line information of the fewer strong lines. For any given molecule over the 0.3-30 μm range, this algorithm reduces the number of lines to a few million, enabling faster radiative-transfer computations without a significant loss of information. The final compression rate depends on how densely populated the spectrum is. I validate this algorithm by comparing Exomol’s HCN extinction-coefficient spectra between the complete (65 million line transitions) and compressed (7.7 million) line lists. Over the 0.6-33 μm range, the average difference between extinction-coefficient values is less than 1%. A Python/C implementation of this algorithm is open-source and available at https://github.com/pcubillos/repack. So far, this code handles the Exomol and HITRAN line-transition format.

  13. Phosphorus Partitioning of Soybean Lines Containing Different Mutant Alleles of Two Soybean Seed-Specific Adenosine Triphosphate-Binding Cassette Phytic Acid Transporter Paralogs

    Directory of Open Access Journals (Sweden)

    Jason D. Gillman

    2013-03-01

    Full Text Available Seed phytate is a repository of P and minerals in soybean [ (L. Merr.] seeds that limits P and mineral bioavailability for monogastric animals (e.g., humans, swine [], and poultry [especially chicken, ] due to insufficient digestive tract phytase activity. We previously identified epistatic recessive mutations affecting two paralogous adenosine triphosphate-binding cassette phytic acid transporter genes (one a nonsense mutation in and the other a missense mutation in as the molecular genetic basis in the ethyl methanesulfonate (EMS-induced mutant low phytate soybean line M153. An additional mutant low phytate line, M766, contained one single nucleotide polymorphism within the ninth intron of the locus as well as a nonsense mutation in . The objectives of this research were to clarify the genetics underlying the low phytate phenotype in line M766 and to determine P partitioning in new combinations of mutant alleles from M766 and M153. Inheritance of nonsense alleles affecting both ( genes (one from M153 and one from M766 led to the production of viable seeds that contained transgressive reductions in total seed phytate and significantly higher levels of inorganic phosphate than has been reported for nontransgenic soybean material and will allow efficient molecular selection of soybeans with even greater reductions of phytate for improved quality soybean meal.

  14. Selecting physician leaders for clinical service lines: critical success factors.

    Science.gov (United States)

    Epstein, Andrew L; Bard, Marc A

    2008-03-01

    Clinical service lines and interdisciplinary centers have emerged as important strategic programs within academic health centers (AHCs). Effective physician leadership is significant to their success, but how these leaders are chosen has not been well studied. The authors conducted a study to identify current models for selecting the physician leaders of clinical service lines, determine critical success factors, and learn how the search process affected service line performance. In 2003 and 2004, the authors interviewed clinical and executive personnel involved in 14 programs to establish, or consider establishing, heart or cancer service lines, at 13 AHCs. The responses were coded to identify and analyze trends and themes. The key findings of the survey were (1) the goals and expectations that AHCs set for their service line leaders vary greatly, depending on both the strategic purpose of the service line in the AHC and the service line's stage of development, (2) the matrix organizational structure employed by most AHCs limits the leader's authority over necessary resources, and calls forth a variety of compensating strategies if the service line is to succeed, (3) the AHCs studied used relatively informal processes to identify, evaluate, and select service line leaders, and (4) the leader's job is vitally shaped by the AHC's strategic, structural, and political context, and selection criteria should be determined accordingly. Institutions should be explicit about the strategic purpose and stage of development of their clinical service lines and be clear about their expectations and requirements in hiring service line leaders.

  15. Influence of process parameters on the weld lines of a micro injection molded component

    DEFF Research Database (Denmark)

    Tosello, Guido; Gava, Alberto; Hansen, Hans Nørgaard

    2007-01-01

    The insufficient entanglement of the molecular chains and the stress amplification at the v-notch of a weld line compromise the mechanical strength of a plastic product, also in the micro scale. To investigate the influence of process parameters on the weld lines formation, a special micro cavity...... was designed and manufactured by µEDM (Electro Discharge Machining). Weld lines were quantitatively characterized both in the two-dimensional (direction and position) and three-dimensional range (surface topography characterization). Results showed that shape and position of weld lines are mainly influenced...

  16. Los resonance lines in promethiumlike heavy ions

    International Nuclear Information System (INIS)

    Nakamura, Nobuyuki; Kobayashi, Yusuke; Kato, Daiji; Sakaue, Hiroyuki A.; Murakami, Izumi

    2016-01-01

    Identifying the ns - np resonance lines in alkali-metal-like ions is an important issue in fusion plasma science in the view of spectroscopic diagnostics and radiation power loss. Whereas for n=2, 3 and 4 these resonances are prominent and well studied, so far no one could clearly identify the resonance lines for n=5 in the promethiumlike sequence. We have now experimentally clarified the reason for the 'lost resonance lines. In the present study, highly-charged bismuth ions have been studied using a compact electron beam ion trap (EBIT). Extreme ultraviolet emission from the bismuth ions produced and trapped in the EBIT is observed with a grazing-incidence flat-field spectrometer. The energy dependent spectra are compared with a collisional-radiative model calculation, and we show that the 5s - 5p resonance lines are very weak in plasma with a wide range of electron density due to the presence of a long-lived metastable state. (author)

  17. MOLECULAR ENVIRONMENTS OF 51 PLANCK COLD CLUMPS IN THE ORION COMPLEX

    International Nuclear Information System (INIS)

    Liu Tie; Wu Yuefang; Zhang Huawei

    2012-01-01

    A mapping survey of 51 Planck cold clumps projected on the Orion complex was performed with J = 1–0 lines of 12 CO and 13 CO with the 13.7 m telescope at the Purple Mountain Observatory. The mean column densities of the Planck gas clumps range from 0.5 to 9.5 × 10 21 cm –2 , with an average value of (2.9 ± 1.9) × 10 21 cm –2 . The mean excitation temperatures of these clumps range from 7.4 to 21.1 K, with an average value of 12.1 ± 3.0 K and the average three-dimensional velocity dispersion σ 3D in these molecular clumps is 0.66 ± 0.24 km s –1 . Most of the clumps have σ NT larger than or comparable to σ Therm . The H 2 column density of the molecular clumps calculated from molecular lines correlates with the aperture flux at 857 GHz of the dust emission. By analyzing the distributions of the physical parameters, we suggest that turbulent flows can shape the clump structure and dominate their density distribution on large scales, but not function on small scales due to local fluctuations. Eighty-two dense cores are identified in the molecular clumps. The dense cores have an average radius and local thermal equilibrium (LTE) mass of 0.34 ± 0.14 pc and 38 +5 –30 M ☉ , respectively. The structures of low column density cores are more affected by turbulence, while the structures of high column density cores are more affected by other factors, especially by gravity. The correlation of velocity dispersion versus core size is very weak for the dense cores. The dense cores are found to be most likely gravitationally bounded rather than pressure confined. The relationship between M vir and M LTE can be well fitted with a power law. The core mass function here is much flatter than the stellar initial mass function. The lognormal behavior of the core mass distribution is most likely determined by internal turbulence.

  18. Physical properties of CO-dark molecular gas with C+ and OH observations

    Science.gov (United States)

    Tang, Ningyu; Li, Di; Heiles, Carl E.; ISM Group in National Astronomical Observatories, CAS

    2017-01-01

    The lifecycle of interstellar medium (ISM) is critical for understanding galaxy evolution. The transition between atomic neutral medium and dense molecular gas, however, cannot be traced adequately by either HI or CO emission. Results from dust observations of Planck all-sky mission and gamma-ray observations of Energetic Gamma Ray Experiment Telescope (EGRET) have revealed the existence of “CO dark molecular gas” (DMG) - molecular gas without CO emission. The physical conditions of DMG including density, temperature, and molecular composition are basis of understanding the ISM evolution. We analyzed physical properties of DMG with HI-self absorption and C+ fine line emission at 158 um toward the lines of sight of Galactic Observations of Terahertz C+ (GOTC+). DMG clouds have a median excitation temperature of 56 K and median volume density of 230 cm2, showing intermediate physical properties between atomic and molecular gas. Sixteen DMG clouds with high visual extinction (AV>=2.7 mag) were found. CO abundance compared to H2 in these clouds is two orders magnitude smaller than the cannonical value in the Milky Way and cannot be explained by the chemical evolutionary model. They may be formed through the agglomeration of pre-existing molecular gas in the Milky Way. We have finished a follow up survey of OH 18 cm lines toward 51 sightlines of GOTC+ including sightlines with DMG clouds through Arecibo telescope. DMG may result in the absence of correlation between CO and OH column density. A possible correlation was found between C+ and OH column density in tracing DMG.

  19. The Cellosaurus, a Cell-Line Knowledge Resource

    Science.gov (United States)

    Bairoch, Amos

    2018-01-01

    The Cellosaurus is a knowledge resource on cell lines. It aims to describe all cell lines used in biomedical research. Its scope encompasses both vertebrates and invertebrates. Currently, information for >100,000 cell lines is provided. For each cell line, it provides a wealth of information, cross-references, and literature citations. The Cellosaurus is available on the ExPASy server (https://web.expasy.org/cellosaurus/) and can be downloaded in a variety of formats. Among its many uses, the Cellosaurus is a key resource to help researchers identify potentially contaminated/misidentified cell lines, thus contributing to improving the quality of research in the life sciences. PMID:29805321

  20. Emergent scar lines in chaotic advection of passive directors

    Science.gov (United States)

    Hejazi, Bardia; Mehlig, Bernhard; Voth, Greg A.

    2017-12-01

    We examine the spatial field of orientations of slender fibers that are advected by a two-dimensional fluid flow. The orientation field of these passive directors are important in a wide range of industrial and geophysical flows. We introduce emergent scar lines as the dominant coherent structures in the orientation field of passive directors in chaotic flows. Previous work has identified the existence of scar lines where the orientation rotates by π over short distances, but the lines that were identified disappeared as time progressed. As a result, earlier work focused on topological singularities in the orientation field, which we find to play a negligible role at long times. We use the standard map as a simple time-periodic two-dimensional flow that produces Lagrangian chaos. This class of flows produces persistent patterns in passive scalar advection and we find that a different kind of persistent pattern develops in the passive director orientation field. We identify the mechanism by which emergent scar lines grow to dominate these patterns at long times in complex flows. Emergent scar lines form where the recent stretching of the fluid element is perpendicular to earlier stretching. Thus these scar lines can be labeled by their age, defined as the time since their stretching reached a maximum.

  1. Composite Materials in Overhead Lines

    DEFF Research Database (Denmark)

    Sørensen, Thomas Kjærsgaard; Holbøll, Joachim

    2009-01-01

    towers and recently conductors based on composite materials are available at transmission levels. In this paper it is investigated which composite based solutions are available in connection with complete overhead line systems including insulators, towers and conductors. The components are reviewed......The use of composite materials, e.g. fibreglass materials, in overhead transmission line systems is nothing new. Composite based insulators have been applied to transmission lines for over 30 years, mainly as suspension and post insulators and often as an option for special applications. Also...... with respect to solved and persisting known failures/problems of both mechanical and electrical nature. Major challenges related to extensive use of composite materials in an overhead line system are identified, as are possible benefits - both when using standard as well as customised composite components, e...

  2. Characterization of some bread wheat genotypes using molecular markers for drought tolerance.

    Science.gov (United States)

    Ateş Sönmezoğlu, Özlem; Terzi, Begüm

    2018-02-01

    Because of its wide geographical adaptation and importance in human nutrition, wheat is one of the most important crops in the world. However, wheat yield has reduced due to drought stress posing threat to sustainability and world food security in agricultural production. The first stage of drought tolerant variety breeding occurs on the molecular and biochemical characterization and classification of wheat genotypes. The aim of the present study is characterization of widely grown bread wheat cultivars and breeding lines for drought tolerance so as to be adapted to different regions in Turkey. The genotypes were screened with molecular markers for the presence of QTLs mapped to different chromosomes. Results of the molecular studies identified and detected 15 polymorphic SSR markers which gave the clearest PCR bands among the control genotypes. At the end of the research, bread wheat genotypes which were classified for tolerance or sensitivity to drought and the genetic similarity within control varieties were determined by molecular markers. According to SSR based dendrogram, two main groups were obtained for drought tolerance. At end of the molecular screening with SSR primers, genetic similarity coefficients were obtained that ranged from 0.14 to 0.71. The ones numbered 8 and 11 were the closest genotypes to drought tolerant cultivar Gerek 79 and the furthest genotypes from this cultivar were number 16 and to drought sensitive cultivar Sultan 95. The genotypes as drought tolerance due to their SSR markers scores are expected to provide useful information for drought related molecular breeding studies.

  3. Coincidences of structural and molecular characters in evolutionary lines of cyanobacteria

    Czech Academy of Sciences Publication Activity Database

    Komárek, Jiří; Kaštovský, J.

    2003-01-01

    Roč. 148, č. 109 (2003), s. 305-325 ISSN 0342-1120. [Symposium of the International Association for Cyanophyte Research /15./. Barcelona, 03.09.2001-07.09.2001] R&D Projects: GA AV ČR KSK6005114 Grant - others:MIDI-CHIP(EU) EVK2 Institutional research plan: CEZ:AV0Z6005908; CEZ:MSM 123100003 Keywords : cyanobacteria * molecular sequencing * taxonomic classification Subject RIV: EF - Botanics

  4. Antibiotic discovery throughout the Small World Initiative: A molecular strategy to identify biosynthetic gene clusters involved in antagonistic activity.

    Science.gov (United States)

    Davis, Elizabeth; Sloan, Tyler; Aurelius, Krista; Barbour, Angela; Bodey, Elijah; Clark, Brigette; Dennis, Celeste; Drown, Rachel; Fleming, Megan; Humbert, Allison; Glasgo, Elizabeth; Kerns, Trent; Lingro, Kelly; McMillin, MacKenzie; Meyer, Aaron; Pope, Breanna; Stalevicz, April; Steffen, Brittney; Steindl, Austin; Williams, Carolyn; Wimberley, Carmen; Zenas, Robert; Butela, Kristen; Wildschutte, Hans

    2017-06-01

    The emergence of bacterial pathogens resistant to all known antibiotics is a global health crisis. Adding to this problem is that major pharmaceutical companies have shifted away from antibiotic discovery due to low profitability. As a result, the pipeline of new antibiotics is essentially dry and many bacteria now resist the effects of most commonly used drugs. To address this global health concern, citizen science through the Small World Initiative (SWI) was formed in 2012. As part of SWI, students isolate bacteria from their local environments, characterize the strains, and assay for antibiotic production. During the 2015 fall semester at Bowling Green State University, students isolated 77 soil-derived bacteria and genetically characterized strains using the 16S rRNA gene, identified strains exhibiting antagonistic activity, and performed an expanded SWI workflow using transposon mutagenesis to identify a biosynthetic gene cluster involved in toxigenic compound production. We identified one mutant with loss of antagonistic activity and through subsequent whole-genome sequencing and linker-mediated PCR identified a 24.9 kb biosynthetic gene locus likely involved in inhibitory activity in that mutant. Further assessment against human pathogens demonstrated the inhibition of Bacillus cereus, Listeria monocytogenes, and methicillin-resistant Staphylococcus aureus in the presence of this compound, thus supporting our molecular strategy as an effective research pipeline for SWI antibiotic discovery and genetic characterization. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  5. Modern quantum kinetic theory and spectral line shapes

    International Nuclear Information System (INIS)

    Monchick, L.

    1991-01-01

    The modern quantum kinetic theory of spectral line shapes is outlined and a typical calculation of a Raman scattered line shape described. The distinguishing feature of this calculation is that it was completely ab initio and therefore constituted a test of modern quantum kinetic theory, the state of the art in computing molecular-scattering cross sections, and novel methods of solving kinetic equations. The computation employed a large assortment of tools: group theory, finite-element methods, classic methods of solving coupled sets of ordinary differential equations, graph methods of combining angular momenta, and matrix methods of solving integral equations. Agreement with experimental results was excellent. 13 refs

  6. Skills Associated with Line Breaks in Elite Rugby Union

    Directory of Open Access Journals (Sweden)

    Steve den Hollander, James Brown, Michael Lambert, Paul Treu, Sharief Hendricks

    2016-09-01

    Full Text Available The ability of the attacking team to break through the defensive line is a key indicator of success as it creates opportunities to score tries. The aim of this study was to analyse line breaks and identify the associated skills and playing characteristics. The 2013 Super Rugby season (125 games was analysed, in which 362 line breaks were identified and coded using variables that assessed team patterns and non-contact attacking skills in the phases preceding the line break. There was an average of 3 line breaks per game, with 39% of line breaks resulting in a try. Line breaks occurred when the ball-carrier was running fast [61%, x2(4 = 25.784, p = 0.000, Cramer’s v = 0.1922, weak]. At a moderate distance, short lateral passes (19% and skip passes (15% attributed to the highest percentage of line breaks [x2(26 = 50.899, p = 0.036, Cramer’s v = 0.2484, moderate]. Faster defensive line speeds resulted in more line breaks [x2(12 = 61.703, p < 0.001, Cramer’s v = 0.3026, moderate]. Line breaks are associated with overall team success and try scoring opportunities. Awareness of the defenders line speed and depth, fast running speed when receiving the ball and quick passing between attackers to the outside backs creates line break opportunities. During training, coaches should emphasise the movement speed of the ball between attackers and manipulate the speed and distance of the defenders.

  7. Multiple Lines of Evidence

    Energy Technology Data Exchange (ETDEWEB)

    Amidan, Brett G. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Venzin, Alexander M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Bramer, Lisa M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2015-06-03

    This paper discusses the process of identifying factors that influence the contamination level of a given decision area and then determining the likelihood that the area remains unacceptable. This process is referred to as lines of evidence. These lines of evidence then serve as inputs for the stratified compliance sampling (SCS) method, which requires a decision area to be divided into strata based upon contamination expectations. This is done in order to focus sampling efforts more within stratum where contamination is more likely and to use the domain knowledge about these likelihoods of the stratum remaining unacceptable to buy down the number of samples necessary, if possible. Two different building scenarios were considered as an example (see Table 3.1). SME expertise was elicited concerning four lines of evidence factors (see Table 3.2): 1) amount of contamination that was seen before decontamination, 2) post-decontamination air sampling information, 3) the applied decontaminant information, and 4) the surface material. Statistical experimental design and logistic regression modelling were used to help determine the likelihood that example stratum remained unacceptable for a given example scenario. The number of samples necessary for clearance was calculated by applying the SCS method to the example scenario, using the estimated likelihood of each stratum remaining unacceptable as was determined using the lines of evidence approach. The commonly used simple random sampling (SRS) method was also used to calculate the number of samples necessary for clearance for comparison purposes. The lines of evidence with SCS approach resulted in a 19% to 43% reduction in total number of samples necessary for clearance (see Table 3.6). The reduction depended upon the building scenario, as well as the level of percent clean criteria. A sensitivity analysis was also performed showing how changing the estimated likelihoods of stratum remaining unacceptable affect the number

  8. Multiple lines of evidence for the origin of domesticated chili pepper, Capsicum annuum, in Mexico

    Science.gov (United States)

    Kraft, Kraig H.; Brown, Cecil H.; Nabhan, Gary P.; Luedeling, Eike; Luna Ruiz, José de Jesús; Coppens d’Eeckenbrugge, Geo; Hijmans, Robert J.; Gepts, Paul

    2014-01-01

    The study of crop origins has traditionally involved identifying geographic areas of high morphological diversity, sampling populations of wild progenitor species, and the archaeological retrieval of macroremains. Recent investigations have added identification of plant microremains (phytoliths, pollen, and starch grains), biochemical and molecular genetic approaches, and dating through 14C accelerator mass spectrometry. We investigate the origin of domesticated chili pepper, Capsicum annuum, by combining two approaches, species distribution modeling and paleobiolinguistics, with microsatellite genetic data and archaeobotanical data. The combination of these four lines of evidence yields consensus models indicating that domestication of C. annuum could have occurred in one or both of two areas of Mexico: northeastern Mexico and central-east Mexico. Genetic evidence shows more support for the more northern location, but jointly all four lines of evidence support central-east Mexico, where preceramic macroremains of chili pepper have been recovered in the Valley of Tehuacán. Located just to the east of this valley is the center of phylogenetic diversity of Proto-Otomanguean, a language spoken in mid-Holocene times and the oldest protolanguage for which a word for chili pepper reconstructs based on historical linguistics. For many crops, especially those that do not have a strong archaeobotanical record or phylogeographic pattern, it is difficult to precisely identify the time and place of their origin. Our results for chili pepper show that expressing all data in similar distance terms allows for combining contrasting lines of evidence and locating the region(s) where cultivation and domestication of a crop began. PMID:24753581

  9. Establishment of immortalized B lymphoblastoid cell lines of old residents in high background radiation area in Guangdong, China

    International Nuclear Information System (INIS)

    Lu Xue; Feng Jiangbing; Chen Deqing; Liu Qingjie; Cha Yongru; Zou Jianming

    2008-01-01

    Objective: To establish the immortalized cell lines of peripheral blood lymphocytes for old male residents in high background radiation area (HBRA) in Guangdong, China, in order to preserve the specific genomic resources of residents in HBRA for the further genetic and molecular biological study on HBRA. Methods: The peripheral blood samples of 20 old male residents in HBRA were collected after informed consent. The immortalized B lymphoblastoid cell lines, 2 fox each resident, were established with Epstein-Barr virus. After being frozen and recovered, the cell viability, the contamination of bacterium and mycoplasma were analyzed. The stabilization of cell lines was decided by comparing the karyotypes of the peripheral blood lymphocytes and the cell lines. Results: 40 cell lines for 20 residents in HBRA were successfully established.. The recovery rate of cell lines after being frozen was 100% . All the cell viablity after recovery was higher than 90%, and no contamination of bacteria and mycoplasma occurred. The karyotypes of the 20th generation cell lines were not change. Conclusion: The immortalized cell lines established in this study could provide biological resources for further study on genetics and molecular biology in HBRA. (authors)

  10. Gas, dust, stars, star formation, and their evolution in M 33 at giant molecular cloud scales

    Science.gov (United States)

    Komugi, Shinya; Miura, Rie E.; Kuno, Nario; Tosaki, Tomoka

    2018-04-01

    We report on a multi-parameter analysis of giant molecular clouds (GMCs) in the nearby spiral galaxy M 33. A catalog of GMCs identifed in 12CO(J = 3-2) was used to compile associated 12CO(J = 1-0), dust, stellar mass, and star formation rate. Each of the 58 GMCs are categorized by their evolutionary stage. Applying the principal component analysis on these parameters, we construct two principal components, PC1 and PC2, which retain 75% of the information from the original data set. PC1 is interpreted as expressing the total interstellar matter content, and PC2 as the total activity of star formation. Young (activity compared to intermediate-age and older clouds. Comparison of average cloud properties in different evolutionary stages imply that GMCs may be heated or grow denser and more massive via aggregation of diffuse material in their first ˜ 10 Myr. The PCA also objectively identified a set of tight relations between ISM and star formation. The ratio of the two CO lines is nearly constant, but weakly modulated by massive star formation. Dust is more strongly correlated with the star formation rate than the CO lines, supporting recent findings that dust may trace molecular gas better than CO. Stellar mass contributes weakly to the star formation rate, reminiscent of an extended form of the Schmidt-Kennicutt relation with the molecular gas term substituted by dust.

  11. Call for papers for special issue of Journal of Molecular Spectroscopy focusing on "Frequency-comb spectroscopy"

    Science.gov (United States)

    Foltynowicz, Aleksandra; Picqué, Nathalie; Ye, Jun

    2018-05-01

    Frequency combs are becoming enabling tools for many applications in science and technology, beyond the original purpose of frequency metrology of simple atoms. The precisely evenly spaced narrow lines of a laser frequency comb inspire intriguing approaches to molecular spectroscopy, designed and implemented by a growing community of scientists. Frequency-comb spectroscopy advances the frontiers of molecular physics across the entire electro-magnetic spectrum. Used as frequency rulers, frequency combs enable absolute frequency measurements and precise line shape studies of molecular transitions, for e.g. tests of fundamental physics and improved determination of fundamental constants. As light sources interrogating the molecular samples, they dramatically improve the resolution, precision, sensitivity and acquisition time of broad spectral-bandwidth spectroscopy and open up new opportunities and applications at the leading edge of molecular spectroscopy and sensing.

  12. Communication: Molecular gears

    Energy Technology Data Exchange (ETDEWEB)

    Burnell, E. Elliott, E-mail: elliott.burnell@ubc.ca [Chemistry Department, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1 (Canada); Lange, Cornelis A. de, E-mail: c.a.de.lange@vu.nl [Atomic, Molecular and Laser Physics, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam (Netherlands); Meerts, W. Leo, E-mail: leo.meerts@science.ru.nl [Atomic, Molecular and Laser Physics, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam (Netherlands); Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, NL-6525 AJ Nijmegen (Netherlands)

    2016-09-07

    The {sup 1}H nuclear magnetic resonance spectrum of hexamethylbenzene orientationally ordered in the nematic liquid crystal ZLI-1132 is analysed using covariance matrix adaptation evolution strategy. The spectrum contains over 350 000 lines with many overlapping transitions, from which four independent direct dipolar couplings are obtained. The rotations of the six methyl groups appear to be correlated due to mutual steric hindrance. Adjacent methyl groups show counter-rotating or geared motion. Hexamethylbenzene thus behaves as a molecular hexagonal gear.

  13. The Genomic and Transcriptomic Landscape of a HeLa Cell Line

    Science.gov (United States)

    Landry, Jonathan J. M.; Pyl, Paul Theodor; Rausch, Tobias; Zichner, Thomas; Tekkedil, Manu M.; Stütz, Adrian M.; Jauch, Anna; Aiyar, Raeka S.; Pau, Gregoire; Delhomme, Nicolas; Gagneur, Julien; Korbel, Jan O.; Huber, Wolfgang; Steinmetz, Lars M.

    2013-01-01

    HeLa is the most widely used model cell line for studying human cellular and molecular biology. To date, no genomic reference for this cell line has been released, and experiments have relied on the human reference genome. Effective design and interpretation of molecular genetic studies performed using HeLa cells require accurate genomic information. Here we present a detailed genomic and transcriptomic characterization of a HeLa cell line. We performed DNA and RNA sequencing of a HeLa Kyoto cell line and analyzed its mutational portfolio and gene expression profile. Segmentation of the genome according to copy number revealed a remarkably high level of aneuploidy and numerous large structural variants at unprecedented resolution. Some of the extensive genomic rearrangements are indicative of catastrophic chromosome shattering, known as chromothripsis. Our analysis of the HeLa gene expression profile revealed that several pathways, including cell cycle and DNA repair, exhibit significantly different expression patterns from those in normal human tissues. Our results provide the first detailed account of genomic variants in the HeLa genome, yielding insight into their impact on gene expression and cellular function as well as their origins. This study underscores the importance of accounting for the strikingly aberrant characteristics of HeLa cells when designing and interpreting experiments, and has implications for the use of HeLa as a model of human biology. PMID:23550136

  14. The HI/OH/Recombination line survey of the inner Milky Way (THOR). Survey overview and data release 1

    Science.gov (United States)

    Beuther, H.; Bihr, S.; Rugel, M.; Johnston, K.; Wang, Y.; Walter, F.; Brunthaler, A.; Walsh, A. J.; Ott, J.; Stil, J.; Henning, Th.; Schierhuber, T.; Kainulainen, J.; Heyer, M.; Goldsmith, P. F.; Anderson, L. D.; Longmore, S. N.; Klessen, R. S.; Glover, S. C. O.; Urquhart, J. S.; Plume, R.; Ragan, S. E.; Schneider, N.; McClure-Griffiths, N. M.; Menten, K. M.; Smith, R.; Roy, N.; Shanahan, R.; Nguyen-Luong, Q.; Bigiel, F.

    2016-10-01

    Context. The past decade has witnessed a large number of Galactic plane surveys at angular resolutions below 20''. However, no comparable high-resolution survey exists at long radio wavelengths around 21 cm in line and continuum emission. Aims: We remedy this situation by studying the northern Galactic plane at 20'' resolution in emission of atomic, molecular, and ionized gas. Methods: Employing the Karl G. Jansky Very Large Array (VLA) in the C-array configuration and a large program, we observe the HI 21 cm line, four OH lines, nineteen Hnα radio recombination lines as well as the continuum emission from 1 to 2 GHz in full polarization over a large part of the first Galactic quadrant. Results: Covering Galactic longitudes from 14.5 to 67.4 deg and latitudes between ± 1.25 deg, we image all of these lines and the continuum at 20'' resolution. These data allow us to study the various components of the interstellar medium (ISM): from the atomic phase, traced by the HI line, to the molecular phase, observed by the OH transitions, to the ionized medium, revealed by the cm continuum and the Hnα radio recombination lines. Furthermore, the polarized continuum emission enables magnetic field studies. In this overview paper, we discuss the survey outline and present the first data release as well as early results from the different datasets. We now release the first half of the survey; the second half will follow later after the ongoing data processing has been completed. The data in fits format (continuum images and line data cubes) can be accessed through the project web-page. Conclusions: The HI/OH/Recombination line survey of the Milky Way (THOR) opens a new window to the different parts of the ISM. It enables detailed studies of molecular cloud formation, conversion of atomic to molecular gas, and feedback from Hii regions as well as the magnetic field in the Milky Way. It is highly complementary to other surveys of our Galaxy, and comparing the different datasets

  15. A review of molecular effects in gas-phase KL X-ray emission

    Energy Technology Data Exchange (ETDEWEB)

    Guillemin, Renaud; Carniato, Stéphane; Journel, Loïc [UPMC Univ Paris 06, UMR 7614, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005 Paris (France); CNRS, UMR 7614, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005 Paris (France); Stolte, Wayne C. [Department of Chemistry, University of Nevada, Las Vegas, NV 89154-4003 (United States); Marchenko, Tatiana; Khoury, Lara El; Kawerk, Elie; Piancastelli, Maria Novella [UPMC Univ Paris 06, UMR 7614, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005 Paris (France); CNRS, UMR 7614, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005 Paris (France); Hudson, Amanda C.; Lindle, Dennis W. [Department of Chemistry, University of Nevada, Las Vegas, NV 89154-4003 (United States); Simon, Marc, E-mail: marc.simon@upmc.fr [UPMC Univ Paris 06, UMR 7614, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005 Paris (France); CNRS, UMR 7614, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005 Paris (France)

    2013-06-15

    The unique capabilities of resonant inelastic X-ray scattering (RIXS) to provide a deep insight into molecular dynamics following core excitation are reviewed here. Characteristic features of molecular X-ray emission are experimentally observed and theoretically interpreted. Some of our most significant results on molecular dynamics following deep core excitation are presented. In particular, we provide several examples of nuclear dynamics on the femtosecond or subfemtosecond time scale; line-narrowing effects related to the quenching of vibrational structure due to parallelism of intermediate and final state curves; anomalous line dispersion across a resonance, which is due to core-hole lifetime effects; spin–orbit-state populations derived from polarized RIXS experiments. We also show how to connect the RIXS results to the general chemical properties of the investigated systems.

  16. A review of molecular effects in gas-phase KL X-ray emission

    International Nuclear Information System (INIS)

    Guillemin, Renaud; Carniato, Stéphane; Journel, Loïc; Stolte, Wayne C.; Marchenko, Tatiana; Khoury, Lara El; Kawerk, Elie; Piancastelli, Maria Novella; Hudson, Amanda C.; Lindle, Dennis W.; Simon, Marc

    2013-01-01

    The unique capabilities of resonant inelastic X-ray scattering (RIXS) to provide a deep insight into molecular dynamics following core excitation are reviewed here. Characteristic features of molecular X-ray emission are experimentally observed and theoretically interpreted. Some of our most significant results on molecular dynamics following deep core excitation are presented. In particular, we provide several examples of nuclear dynamics on the femtosecond or subfemtosecond time scale; line-narrowing effects related to the quenching of vibrational structure due to parallelism of intermediate and final state curves; anomalous line dispersion across a resonance, which is due to core-hole lifetime effects; spin–orbit-state populations derived from polarized RIXS experiments. We also show how to connect the RIXS results to the general chemical properties of the investigated systems

  17. Photon-dominated region modeling of the [C I], [C II], and CO Line Emission From A Boundary In The Taurus molecular cloud

    Energy Technology Data Exchange (ETDEWEB)

    Orr, Matthew E. [Physics and Astronomy Department, University of Southern California, Los Angeles, CA 90089 (United States); Pineda, Jorge L.; Goldsmith, Paul F. [Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA 91109-8099 (United States)

    2014-11-01

    We present [C I] and [C II] observations of a linear edge region in the Taurus molecular cloud, and model this region as a cylindrically symmetric photon-dominated region (PDR) exposed to a low-intensity UV radiation field. The sharp, long profile of the linear edge makes it an ideal case to test PDR models and determine cloud parameters. We compare observations of the [C I], {sup 3} P {sub 1} → {sup 3} P {sub 0} (492 GHz), [C I] {sup 3} P {sub 2} → {sup 3} P {sub 1} (809 GHz), and [C II] {sup 2} P {sub 3/2} → {sup 2} P {sub 1/2} (1900 GHz) transitions, as well as the lowest rotational transitions of {sup 12}CO and {sup 13}CO, with line intensities produced by the RATRAN radiative transfer code from the results of the Meudon PDR code. We constrain the density structure of the cloud by fitting a cylindrical density function to visual extinction data. We study the effects of variation of the FUV field, {sup 12}C/{sup 13}C isotopic abundance ratio, sulfur depletion, cosmic ray ionization rate, and inclination of the filament relative to the sky-plane on the chemical network of the PDR model and resulting line emission. We also consider the role of suprathermal chemistry and density inhomogeneities. We find good agreement between the model and observations, and that the integrated line intensities can be explained by a PDR model with an external FUV field of 0.05 G {sub 0}, a low ratio of {sup 12}C to {sup 13}C ∼43, a highly depleted sulfur abundance (by a factor of at least 50), a cosmic ray ionization rate (3-6) × 10{sup –17} s{sup –1}, and without significant effects from inclination, clumping or suprathermal chemistry.

  18. Harnessing Thin-Film Continuous-Flow Assembly Lines.

    Science.gov (United States)

    Britton, Joshua; Castle, Jared W; Weiss, Gregory A; Raston, Colin L

    2016-07-25

    Inspired by nature's ability to construct complex molecules through sequential synthetic transformations, an assembly line synthesis of α-aminophosphonates has been developed. In this approach, simple starting materials are continuously fed through a thin-film reactor where the intermediates accrue molecular complexity as they progress through the flow system. Flow chemistry allows rapid multistep transformations to occur via reaction compartmentalization, an approach not amenable to using conventional flasks. Thin film processing can also access facile in situ solvent exchange to drive reaction efficiency, and through this method, α-aminophosphonate synthesis requires only 443 s residence time to produce 3.22 g h(-1) . Assembly-line synthesis allows unprecedented reaction flexibility and processing efficiency. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. State Estimation-based Transmission line parameter identification

    Directory of Open Access Journals (Sweden)

    Fredy Andrés Olarte Dussán

    2010-01-01

    Full Text Available This article presents two state-estimation-based algorithms for identifying transmission line parameters. The identification technique used simultaneous state-parameter estimation on an artificial power system composed of several copies of the same transmission line, using measurements at different points in time. The first algorithm used active and reactive power measurements at both ends of the line. The second method used synchronised phasor voltage and current measurements at both ends. The algorithms were tested in simulated conditions on the 30-node IEEE test system. All line parameters for this system were estimated with errors below 1%.

  20. LARGE-SCALE CO MAPS OF THE LUPUS MOLECULAR CLOUD COMPLEX

    International Nuclear Information System (INIS)

    Tothill, N. F. H.; Loehr, A.; Stark, A. A.; Lane, A. P.; Harnett, J. I.; Bourke, T. L.; Myers, P. C.; Parshley, S. C.; Wright, G. A.; Walker, C. K.

    2009-01-01

    Fully sampled degree-scale maps of the 13 CO 2-1 and CO 4-3 transitions toward three members of the Lupus Molecular Cloud Complex-Lupus I, III, and IV-trace the column density and temperature of the molecular gas. Comparison with IR extinction maps from the c2d project requires most of the gas to have a temperature of 8-10 K. Estimates of the cloud mass from 13 CO emission are roughly consistent with most previous estimates, while the line widths are higher, around 2 km s -1 . CO 4-3 emission is found throughout Lupus I, indicating widespread dense gas, and toward Lupus III and IV. Enhanced line widths at the NW end and along the edge of the B 228 ridge in Lupus I, and a coherent velocity gradient across the ridge, are consistent with interaction between the molecular cloud and an expanding H I shell from the Upper-Scorpius subgroup of the Sco-Cen OB Association. Lupus III is dominated by the effects of two HAe/Be stars, and shows no sign of external influence. Slightly warmer gas around the core of Lupus IV and a low line width suggest heating by the Upper-Centaurus-Lupus subgroup of Sco-Cen, without the effects of an H I shell.

  1. Mordred: a molecular descriptor calculator.

    Science.gov (United States)

    Moriwaki, Hirotomo; Tian, Yu-Shi; Kawashita, Norihito; Takagi, Tatsuya

    2018-02-06

    Molecular descriptors are widely employed to present molecular characteristics in cheminformatics. Various molecular-descriptor-calculation software programs have been developed. However, users of those programs must contend with several issues, including software bugs, insufficient update frequencies, and software licensing constraints. To address these issues, we propose Mordred, a developed descriptor-calculation software application that can calculate more than 1800 two- and three-dimensional descriptors. It is freely available via GitHub. Mordred can be easily installed and used in the command line interface, as a web application, or as a high-flexibility Python package on all major platforms (Windows, Linux, and macOS). Performance benchmark results show that Mordred is at least twice as fast as the well-known PaDEL-Descriptor and it can calculate descriptors for large molecules, which cannot be accomplished by other software. Owing to its good performance, convenience, number of descriptors, and a lax licensing constraint, Mordred is a promising choice of molecular descriptor calculation software that can be utilized for cheminformatics studies, such as those on quantitative structure-property relationships.

  2. Automatic yield-line analysis of slabs using discontinuity layout optimization.

    Science.gov (United States)

    Gilbert, Matthew; He, Linwei; Smith, Colin C; Le, Canh V

    2014-08-08

    The yield-line method of analysis is a long established and extremely effective means of estimating the maximum load sustainable by a slab or plate. However, although numerous attempts to automate the process of directly identifying the critical pattern of yield-lines have been made over the past few decades, to date none has proved capable of reliably analysing slabs of arbitrary geometry. Here, it is demonstrated that the discontinuity layout optimization (DLO) procedure can successfully be applied to such problems. The procedure involves discretization of the problem using nodes inter-connected by potential yield-line discontinuities, with the critical layout of these then identified using linear programming. The procedure is applied to various benchmark problems, demonstrating that highly accurate solutions can be obtained, and showing that DLO provides a truly systematic means of directly and reliably automatically identifying yield-line patterns. Finally, since the critical yield-line patterns for many problems are found to be quite complex in form, a means of automatically simplifying these is presented.

  3. Metabolic labeling of sialic acids in tissue culture cell lines: methods to identify substituted and modified radioactive neuraminic acids

    International Nuclear Information System (INIS)

    Diaz, S.; Varki, A.

    1985-01-01

    The parent sialic acid N-acetylneuraminic acid can be modified or substituted in various ways, giving rise to a family of more than 25 compounds. The definitive identification of these compounds has previously required isolation of nanomole amounts for mass spectrometry or NMR. We have explored the possibility of using the known metabolic precursors of the sialic acids, particularly N-acetyl-[6-3H]mannosamine, to label and identify various forms of sialic acids in tissue culture cells. Firstly, we defined several variables that affect the labeling of sialic acids with N-acetyl-[6-3H]mannosamine. Secondly, we have devised a simple screening method to identify cell lines that synthesize substituted or modified sialic acids. We next demonstrate that it is possible to definitively identify the natures of the various labeled sialic acids without the use of mass spectrometry, even though they are present only in tracer amounts. The methods used include paper chromatography, analytical de-O-acetylation, periodate release of the 9-3H as [3H]formaldehyde (which is subsequently converted to a specific 3H-labeled chromophore), acylneuraminate pyruvate lyase treatment with identification of [3H]acylmannosamines, gas-liquid chromatography with radioactive detection, and two new high-pressure liquid chromatography methods utilizing the amine-adsorption:ion suppression and ion-pair principles. The use of an internal N-acetyl-[4-14C]neuraminic acid standard in each of these methods assures precision and accuracy. The combined use of these methods now allows the identification of radioactive tracer amounts of the various types of sialic acids in well-defined populations of tissue culture cells; it may also allow the identification of hitherto unknown forms of sialic acids

  4. Cytogenetic and molecular genetic characterization of immortalized human ovarian surface epithelial cell lines: consistent loss of chromosome 13 and amplification of chromosome 20.

    Science.gov (United States)

    Jin, Yuesheng; Zhang, Hao; Tsao, Sai Wah; Jin, Charlotte; Lv, Mei; Strömbeck, Bodil; Wiegant, Joop; Wan, Thomas Shek Kong; Yuen, Po Wing; Kwong, Yok-Lam

    2004-01-01

    This study aimed at identifying the genetic events involved in immortalization of ovarian epithelial cells, which might be important steps in ovarian carcinogenesis. The genetic profiles of five human ovarian surface epithelial (HOSE) cell lines immortalized by retroviral transfection of the human papillomavirus (HPV) E6/E7 genes were thoroughly characterized by chromosome banding and fluorescence in situ hybridization (FISH), at various passages pre- and post-crisis. In pre-crisis, most cells had simple, non-clonal karyotypic changes. Telomere association was the commonest aberration, suggesting that tolermase dysfunction might be an important genetic event leading to cellular crisis. After immortalization post-crisis, however, the karyotypic patterns were non-random. Loss of genetic materials was a characteristic feature. The commonest numerical aberrations were -13, -14, -16, -17, -18, and +5. Among them, loss of chromosome 13 was common change observed in all lines. The only recurrent structural aberration was homogeneously staining regions (hsr) observed in three lines. FISH and combined binary ratio labeling (COBRA)-FISH showed in two cases that the hsrs were derived from chromosome 20. Clonal evolution was observed in four of the lines. In one line, hsr was the only change shared by all subclones, suggesting that it might be a primary event in cell immortalization. The results of the present study suggested that loss of chromosome 13 and the amplification of chromosome 20 might be early genetic events involved in ovarian cell immortalization, and might be useful targets for the study of genomic aberrations in ovarian carcinogenesis.

  5. Molecular cytogenetic characterization of a new wheat-rye 4R chromosome translocation line resistant to powdery mildew.

    Science.gov (United States)

    An, Diaoguo; Zheng, Qi; Zhou, Yilin; Ma, Pengtao; Lv, Zhenling; Li, Lihui; Li, Bin; Luo, Qiaoling; Xu, Hongxing; Xu, Yunfeng

    2013-07-01

    Rye is an important and valuable gene resource for wheat improvement. However, due to extensive growing of cultivars with disease resistance genes from short arm of rye chromosome 1R and coevolution of pathogen virulence and host resistance, these cultivars successively lost resistance to pathogens. Identification and deployment of new resistance gene sources in rye are, therefore, of especial importance and urgency. A new wheat-rye line, designated as WR41-1, was produced through distant hybridization and chromosome engineering protocols between common wheat cultivar Xiaoyan 6 and rye cultivar German White. It was proved to be a new wheat-rye T4BL·4RL and T7AS·4RS translocation line using sequential genomic in situ hybridization (GISH), multicolor fluorescence in situ hybridization (mc-FISH), and expressed sequence tag-simple sequence repeat (EST-SSR) marker analysis. WR41-1 showed high levels of resistance to powdery mildew (Blumeria graminis f. sp. tritici, Bgt) pathogens prevalent in China at the adult growth stage and 13 of 23 Bgt isolates tested at the seedling stage. According to its resistant pattern to 23 different Bgt isolates, WR41-1 may possess new gene(s) for resistance to powdery mildew, which differed from previously identified and known powdery mildew genes from rye (Pm7, Pm8, Pm17, and Pm20). In addition, WR41-1 was cytologically stable, had a desirable fertility, and is expected to be useful in wheat improvement.

  6. ApoE4-specific Misfolded Intermediate Identified by Molecular Dynamics Simulations.

    Directory of Open Access Journals (Sweden)

    Benfeard Williams

    2015-10-01

    Full Text Available The increased risk of developing Alzheimer's disease (AD is associated with the APOE gene, which encodes for three variants of Apolipoprotein E, namely E2, E3, E4, differing only by two amino acids at positions 112 and 158. ApoE4 is known to be the strongest risk factor for AD onset, while ApoE3 and ApoE2 are considered to be the AD-neutral and AD-protective isoforms, respectively. It has been hypothesized that the ApoE isoforms may contribute to the development of AD by modifying the homeostasis of ApoE physiological partners and AD-related proteins in an isoform-specific fashion. Here we find that, despite the high sequence similarity among the three ApoE variants, only ApoE4 exhibits a misfolded intermediate state characterized by isoform-specific domain-domain interactions in molecular dynamics simulations. The existence of an ApoE4-specific intermediate state can contribute to the onset of AD by altering multiple cellular pathways involved in ApoE-dependent lipid transport efficiency or in AD-related protein aggregation and clearance. We present what we believe to be the first structural model of an ApoE4 misfolded intermediate state, which may serve to elucidate the molecular mechanism underlying the role of ApoE4 in AD pathogenesis. The knowledge of the structure for the ApoE4 folding intermediate provides a new platform for the rational design of alternative therapeutic strategies to fight AD.

  7. Characterization of a Merkel Cell Polyomavirus-Positive Merkel Cell Carcinoma Cell Line CVG-1.

    Science.gov (United States)

    Velásquez, Celestino; Amako, Yutaka; Harold, Alexis; Toptan, Tuna; Chang, Yuan; Shuda, Masahiro

    2018-01-01

    Merkel cell polyomavirus (MCV) plays a causal role in ∼80% of Merkel cell carcinomas (MCC). MCV is clonally integrated into the MCC tumor genome, which results in persistent expression of large T (LT) and small T (sT) antigen oncoproteins encoded by the early locus. In MCV-positive MCC tumors, LT is truncated by premature stop codons or deletions that lead to loss of the C-terminal origin binding (OBD) and helicase domains important for replication. The N-terminal Rb binding domain remains intact. MCV-positive cell lines derived from MCC explants have been valuable tools to study the molecular mechanism of MCV-induced Merkel cell carcinogenesis. Although all cell lines have integrated MCV and express truncated LT antigens, the molecular sizes of the LT proteins differ between cell lines. The copy number of integrated viral genome also varies across cell lines, leading to significantly different levels of viral protein expression. Nevertheless, these cell lines share phenotypic similarities in cell morphology, growth characteristics, and neuroendocrine marker expression. Several low-passage MCV-positive MCC cell lines have been established since the identification of MCV. We describe a new MCV-positive MCV cell line, CVG-1, with features distinct from previously reported cell lines. CVG-1 tumor cells grow in more discohesive clusters in loose round cell suspension, and individual cells show dramatic size heterogeneity. It is the first cell line to encode an MCV sT polymorphism resulting in a unique leucine (L) to proline (P) substitution mutation at amino acid 144. CVG-1 possesses a LT truncation pattern near identical to that of MKL-1 cells differing by the last two C-terminal amino acids and also shows an LT protein expression level similar to MKL-1. Viral T antigen knockdown reveals that, like other MCV-positive MCC cell lines, CVG-1 requires T antigen expression for cell proliferation.

  8. Quantum oscillations in nodal line systems

    Science.gov (United States)

    Yang, Hui; Moessner, Roderich; Lim, Lih-King

    2018-04-01

    We study signatures of magnetic quantum oscillations in three-dimensional nodal line semimetals at zero temperature. The extended nature of the degenerate bands can result in a Fermi surface geometry with topological genus one, as well as a Fermi surface of electron and hole pockets encapsulating the nodal line. Moreover, the underlying two-band model to describe a nodal line is not unique, in that there are two classes of Hamiltonian with distinct band topology giving rise to the same Fermi-surface geometry. After identifying the extremal cyclotron orbits in various magnetic field directions, we study their concomitant Landau levels and resulting quantum oscillation signatures. By Landau-fan-diagram analyses, we extract the nontrivial π Berry phase signature for extremal orbits linking the nodal line.

  9. On the theory of a dissociative recombination of electrons and molecular ions

    International Nuclear Information System (INIS)

    Golubkov, G.V.; Drygin, S.V.; Ivanov, G.K.

    1995-01-01

    The present paper deals with a detailed description of molecular recombination of the electron and two-atom molecular ion, as well as with consideration of the this complex quantum-mechanical process. It is shown that this relationship results in a displacement of vibrational resonance levels and deformation of line contour

  10. Molecular Imaging to Identify Tumor Recurrence following Chemoradiation in a Hostile Surgical Environment

    Directory of Open Access Journals (Sweden)

    Olugbenga T. Okusanya

    2015-01-01

    Full Text Available Surgical biopsy of potential tumor recurrence is a common challenge facing oncologists, surgeons, and cancer patients. Imaging modalities have limited ability to accurately detect recurrent cancer in fields affected by previous surgery, chemotherapy, or radiation. However, definitive tissue diagnosis is often needed to initiate treatment and to direct therapy. We sought to determine if a targeted fluorescent intraoperative molecular imaging technique could be applied in a clinical setting to assist a surgical biopsy in a “hostile” field. We describe the use of a folate-fluorescein conjugate to direct the biopsy of a suspected recurrent lung adenocarcinoma invading the mediastinum that had been previously treated with chemoradiation. We found that intraoperative imaging allowed the identification of small viable tumor deposits that were otherwise indistinguishable from scar and necrosis. Our operative observations were confirmed by histology, fluorescence microscopy, and immunohistochemistry. Our results demonstrate one possible application and clinical value of intraoperative molecular imaging.

  11. Integrated Bioinformatics, Environmental Epidemiologic and Genomic Approaches to Identify Environmental and Molecular Links between Endometriosis and Breast Cancer

    Directory of Open Access Journals (Sweden)

    Deodutta Roy

    2015-10-01

    Full Text Available We present a combined environmental epidemiologic, genomic, and bioinformatics approach to identify: exposure of environmental chemicals with estrogenic activity; epidemiologic association between endocrine disrupting chemical (EDC and health effects, such as, breast cancer or endometriosis; and gene-EDC interactions and disease associations. Human exposure measurement and modeling confirmed estrogenic activity of three selected class of environmental chemicals, polychlorinated biphenyls (PCBs, bisphenols (BPs, and phthalates. Meta-analysis showed that PCBs exposure, not Bisphenol A (BPA and phthalates, increased the summary odds ratio for breast cancer and endometriosis. Bioinformatics analysis of gene-EDC interactions and disease associations identified several hundred genes that were altered by exposure to PCBs, phthalate or BPA. EDCs-modified genes in breast neoplasms and endometriosis are part of steroid hormone signaling and inflammation pathways. All three EDCs–PCB 153, phthalates, and BPA influenced five common genes—CYP19A1, EGFR, ESR2, FOS, and IGF1—in breast cancer as well as in endometriosis. These genes are environmentally and estrogen responsive, altered in human breast and uterine tumors and endometriosis lesions, and part of Mitogen Activated Protein Kinase (MAPK signaling pathways in cancer. Our findings suggest that breast cancer and endometriosis share some common environmental and molecular risk factors.

  12. Net emission coefficient for CO–H2 thermal plasmas with the consideration of molecular systems

    International Nuclear Information System (INIS)

    Billoux, T.; Cressault, Y.; Gleizes, A.

    2015-01-01

    This paper deals with the calculation of net emission coefficients (NECs) for CO–H 2 thermal plasmas. This task required the elaboration of a complete spectroscopic database including atoms and molecules formed by carbon, oxygen and hydrogen elements. We have used a systematic line by line method to calculate all the main radiative contributions which are the atomic and molecular continua, the atomic lines and the molecular (diatomic and polyatomic) lines. The main diatomic electronic systems for CO–H 2 plasmas and the triatomic molecular bands were considered. We present some variations of the net emission coefficient versus temperature, for various pressures and for two relative proportions of the components. The role of the diatomic molecules is important at temperatures lower than 5000 K whereas the net emission coefficient presents an unusual peak at temperature around 1000 K, due to the presence of the CO 2 molecule presenting a strong infrared radiation. Finally, the results show that the NEC slightly depends on the relative proportion of CO and H 2 . - highlights: • We calculate radiative losses from CO–H 2 thermal plasmas. • We use the up-to-date atomic and molecular databases. • The influence of CO 2 molecule is very important at low temperature. • The relative maximum of the net emission coefficient at low temperature is unusual

  13. Distinct Molecular Signature of Murine Fetal Liver and Adult Hematopoietic Stem Cells Identify Novel Regulators of Hematopoietic Stem Cell Function.

    Science.gov (United States)

    Manesia, Javed K; Franch, Monica; Tabas-Madrid, Daniel; Nogales-Cadenas, Ruben; Vanwelden, Thomas; Van Den Bosch, Elisa; Xu, Zhuofei; Pascual-Montano, Alberto; Khurana, Satish; Verfaillie, Catherine M

    2017-04-15

    During ontogeny, fetal liver (FL) acts as a major site for hematopoietic stem cell (HSC) maturation and expansion, whereas HSCs in the adult bone marrow (ABM) are largely quiescent. HSCs in the FL possess faster repopulation capacity as compared with ABM HSCs. However, the molecular mechanism regulating the greater self-renewal potential of FL HSCs has not yet extensively been assessed. Recently, we published RNA sequencing-based gene expression analysis on FL HSCs from 14.5-day mouse embryo (E14.5) in comparison to the ABM HSCs. We reanalyzed these data to identify key transcriptional regulators that play important roles in the expansion of HSCs during development. The comparison of FL E14.5 with ABM HSCs identified more than 1,400 differentially expressed genes. More than 200 genes were shortlisted based on the gene ontology (GO) annotation term "transcription." By morpholino-based knockdown studies in zebrafish, we assessed the function of 18 of these regulators, previously not associated with HSC proliferation. Our studies identified a previously unknown role for tdg, uhrf1, uchl5, and ncoa1 in the emergence of definitive hematopoiesis in zebrafish. In conclusion, we demonstrate that identification of genes involved in transcriptional regulation differentially expressed between expanding FL HSCs and quiescent ABM HSCs, uncovers novel regulators of HSC function.

  14. THE SDSS-III APOGEE SPECTRAL LINE LIST FOR H-BAND SPECTROSCOPY

    Energy Technology Data Exchange (ETDEWEB)

    Shetrone, M. [University of Texas at Austin, McDonald Observatory (United States); Bizyaev, D.; Chojnowski, D. [Apache Point Observatory and New Mexico State University, P.O. Box 59, Sunspot, NM, 88349-0059 (United States); Lawler, J. E. [Department of Physics, University of Wisconsin-Madison, 1150 University Avenue, Madison, WI 53706 (United States); Prieto, C. Allende; Zamora, O.; García-Hernández, D. A.; Souto, D. [Instituto de Astrofísica de Canarias, Calle Vía Lactea s/n, E-38205 La Laguna, Tenerife (Spain); Johnson, J. A. [Department of Astronomy, The Ohio State University, Columbus, OH 43210 (United States); Smith, V. V. [National Optical Astronomy Observatory, 950 North Cherry Avenue, Tucson, AZ 85719 (United States); Cunha, K. [Observatório Nacional, Rua General Jose Cristino, 77, 20921-400 São Cristóvão, Rio de Janeiro, RJ (Brazil); Holtzman, J. [Department of Astronomy, New Mexico State University, Las Cruces, NM 88003 (United States); Pérez, A. E. García; Sobeck, J.; Majewski, S. [Department of Astronomy, University of Virginia, P.O. Box 400325, Charlottesville, VA 22904-4325 (United States); Mészáros, Sz. [ELTE Gothard Astrophysical Observatory, H-9704 Szombathely, Szent Imre herceg st. 112 (Hungary); Koesterke, L. [The University of Texas at Austin, Texas Advanced Computing Center (United States); Zasowski, G. [Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD 21218 (United States)

    2015-12-15

    We present the H-band spectral line lists adopted by the Apache Point Observatory Galactic Evolution Experiment (APOGEE). The APOGEE line lists comprise astrophysical, theoretical, and laboratory sources from the literature, as well as newly evaluated astrophysical oscillator strengths and damping parameters. We discuss the construction of the APOGEE line list, which is one of the critical inputs for the APOGEE Stellar Parameters and Chemical Abundances Pipeline, and present three different versions that have been used at various stages of the project. The methodology for the newly calculated astrophysical line lists is reviewed. The largest of these three line lists contains 134,457 molecular and atomic transitions. In addition to the format adopted to store the data, the line lists are available in MOOG, Synspec, and Turbospectrum formats. The limitations of the line lists along with guidance for its use on different spectral types are discussed. We also present a list of H-band spectral features that are either poorly represented or completely missing in our line list. This list is based on the average of a large number of spectral fit residuals for APOGEE observations spanning a wide range of stellar parameters.

  15. Physiological and molecular analysis of selected Kenyan maize lines for aluminum tolerance

    Science.gov (United States)

    Aluminum (Al) toxicity is an important limitation to maize production in many tropical and sub-tropical acid soil areas. The aim of this study was to survey the variation in Al tolerance in a panel of maize lines adapted for Kenya and look for novel sources of Al tolerance. 112 Kenyan maize accessio...

  16. Rotational Raman scattering using molecular nitrogen gas for calibration of Thomson-scattering apparatus

    International Nuclear Information System (INIS)

    Yamauchi, Toshihiko; Nakazawa, Ichiro

    1987-01-01

    Anti-Stokes rotational Raman lines in molecular nitrogen gas were used for the calibration of Thomson-scattering apparatus. It was found that molecular nitrogen gas is suitable for a vessel having strong stray light. The polarization ratio was 0.16 using linear-polarized laser light. (author)

  17. Classical and quantum molecular dynamics in NMR spectra

    CERN Document Server

    Szymański, Sławomir

    2018-01-01

    The book provides a detailed account of how condensed-phase molecular dynamics are reflected in the line shapes of NMR spectra. The theories establishing connections between random, time-dependent molecular processes and lineshape effects are exposed in depth. Special emphasis is placed on the theoretical aspects, involving in particular intermolecular processes in solution, and molecular symmetry issues. The Liouville super-operator formalism is briefly introduced and used wherever it is beneficial for the transparency of presentation. The proposed formal descriptions of the discussed problems are sufficiently detailed to be implemented on a computer. Practical applications of the theory in solid- and liquid-phase studies are illustrated with appropriate experimental examples, exposing the potential of the lineshape method in elucidating molecular dynamics NMR-observable molecular phenomena where quantization of the spatial nuclear degrees of freedom is crucial are addressed in the last part of the book. As ...

  18. Transcriptional profiling at whole population and single cell levels reveals somatosensory neuron molecular diversity

    Science.gov (United States)

    Chiu, Isaac M; Barrett, Lee B; Williams, Erika K; Strochlic, David E; Lee, Seungkyu; Weyer, Andy D; Lou, Shan; Bryman, Gregory S; Roberson, David P; Ghasemlou, Nader; Piccoli, Cara; Ahat, Ezgi; Wang, Victor; Cobos, Enrique J; Stucky, Cheryl L; Ma, Qiufu; Liberles, Stephen D; Woolf, Clifford J

    2014-01-01

    The somatosensory nervous system is critical for the organism's ability to respond to mechanical, thermal, and nociceptive stimuli. Somatosensory neurons are functionally and anatomically diverse but their molecular profiles are not well-defined. Here, we used transcriptional profiling to analyze the detailed molecular signatures of dorsal root ganglion (DRG) sensory neurons. We used two mouse reporter lines and surface IB4 labeling to purify three major non-overlapping classes of neurons: 1) IB4+SNS-Cre/TdTomato+, 2) IB4−SNS-Cre/TdTomato+, and 3) Parv-Cre/TdTomato+ cells, encompassing the majority of nociceptive, pruriceptive, and proprioceptive neurons. These neurons displayed distinct expression patterns of ion channels, transcription factors, and GPCRs. Highly parallel qRT-PCR analysis of 334 single neurons selected by membership of the three populations demonstrated further diversity, with unbiased clustering analysis identifying six distinct subgroups. These data significantly increase our knowledge of the molecular identities of known DRG populations and uncover potentially novel subsets, revealing the complexity and diversity of those neurons underlying somatosensation. DOI: http://dx.doi.org/10.7554/eLife.04660.001 PMID:25525749

  19. Systems Genetics Reveals the Functional Context of PCOS Loci and Identifies Genetic and Molecular Mechanisms of Disease Heterogeneity

    Science.gov (United States)

    Xu, Ning; Cui, Jinrui; Mengesha, Emebet; Chen, Yii-Der I.; Taylor, Kent D.; Azziz, Ricardo; Goodarzi, Mark O.

    2015-01-01

    Genome wide association studies (GWAS) have revealed 11 independent risk loci for polycystic ovary syndrome (PCOS), a common disorder in young women characterized by androgen excess and oligomenorrhea. To put these risk loci and the single nucleotide polymorphisms (SNPs) therein into functional context, we measured DNA methylation and gene expression in subcutaneous adipose tissue biopsies to identify PCOS-specific alterations. Two genes from the LHCGR region, STON1-GTF2A1L and LHCGR, were overexpressed in PCOS. In analysis stratified by obesity, LHCGR was overexpressed only in non-obese PCOS women. Although not differentially expressed in the entire PCOS group, INSR was underexpressed in obese PCOS subjects only. Alterations in gene expression in the LHCGR, RAB5B and INSR regions suggest that SNPs in these loci may be functional and could affect gene expression directly or indirectly via epigenetic alterations. We identified reduced methylation in the LHCGR locus and increased methylation in the INSR locus, changes that are concordant with the altered gene expression profiles. Complex patterns of meQTL and eQTL were identified in these loci, suggesting that local genetic variation plays an important role in gene regulation. We propose that non-obese PCOS women possess significant alterations in LH receptor expression, which drives excess androgen secretion from the ovary. Alternatively, obese women with PCOS possess alterations in insulin receptor expression, with underexpression in metabolic tissues and overexpression in the ovary, resulting in peripheral insulin resistance and excess ovarian androgen production. These studies provide a genetic and molecular basis for the reported clinical heterogeneity of PCOS. PMID:26305227

  20. Systems Genetics Reveals the Functional Context of PCOS Loci and Identifies Genetic and Molecular Mechanisms of Disease Heterogeneity.

    Science.gov (United States)

    Jones, Michelle R; Brower, Meredith A; Xu, Ning; Cui, Jinrui; Mengesha, Emebet; Chen, Yii-Der I; Taylor, Kent D; Azziz, Ricardo; Goodarzi, Mark O

    2015-08-01

    Genome wide association studies (GWAS) have revealed 11 independent risk loci for polycystic ovary syndrome (PCOS), a common disorder in young women characterized by androgen excess and oligomenorrhea. To put these risk loci and the single nucleotide polymorphisms (SNPs) therein into functional context, we measured DNA methylation and gene expression in subcutaneous adipose tissue biopsies to identify PCOS-specific alterations. Two genes from the LHCGR region, STON1-GTF2A1L and LHCGR, were overexpressed in PCOS. In analysis stratified by obesity, LHCGR was overexpressed only in non-obese PCOS women. Although not differentially expressed in the entire PCOS group, INSR was underexpressed in obese PCOS subjects only. Alterations in gene expression in the LHCGR, RAB5B and INSR regions suggest that SNPs in these loci may be functional and could affect gene expression directly or indirectly via epigenetic alterations. We identified reduced methylation in the LHCGR locus and increased methylation in the INSR locus, changes that are concordant with the altered gene expression profiles. Complex patterns of meQTL and eQTL were identified in these loci, suggesting that local genetic variation plays an important role in gene regulation. We propose that non-obese PCOS women possess significant alterations in LH receptor expression, which drives excess androgen secretion from the ovary. Alternatively, obese women with PCOS possess alterations in insulin receptor expression, with underexpression in metabolic tissues and overexpression in the ovary, resulting in peripheral insulin resistance and excess ovarian androgen production. These studies provide a genetic and molecular basis for the reported clinical heterogeneity of PCOS.