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Sample records for analysis molecular investigation

  1. Spectroscopic analysis and molecular docking of imidazole derivatives and investigation of its reactive properties by DFT and molecular dynamics simulations

    Science.gov (United States)

    Thomas, Renjith; Hossain, Mossaraf; Mary, Y. Sheena; Resmi, K. S.; Armaković, Stevan; Armaković, Sanja J.; Nanda, Ashis Kumar; Ranjan, Vivek Kumar; Vijayakumar, G.; Van Alsenoy, C.

    2018-04-01

    Solvent-free synthesis pathway for obtaining two imidazole derivatives (2-chloro-1-(4-methoxyphenyl)-4,5-dimethyl-1H-imidazole (CLMPDI) and 1-(4-bromophenyl)-2-chloro-4,5-dimethyl-1H-imidazole (BPCLDI) has been reported in this work, followed by detailed experimental and computational spectroscopic characterization and reactivity study. Spectroscopic methods encompassed IR, FT-Raman and NMR techniques, with the mutual comparison of experimentally and computationally obtained results at DFT/B3LYP level of theory. Reactivity study based on DFT calculations encompassed molecular orbitals analysis, followed by calculations of molecular electrostatic potential (MEP) and average local ionization energy (ALIE) values, Fukui functions and bond dissociation energies (BDE). Additionally, the stability of title molecules in water has been investigated via molecular dynamics (MD) simulations, while interactivity with aspulvinonedimethylallyl transferase protein has been evaluated by molecular docking procedure. CLMPDI compound showed antimicrobial activity against all four bacterial strain in both gram positive and gram negative bacteria while, BPCLDI showed only in gram positive bacteria, Staphylococcus Aureus (MTCC1144). The first order hyperpolarizability of CLMPDI and BPCLDI are 20.15 and 6.10 times that of the standard NLO material urea.

  2. Molecular structure, vibrational analysis (IR and Raman) and quantum chemical investigations of 1-aminoisoquinoline

    Science.gov (United States)

    Sivaprakash, S.; Prakash, S.; Mohan, S.; Jose, Sujin P.

    2017-12-01

    Quantum chemical calculations of energy and geometrical parameters of 1-aminoisoquinoline [1-AIQ] were carried out by using DFT/B3LYP method using 6-311G (d,p), 6-311G++(d,p) and cc-pVTZ basis sets. The vibrational wavenumbers were computed for the energetically most stable, optimized geometry. The vibrational assignments were performed on the basis of potential energy distribution (PED) using VEDA program. The NBO analysis was done to investigate the intra molecular charge transfer of the molecule. The frontier molecular orbital (FMO) analysis was carried out and the chemical reactivity descriptors of the molecule were studied. The Mulliken charge analysis, molecular electrostatic potential (MEP), HOMO-LUMO energy gap and the related properties were also investigated at B3LYP level. The absorption spectrum of the molecule was studied from UV-Visible analysis by using time-dependent density functional theory (TD-DFT). Fourier Transform Infrared spectrum (FT-IR) and Raman spectrum of 1-AIQ compound were analyzed and recorded in the range 4000-400 cm-1 and 3500-100 cm-1 respectively. The experimentally determined wavenumbers were compared with those calculated theoretically and they complement each other.

  3. 3D-QSAR Investigation of Synthetic Antioxidant Chromone Derivatives by Molecular Field Analysis

    Directory of Open Access Journals (Sweden)

    Jiraporn Ungwitayatorn

    2008-02-01

    Full Text Available A series of 7-hydroxy, 8-hydroxy and 7,8-dihydroxy synthetic chromone derivatives was evaluated for their DPPH free radical scavenging activities. A training set of 30 synthetic chromone derivatives was subject to three-dimensional quantitative structure-activity relationship (3D-QSAR studies using molecular field analysis (MFA. The substitutional requirements for favorable antioxidant activity were investigated and a predictive model that could be used for the design of novel antioxidants was derived. Regression analysis was carried out using genetic partial least squares (G/PLS method. A highly predictive and statistically significant model was generated. The predictive ability of the developed model was assessed using a test set of 5 compounds (r2pred = 0.924. The analyzed MFA model demonstrated a good fit, having r2 value of 0.868 and crossvalidated coefficient r2cv value of 0.771.

  4. Investigating Molecular Interactions

    DEFF Research Database (Denmark)

    Clausen, Henrik Fanø

    2010-01-01

    ···π interactions are accommodated by electrostatic complementarity. The crystal structure of both the α- and the β-polymorph of hydroquinone is presented in Chapter 6 with focus on close intermolecular contacts between the molecules via Hirshfeld surface analysis. The charge density distribution of the empty β....... The last chapter of this dissertation presents the analysis of intermolecular interaction using both the Hirshfeld surface and charge density distribution of the acetonitrile β-hydroquinone clathrate. The local packing and related close contacts are examined by breakdown of the fingerprint plots revealing......, are also introduced, as a goal of the analysis of charge density distributions is to obtain further understanding of these macroscopic properties. Neutron diffraction will be used as a complementary tool to the X-ray diffraction experiment, as positional and thermal parameters of hydrogen atoms can...

  5. Mutation analysis and molecular modeling for the investigation of ligand-binding modes of GPR84.

    Science.gov (United States)

    Nikaido, Yoshiaki; Koyama, Yuuta; Yoshikawa, Yasushi; Furuya, Toshio; Takeda, Shigeki

    2015-05-01

    GPR84 is a G protein-coupled receptor for medium-chain fatty acids. Capric acid and 3,3'-diindolylmethane are specific agonists for GPR84. We built a homology model of a GPR84-capric acid complex to investigate the ligand-binding mode using the crystal structure of human active-state β2-adrenergic receptor. We performed site-directed mutagenesis to subject ligand-binding sites to our model using GPR84-Giα fusion proteins and a [(35)S]GTPγS-binding assay. We compared the activity of the wild type and mutated forms of GPR84 by [(35)S]GTPγS binding to capric acid and diindolylmethane. The mutations L100D `Ballesteros-Weinstein numbering: 3.32), F101Y (3.33) and N104Q (3.36) in the transmembrane helix III and N357D (7.39) in the transmembrane helix VII resulted in reduced capric acid activity but maintained the diindolylmethane responses. Y186F (5.46) and Y186H (5.46) mutations had no characteristic effect on capric acid but with diindolylmethane they significantly affected the G protein activation efficiency. The L100D (3.32) mutant responded to decylamine, a fatty amine, instead of a natural agonist, the fatty acid capric acid, suggesting that we have identified a mutated G protein-coupled receptor-artificial ligand pairing. Our molecular model provides an explanation for these results and interactions between GPR84 and capric acid. Further, from the results of a double stimulation assay, we concluded that diindolylmethane was a positive allosteric modulator for GPR84. © The Authors 2014. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

  6. Spectroscopic analysis of 8-hydroxyquinoline derivatives and investigation of its reactive properties by DFT and molecular dynamics simulations

    Science.gov (United States)

    Sureshkumar, B.; Mary, Y. Sheena; Resmi, K. S.; Panicker, C. Yohannan; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, C.; Narayana, B.; Suma, S.

    2018-03-01

    Two 8-hydroxyquinoline derivatives, 5,7-dichloro-8-hydroxyquinoline (57DC8HQ) and 5-chloro-7-iodo-8-hydroxy quinoline (5CL7I8HQ) have been investigated in details by means of spectroscopic characterization and computational molecular modelling techniques. FT-IR and FT-Raman experimental spectroscopic approaches have been utilized in order to obtain detailed spectroscopic signatures of title compounds, while DFT calculations have been used in order to visualize and assign vibrations. The computed values of dipole moment, polarizability and hyperpolarizability indicate that the title molecules exhibit NLO properties. The evaluated HOMO and LUMO energies demonstrate the chemical stability of the molecules. NBO analysis is made to study the stability of the molecules arising from hyperconjugative interactions and charge delocalization. DFT calculations have been also used jointly with MD simulations in order to investigate in details global and local reactivity properties of title compounds. Also, molecular docking has been also used in order to investigate affinity of title compounds against decarboxylase inhibitor and quinoline derivatives can be a lead compounds for developing new antiparkinsonian drug.

  7. Density functional theoretical analysis with experimental, invitro bioactivity and molecular docking investigations on the pesticide Albendazole

    Science.gov (United States)

    Divya, P.; Bena Jothy, V.

    2018-03-01

    Optimized structural parameters of Albendazole and corresponding vibrational assignments have been studied using infrared and Raman spectroscopy combined with quantum-chemical calculations. Results of these spectroscopic studies have been successfully compared against obtained experimental data. Difference between experimental and calculated CH3 group wavenumbers was blue-shifted by 58 cm-1 and 43 cm-1, respectively due to electronic effects. In NBO analysis the increase in energies and the shortening of Csbnd N and Cdbnd O bonds gives clear evidence that the resonance of the benzimidazole ring is increased by the groups. Best binding score of Albendazole was obtained with protein 4NQ6 (-5.58 kcal/mol).

  8. Numerical Investigation of the Microscopic Heat Current Inside a Nanofluid System Based on Molecular Dynamics Simulation and Wavelet Analysis.

    Science.gov (United States)

    Jia, Tao; Gao, Di

    2018-04-03

    Molecular dynamics simulation is employed to investigate the microscopic heat current inside an argon-copper nanofluid. Wavelet analysis of the microscopic heat current inside the nanofluid system is conducted. The signal of the microscopic heat current is decomposed into two parts: one is the approximation part; the other is the detail part. The approximation part is associated with the low-frequency part of the signal, and the detail part is associated with the high-frequency part of the signal. Both the probability distributions of the high-frequency and the low-frequency parts of the signals demonstrate Gaussian-like characteristics. The curves fit to data of the probability distribution of the microscopic heat current are established, and the parameters including the mean value and the standard deviation in the mathematical formulas of the curves show dramatic changes for the cases before and after adding copper nanoparticles into the argon base fluid.

  9. Molecular investigation of mental retardation locus gene PRSS12 by linkage analysis.

    Science.gov (United States)

    Ali, Zafar; Babar, Masroor Ellahi; Ahmad, Jamil; Yousaf, Muhammad Zubair; Asif, Muhammad; Shah, Sajjad Ali

    2011-05-01

    The present study was carried out to determine the prevalence of families having mental retardation in Pakistani population. We enrolled seven mentally retarded (MR) families with two or more affected individuals. Family history was taken to minimize the chances of other abnormalities. Pedigrees were drawn using the Cyrillic software (version 2.1). The structure of pedigrees shows that all the marriages are consanguineous and the families have recessive mode of inheritance. All the families were studied by linkage analysis to mental retardation locus (MRT1)/gene PRSS12. Three STR markers (D4S191, D4S2392, and D4S3024) in vicinity of mental retardation (MR) locus (MRT1)/gene PRSS12 were amplified on all the sample of each family by PCR. The PCR products were then genotyped on non denaturing polyacrylamide gel electrophoresis (PAGE). The Haplotype were constructed to determine the pattern of inheritance and also to determine that a family was linked or unlinked to gene PRSS12. One out of the seven families was potentially linked to gene PRSS12, while the other six families remain unlinked.

  10. Techniques for Investigating Molecular Toxicology of Nanomaterials.

    Science.gov (United States)

    Wang, Yanli; Li, Chenchen; Yao, Chenjie; Ding, Lin; Lei, Zhendong; Wu, Minghong

    2016-06-01

    Nanotechnology has been a rapidly developing field in the past few decades, resulting in the more and more exposure of nanomaterials to human. The increased applications of nanomaterials for industrial, commercial and life purposes, such as fillers, catalysts, semiconductors, paints, cosmetic additives and drug carriers, have caused both obvious and potential impacts on human health and environment. Nanotoxicology is used to study the safety of nanomaterials and has grown at the historic moment. Molecular toxicology is a new subdiscipline to study the interactions and impacts of materials at the molecular level. To better understand the relationship between the molecular toxicology and nanomaterials, this review summarizes the typical techniques and methods in molecular toxicology which are applied when investigating the toxicology of nanomaterials and include six categories: namely; genetic mutation detection, gene expression analysis, DNA damage detection, chromosomal aberration analysis, proteomics, and metabolomics. Each category involves several experimental techniques and methods.

  11. NMR investigations of molecular dynamics

    Science.gov (United States)

    Palmer, Arthur

    2011-03-01

    NMR spectroscopy is a powerful experimental approach for characterizing protein conformational dynamics on multiple time scales. The insights obtained from NMR studies are complemented and by molecular dynamics (MD) simulations, which provide full atomistic details of protein dynamics. Homologous mesophilic (E. coli) and thermophilic (T. thermophilus) ribonuclease H (RNase H) enzymes serve to illustrate how changes in protein sequence and structure that affect conformational dynamic processes can be monitored and characterized by joint analysis of NMR spectroscopy and MD simulations. A Gly residue inserted within a putative hinge between helices B and C is conserved among thermophilic RNases H, but absent in mesophilic RNases H. Experimental spin relaxation measurements show that the dynamic properties of T. thermophilus RNase H are recapitulated in E. coli RNase H by insertion of a Gly residue between helices B and C. Additional specific intramolecular interactions that modulate backbone and sidechain dynamical properties of the Gly-rich loop and of the conserved Trp residue flanking the Gly insertion site have been identified using MD simulations and subsequently confirmed by NMR spin relaxation measurements. These results emphasize the importance of hydrogen bonds and local steric interactions in restricting conformational fluctuations, and the absence of such interactions in allowing conformational adaptation to substrate binding.

  12. Theoretical investigations of two adamantane derivatives: A combined X-ray, DFT, QTAIM analysis and molecular docking

    Science.gov (United States)

    Al-Wahaibi, Lamya H.; Sujay, Subramaniam; Muthu, Gangadharan Ganesh; El-Emam, Ali A.; Venkataramanan, Natarajan S.; Al-Omary, Fatmah A. M.; Ghabbour, Hazem A.; Percino, Judith; Thamotharan, Subbiah

    2018-05-01

    A detailed structural analysis of two adamantane derivatives namely, ethyl 2-[(Z)-1-(adamantan-1-yl)-3-(phenyl)isothioureido]acetate I and ethyl 2-[(Z)-1-(adamantan-1-yl)-3-(4-fluorophenyl)isothioureido]acetate II is carried out to understand the effect of fluorine substitution. The introduction of fluorine atom alters the crystal packing and is completely different from its parent compound. The fluorine substitution drastically reduced the intermolecular H⋯H contacts and this reduction is compensated by intermolecular F⋯H and F⋯F contacts. The relative contributions of various intermolecular contacts present in these structures were quantified using Hirshfeld surface analysis. Energetically significant molecular pairs were identified from the crystal structures of these compounds using PIXEL method. The structures of I and II are optimized in gas and solvent phases using the B3LYP-D3/6-311++G(d,p) level of theory. The quantum theory of atoms-in-molecules (QTAIM) analysis was carried out to estimate the strengths of various intermolecular contacts present in these molecular dimers. The results suggest that the Hsbnd H bonding take part in the stabilization of crystal structures. The experimental and theoretical UV-Vis results show the variations in HOMO and LUMO energy levels. In silico docking analysis indicates that both compounds I and II may exhibit inhibitory activity against 11-β-hydroxysteroid dehydrogenase 1 (11-β-HSD1).

  13. Spectroscopic analysis of 8-hydroxyquinoline-5-sulphonic acid and investigation of its reactive properties by DFT and molecular dynamics simulations

    Science.gov (United States)

    Sureshkumar, B.; Sheena Mary, Y.; Panicker, C. Yohannan; Resmi, K. S.; Suma, S.; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, C.

    2017-12-01

    A detailed interpretation of the FT-IR and FT-Raman spectra has been performed on the basis of the observed and calculated infrared and Raman spectra as well as calculated potential energy distribution values. Comparison of Raman and SERS spectra suggests a tilted orientation of the rings on the metal surface. The dipole moment, polarizability and first and second order hyperpolarizability values of the molecule were calculated. Global reactivity parameters were predicted. The relative reactivities towards electrophilic and nucleophilic attack are predicted using molecular electrostatic potential map. Average local ionization energy (ALIE) and Fukui functions have been inspected in order to investigate local reactivity properties of title molecule. The importance of autoxidation and hydrolysis mechanisms for the title molecule has been assessed by DFT calculations of bond dissociation energies (BDE) and by calculations of radial distribution functions (RDFs) after molecular dynamics (MD) simulations. Molecular docking studies suggest that the title compound can be a lead compound for developing new anti-cancerous drug.

  14. Investigation and Analysis of Genetic Diversity of Diospyros Germplasms Using SCoT Molecular Markers in Guangxi.

    Science.gov (United States)

    Deng, Libao; Liang, Qingzhi; He, Xinhua; Luo, Cong; Chen, Hu; Qin, Zhenshi

    2015-01-01

    Knowledge about genetic diversity and relationships among germplasms could be an invaluable aid in diospyros improvement strategies. This study was designed to analyze the genetic diversity and relationship of local and natural varieties in Guangxi Zhuang Autonomous Region of China using start codon targeted polymorphism (SCoT) markers. The accessions of 95 diospyros germplasms belonging to four species Diospyros kaki Thunb, D. oleifera Cheng, D. kaki var. silverstris Mak, and D. lotus Linn were collected from different eco-climatic zones in Guangxi and were analyzed using SCoT markers. Results indicated that the accessions of 95 diospyros germplasms could be distinguished using SCoT markers, and were divided into three groups at similarity coefficient of 0.608; these germplasms that belong to the same species were clustered together; of these, the degree of genetic diversity of the natural D. kaki var. silverstris Mak population was richest among the four species; the geographical distance showed that the 12 natural populations of D. kaki var. silverstris Mak were divided into two groups at similarity coefficient of 0.19. Meanwhile, in order to further verify the stable and useful of SCoT markers in diospyros germplasms, SSR markers were also used in current research to analyze the genetic diversity and relationship in the same diospyros germplasms. Once again, majority of germplasms that belong to the same species were clustered together. Thus SCoT markers were stable and especially useful for analysis of the genetic diversity and relationship in diospyros germplasms. The molecular characterization and diversity assessment of diospyros were very important for conservation of diospyros germplasm resources, meanwhile for diospyros improvement.

  15. Investigation of chemical modifiers for sulfur determination in diesel fuel samples by high-resolution continuum source graphite furnace molecular absorption spectrometry using direct analysis

    Energy Technology Data Exchange (ETDEWEB)

    Huber, Charles S. [Instituto Federal Sul-rio-grandense, Câmpus Pelotas, Pelotas, RS (Brazil); Universidade Federal do Rio Grande do Sul, Instituto de Química, Porto Alegre, RS (Brazil); Vale, Maria Goreti R. [Universidade Federal do Rio Grande do Sul, Instituto de Química, Porto Alegre, RS (Brazil); Instituto Nacional de Ciência e Tecnologia do CNPq, INCT de Energia e Ambiente, Universidade Federal da Bahia, Salvador, BA (Brazil); Welz, Bernhard [Instituto Nacional de Ciência e Tecnologia do CNPq, INCT de Energia e Ambiente, Universidade Federal da Bahia, Salvador, BA (Brazil); Universidade Federal de Santa Catarina, Departamento de Química, Florianópolis, SC (Brazil); Andrade, Jailson B. [Instituto Nacional de Ciência e Tecnologia do CNPq, INCT de Energia e Ambiente, Universidade Federal da Bahia, Salvador, BA (Brazil); Dessuy, Morgana B., E-mail: mbdessuy@ufrgs.br [Universidade Federal do Rio Grande do Sul, Instituto de Química, Porto Alegre, RS (Brazil); Instituto Nacional de Ciência e Tecnologia do CNPq, INCT de Energia e Ambiente, Universidade Federal da Bahia, Salvador, BA (Brazil)

    2015-06-01

    High-resolution continuum source graphite furnace molecular absorption spectrometry has been applied for sulfur determination in diesel fuel. The sharp rotational lines of the carbon monosulfide molecule (formed during the vaporization step) were used to measure the absorbance. The analytical line at 258.056 nm was monitored using the sum of three pixels. Different chemical modifiers were investigated and the mixture of palladium and magnesium was used as chemical modifier in combination with iridium as permanent modifier. L-Cysteine was chosen as sulfur standard and the calibration was done against aqueous standard solutions. The proposed method was applied for the analyses of four diesel samples: two S10 samples and two S500 samples. The trueness of the method was checked with a certified reference material (CRM) of sulfur in diesel fuel (NIST 2724b). Accurate results, for samples and CRM, were achieved after a dilution with propan-1-ol. The following figures of merit were obtained: characteristic mass of 17 ± 3 ng, limit of detection and limit of quantification of 1.4 mg kg{sup −1} and 4.7 mg kg{sup −1}, respectively. - Highlights: • Ir, Ru and Zr were investigated as permanent modifiers. • Ca, Mg, Pd and Pd/Mg were investigated as modifiers in solution. • Indirect determination of sulfur monitoring the molecular absorbance of the CS • Direct analysis of diesel samples using a dilution in propan-1-ol.

  16. 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:

  17. Molecular analysis of thymoma.

    Directory of Open Access Journals (Sweden)

    Sunil Badve

    Full Text Available Histologic classification of thymomas has significant limitations with respect to both subtype definitions and consistency. In order to better understand the biology of the disease processes, we performed whole genome gene expression analysis. RNA was extracted from fresh frozen tumors from 34 patients with thymomas and followup data was available. Using the Illumina BeadStudio® platform and Human Ref-8 Beadchip, gene expression data was analyzed with Partek Genomics Suite®, and Ingenuity Pathways Analysis (IPA. Unsupervised clustering of gene expression data, representing one of the largest series in literature, resulted in identification of four molecular clusters of tumors (C1-C4, which correlated with histology (P = 0.002. However, neither histology nor clusters correlated with clinical outcomes. Correlation of gene expression data with clinical data showed that a number of genes were associated with either advanced stage at diagnosis or development of recurrence or metastases. The top pathways associated with metastases were amino acid metabolisms, biosynthesis of steroids and glycosphingolipids, cell cycle checkpoint proteins and Notch signaling. The differential expression of some of the top genes related to both metastases and stage was confirmed by RT-PCR in all cases of metastases and matched nonmetastatic cases. A number of potential candidates for therapeutics were also identified.

  18. "Mini-Array" Transcriptional Analysis of the "Listeria Monocytogenes" Lecithinase Operon as a Class Project: A Student Investigative Molecular Biology Laboratory Experience

    Science.gov (United States)

    Christensen, Douglas; Jovic, Marko

    2006-01-01

    This report describes a molecular biotechnology-based laboratory curriculum developed to accompany an undergraduate genetics course. During the course of a semester, students researched the pathogen, developed a research question, designed experiments, and performed transcriptional analysis of a set of genes that confer virulence to the food-borne…

  19. Investigation of Galactosylated Low Molecular Weight Chitosan ...

    African Journals Online (AJOL)

    was coupled with low molecular weight chitosan (LMWC) using carbodiimide chemistry. .... High molecular weight chitosan (minimum 85% ..... membrane permeability of drug and mutual repulsion ... coating thickness and the lower solubility of.

  20. Investigating Ebola virus pathogenicity using molecular dynamics.

    Science.gov (United States)

    Pappalardo, Morena; Collu, Francesca; Macpherson, James; Michaelis, Martin; Fraternali, Franca; Wass, Mark N

    2017-08-11

    Ebolaviruses have been known to cause deadly disease in humans for 40 years and have recently been demonstrated in West Africa to be able to cause large outbreaks. Four Ebolavirus species cause severe disease associated with high mortality in humans. Reston viruses are the only Ebolaviruses that do not cause disease in humans. Conserved amino acid changes in the Reston virus protein VP24 compared to VP24 of other Ebolaviruses have been suggested to alter VP24 binding to host cell karyopherins resulting in impaired inhibition of interferon signalling, which may explain the difference in human pathogenicity. Here we used protein structural analysis and molecular dynamics to further elucidate the interaction between VP24 and KPNA5. As a control experiment, we compared the interaction of wild-type and R137A-mutant (known to affect KPNA5 binding) Ebola virus VP24 with KPNA5. Results confirmed that the R137A mutation weakens direct VP24-KPNA5 binding and enables water molecules to penetrate at the interface. Similarly, Reston virus VP24 displayed a weaker interaction with KPNA5 than Ebola virus VP24, which is likely to reduce the ability of Reston virus VP24 to prevent host cell interferon signalling. Our results provide novel molecular detail on the interaction of Reston virus VP24 and Ebola virus VP24 with human KPNA5. The results indicate a weaker interaction of Reston virus VP24 with KPNA5 than Ebola virus VP24, which is probably associated with a decreased ability to interfere with the host cell interferon response. Hence, our study provides further evidence that VP24 is a key player in determining Ebolavirus pathogenicity.

  1. Binding affinities of Schiff base Fe(II) complex with BSA and calf-thymus DNA: Spectroscopic investigations and molecular docking analysis

    Science.gov (United States)

    Rudra, Suparna; Dasmandal, Somnath; Patra, Chiranjit; Kundu, Arjama; Mahapatra, Ambikesh

    2016-09-01

    The binding interaction of a synthesized Schiff base Fe(II) complex with biological macromolecules viz., bovine serum albumin (BSA) and calf thymus(ct)-DNA have been investigated using different spectroscopic techniques coupled with viscosity measurements at physiological pH and 298 K. Regular amendments in emission intensities of BSA upon the action of the complex indicate significant interaction between them, and the binding interaction have been characterized by Stern Volmer plots and thermodynamic binding parameters. On the basis of this quenching technique one binding site with binding constant (Kb = (7.6 ± 0.21) × 105) between complex and protein have been obtained at 298 K. Time-resolved fluorescence studies have also been encountered to understand the mechanism of quenching induced by the complex. Binding affinities of the complex to the fluorophores of BSA namely tryptophan (Trp) and tyrosine (Tyr) have been judged by synchronous fluorescence studies. Secondary structural changes of BSA rooted by the complex has been revealed by CD spectra. On the other hand, hypochromicity of absorption spectra of the complex with the addition of ct-DNA and the gradual reduction in emission intensities of ethidium bromide bound ct-DNA in presence of the complex indicate noticeable interaction between ct-DNA and the complex with the binding constant (4.2 ± 0.11) × 106 M- 1. Life-time measurements have been studied to determine the relative amplitude of binding of the complex to ct-DNA base pairs. Mode of binding interaction of the complex with ct-DNA has been deciphered by viscosity measurements. CD spectra have also been used to understand the changes in ct-DNA structure upon binding with the metal complex. Density functional theory (DFT) and molecular docking analysis have been employed in highlighting the interactive phenomenon and binding location of the complex with the macromolecules.

  2. Spectroscopic investigation on structure (monomer and dimer), molecular characteristics and comparative study on vibrational analysis of picolinic and isonicotinic acids using experimental and theoretical (DFT & IVP) methods

    Science.gov (United States)

    Ramesh, Gaddam; Reddy, Byru Venkatram

    2018-05-01

    In this investigation, the monomeric structure is determined for picolinic and isonicotinic acids based on geometry optimization for one of the four possible conformers and intramolecular hydrogen bond of Osbnd H⋯O using density functional theory (DFT) employing B3LYP functional supplemented with 6-311++G(d,p) basis set. Using this optimized monomeric form, the dimer structure is determined based on minimum energy and length of hydrogen bonds obtained for two possible dimeric forms yielded due to head-to-tail intermolecular Osbnd H⋯N hydrogen bond (dimer 1) linkage and tail-to -tail intermolecular Osbnd H⋯O hydrogen bond (dimer 2) linkage between pyridine ring and carboxyl group. The structure parameters obtained for monomer and dimer forms are in good agreement with the experimental literature values. The vibrational assignments have been made unambiguously for all the vibrations from FTIR and FT-Raman spectra based on the potential energy distribution (PED) and eigen vectors obtained in DFT and inverse vibrational problem (IVP) computations. The rms error between the observed and scaled frequencies is 7.7 and 9.4 cm-1 for PIA and INA, respectively. A 74-element modified valence force field is derived by Wilson's GF matrix method using 58 experimental frequencies of the two molecules in overlay least-squares technique. The average error between observed and computed frequencies by this method is calculated to be 10.39 cm-1. The results of both DFT and IVP computations yielded good agreement between observed and calculated frequencies. The NLO behaviour using hyperpolarizability values; and HOMO and LUMO energies; of the two molecules are investigated by DFT. Charge density distribution and site of chemical reactivity of the molecules are studied by molecular electrostatic surface potential (MESP). Stability of the molecules arising from hyper conjugative interactions and charge delocalization has been analyzed using natural bond orbital (NBO

  3. Spectroscopic investigation (FT-IR, FT-Raman), HOMO-LUMO, NBO, and molecular docking analysis of N-ethyl-N-nitrosourea, a potential anticancer agent

    Science.gov (United States)

    Singh, Priyanka; Islam, S. S.; Ahmad, Hilal; Prabaharan, A.

    2018-02-01

    Nitrosourea plays an important role in the treatment of cancer. N-ethyl-N-nitrosourea, also known as ENU, (chemical formula C3H7N3O2), is a highly potent mutagen. The chemical is an alkylating agent and acts by transferring the ethyl group of ENU to nucleobases (usually thymine) in nucleic acids. The molecular structure of N-ethyl-N-nitrosourea has been elucidated using experimental (FT-IR and FT-Raman) and theoretical (DFT) techniques. APT charges, Mulliken atomic charges, Natural bond orbital, Electrostatic potential, HOMO-LUMO and AIM analysis were performed to identify the reactive sites and charge transfer interactions. Furthermore, to evaluate the anticancer activity of ENU molecular docking studies were carried out against 2JIU protein.

  4. Molecular Contamination Investigation Facility (MCIF) Capabilities

    Science.gov (United States)

    Soules, David M.

    2013-01-01

    This facility was used to guide the development of ASTM E 1559 center dot Multiple Quartz Crystal Microbalances (QCMs), large sample and spectral effects capability center dot Several instrumented, high vacuum chamber systems are used to evaluate the molecular outgassing characteristics of materials, flight components and other sensitive surfaces. Test materials for spacecraft/instrument selection center.Test flight components for acceptable molecular outgas levels center dot Determine time/temperature vacuum bake-out requirements center. Data used to set limits for use of materials and specific components center. Provide Input Data to Contamination Transport Models -Applied to numerous flight projects over the past 20 years.

  5. Molecular & Genetic Investigation of Tau in Chronic Traumatic Encephalopathy

    Science.gov (United States)

    2015-10-01

    AWARD NUMBER: W81XWH-14-1-0399 TITLE: Molecular & Genetic Investigation of Tau in Chronic Traumatic Encephalopathy PRINCIPAL INVESTIGATOR: John F...Include area code) October 2015 Annual Report 30 Sep 2014 - 29 Sep 2015 Molecular & Genetic Investigation of Tau in Chronic Traumatic Encephalopathy John... encephalopathy (CTE), but the underlying molecular changes remain unclear. Here, biochemical and genetic studies that deepen our understanding of the

  6. Conformation analysis of trehalose. Molecular dynamics simulation and molecular mechanics

    International Nuclear Information System (INIS)

    Donnamaira, M.C.; Howard, E.I.; Grigera, J.R.

    1992-09-01

    Conformational analysis of the disaccharide trehalose is done by molecular dynamics and molecular mechanics. In spite of the different force fields used in each case, comparison between the molecular dynamics trajectories of the torsional angles of glycosidic linkage and energy conformational map shows a good agreement between both methods. By molecular dynamics it is observed a moderate mobility of the glycosidic linkage. The demands of computer time is comparable in both cases. (author). 6 refs, 4 figs

  7. RFLP Analysis and Allelic Discrimination with Real-Time PCR Using the Human Lactase Persistence Trait: A Pair of Molecular Genetic Investigations

    Science.gov (United States)

    Weinlander, Kenneth M.; Hall, David J.; De Stasio, Elizabeth A.

    2010-01-01

    We describe here two open-ended laboratory investigations for an undergraduate laboratory course that uses students' DNA as templates for quantitative real-time PCR and for traditional PCR followed by RFLP analysis. Students are captivated by the immediacy of the application and the relevance of the genotypes and traits, lactase persistence or…

  8. Spectroscopic investigations (FT-IR & FT-Raman) and molecular docking analysis of 6-[1-methyl-4-nitro-1H-imidazol-5-yl) sulfonyl]-7H-purine

    Science.gov (United States)

    Prasath, M.; Govindammal, M.; Sathya, B.

    2017-10-01

    The Azathioprine is used as anticancer agent. Azathioprine is chemically called 6-[1-methyl-4-nitro-1H-imidazol-5-yl) sulfonyl]-7H-purine (6M4N5P). The vibrational analysis of the 6M4N5P compound was carried out by using FT-IR and FT-Raman spectroscopic techniques and compared with aspects. The optimized geometry, frequency and intensity of the vibrational bands of 6M4N5P were obtained from the HF and DFT methods with 6-31G (d,p) basis set. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FT-IR and FT-Raman spectra. The calculated Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO) energies show that charge transfer occur within the molecule. MEP (Molecular Electrostatic Potential) is very useful in the investigation of the charge distributions and molecular structure. The molecule orbital contributions were determined by using the total density of states (TDOS). A molecular docking analysis has been carried out to understand the conformational change and electrostatic properties of 6M4N5P in the active site of Rac1-Receptor.

  9. Analysis Components Investigation Report

    Science.gov (United States)

    2014-10-01

    integration n (1.4.1) t r to integra Solr separa nstrate the resco. Ther e file system f 22 ATION context, ocument software ased on visualize d offers...query. NLTK8 libr uments. Th locations, b neral Ling rdNet9 is a ts of spee tionships. aning of a w approach rdnet sema ween two w ilar words...Te The this doc The nam inte Mo sea exa this gro .2.4 Do A m que lea An Fea que If w wh libr out Vow Mic nam com 2 http://zinko s Investigation MENT

  10. RESEARCH NOTE Molecular genetic analysis of consanguineous ...

    Indian Academy of Sciences (India)

    Navya

    Molecular genetic analysis of consanguineous families with primary microcephaly ... Translational Research Institute, Academic Health System, Hamad Medical ..... bridging the gap between homozygosity mapping and deep sequencing.

  11. One Pot Selective Arylation of 2-Bromo-5-Chloro Thiophene; Molecular Structure Investigation via Density Functional Theory (DFT), X-ray Analysis, and Their Biological Activities.

    Science.gov (United States)

    Rasool, Nasir; Kanwal, Aqsa; Rasheed, Tehmina; Ain, Quratulain; Mahmood, Tariq; Ayub, Khurshid; Zubair, Muhammad; Khan, Khalid Mohammed; Arshad, Muhammad Nadeem; M Asiri, Abdullah; Zia-Ul-Haq, Muhammad; Jaafar, Hawa Z E

    2016-06-28

    Synthesis of 2,5-bisarylthiophenes was accomplished by sequential Suzuki cross coupling reaction of 2-bromo-5-chloro thiophenes. Density functional theory (DFT) studies were carried out at the B3LYP/6-31G(d, p) level of theory to compare the geometric parameters of 2,5-bisarylthiophenes with those from X-ray diffraction results. The synthesized compounds are screened for in vitro bacteria scavenging abilities. At the concentration of 50 and 100 μg/mL, compounds 2b, 2c, 2d, 3c, and 3f with IC50-values of 51.4, 52.10, 58.0, 56.2, and 56.5 μg/mL respectively, were found most potent against E. coli. Among all the synthesized compounds 2a, 2d, 3c, and 3e with the least values of IC50 77, 76.26, 79.13 μg/mL respectively showed significant antioxidant activities. Almost all of the compounds showed good antibacterial activity against Escherichia coli, whereas 2-chloro-5-(4-methoxyphenyl) thiophene (2b) was found most active among all synthesized compound with an IC50 value of 51.4 μg/mL. All of the synthesized compounds were screened for nitric oxide scavenging activity as well. Frontier molecular orbitals (FMOs) and molecular electrostatic potentials of the target compounds were also studied theoretically to account for their relative reactivity.

  12. Molecular investigations on grain filling rate under terminal heat ...

    African Journals Online (AJOL)

    Grain yield under post anthesis high temperature stress is largely influenced by grain filling rate (GFR). To investigate molecular basis of this trait, a set of 111 recombinant inbred lines (RILs) derived from Raj 4014, a heat sensitive genotype and WH 730, heat tolerant cultivar was phenotyped during 2009-2010 and ...

  13. Molecular DNA Analysis in Forensic Identification.

    Science.gov (United States)

    Dumache, Raluca; Ciocan, Veronica; Muresan, Camelia; Enache, Alexandra

    2016-01-01

    Serological and biochemical identification methods used in forensics have several major disadvantages, such as: long time in processing biological sample and lack of sensitivity and specificity. In the last 30 years, DNA molecular analysis has become an important tool in forensic investigations. DNA profiling is based on the short tandem repeats (STR) and aids in human identification from biological samples. Forensic genetics, can provide information on the events which occurred at the crime scene or to supplement other methods of forensic identification. Currently, the methods used in identification are based on polymerase chain reaction (PCR) analyses. This method analyses the autosomal STRs, the Y-chromosome, and the mitochondrial DNA. Correlation of biological samples present at the crime scene with identification, selection, and the probative value factor is therefore the first aspect to be taken into consideration in the forensic genetic analysis. In the last decade, because of the advances in the field of molecular biology, new biomarkers such as: microRNAs (miR), messenger RNA (mRNA), and DNA methylation have been studied and proposed to be used in the forensic identifications of body fluids.

  14. Investigation of pollutant gases with molecular absorption spectroscopy

    International Nuclear Information System (INIS)

    Izairi, N; Ajredini, F.; Shehabi, M.

    2011-01-01

    This paper contains the molecular absorption spectroscopic investigation on environmental pollution by many pollutants. For this purpose a laser absorption spectroscopy at 630 nm wavelength has been applied to excite the molecular spectra in order to identify the presence of main gas pollutants. The following was the experimental procedure. Preliminary the presence of pollutants was identified. The gas champions were taken in live environment, in Tetovo streets where cars moved, and in some points in Tetovo suburbia, during different periods of the day. A special civet, part of the apparatus, has been filled by environmental air, and latter, put into the apparatus. A laser beam pulse passes throughout absorbing gas medium in the civet to excite the gas, and the absorbing spectra were automatically registered. The molecular band spectra registration has been performed by an FT-IR Spectrometer (Spectrum BX FT-IR Perkin Elmer). For this purpose the measurements were focused in spectral region of 2075 cm -1 to 2384 cm -1 for CO 2 and CO bands investigation. The importance of such measurements is to investigate the spectral properties of absorption spectra and molecular structure, and for monitoring the environmental pollution. (Author)

  15. Wavelet Analysis for Molecular Dynamics

    Science.gov (United States)

    2015-06-01

    Our method takes as input the topology and sparsity of the bonding structure of a molecular system, and returns a hierarchical set of system-specific...problems, such as modeling crack initiation and propagation, or interfacial phenomena. In the present work, we introduce a wavelet-based approach to extend...Several functional forms are common for angle poten- tials complicating not only implementation but also choice of approximation. In all cases, the

  16. New Pyrazole-Hydrazone Derivatives: X-ray Analysis, Molecular Structure Investigation via Density Functional Theory (DFT) and Their High In-Situ Catecholase Activity.

    Science.gov (United States)

    Karrouchi, Khalid; Yousfi, El Bekkaye; Sebbar, Nada Kheira; Ramli, Youssef; Taoufik, Jamal; Ouzidan, Younes; Ansar, M'hammed; Mabkhot, Yahia N; Ghabbour, Hazem A; Radi, Smaail

    2017-10-25

    The development of low-cost catalytic systems that mimic the activity of tyrosinase enzymes (Catechol oxidase) is of great promise for future biochemistry technologic demands. Herein, we report the synthesis of new biomolecules systems based on hydrazone derivatives containing a pyrazole moiety ( L1 - L6 ) with superior catecholase activity. Crystal structures of L1 and L2 biomolecules were determined by X-ray single crystal diffraction (XRD). Optimized geometrical parameters were calculated by density functional theory (DFT) at B3LYP/6-31G (d, p) level and were found to be in good agreement with single crystal XRD data. Copper (II) complexes of the compounds ( L1 - L6 ), generated in-situ, were investigated for their catalytic activities towards the oxidation reaction of catechol to ortho -quinone with the atmospheric dioxygen, in an attempt to model the activity of the copper containing enzyme tyrosinase. The studies showed that the activities depend on four parameters: the nature of the ligand, the nature of counter anion, the nature of solvent and the concentration of ligand. The Cu(II)-ligands, given here, present the highest catalytic activity (72.920 μmol·L -1 ·min -1 ) among the catalysts recently reported in the existing literature.

  17. Investigation of uranium molecular species using laser ablation

    Energy Technology Data Exchange (ETDEWEB)

    Curreli, Davide [Univ. of Illinois, Urbana, IL (United States). Dept. of Nuclear, Plasma, and Radiological Engineering

    2017-07-12

    The goal of this project is to investigate the dynamic evolution of uranium oxide (UOx) molecular species in a rapidly cooling low-temperature plasma using a coupled experimental and modeling approach. Our purpose is to develop quantitative constraints on the UOx phase chemistry under physical conditions similar to that of a nuclear fireball at the time of debris condensation. This work is motivated by a need to better understand the factors controlling uranium chemical fractionation in post-detonation nuclear debris.

  18. Investigation of gamma spectra analysis

    International Nuclear Information System (INIS)

    Wu Huailong; Liu Suping; Hao Fanhua; Gong Jian; Liu Xiaoya

    2006-01-01

    In the investigation of radiation fingerprint comparison, it is found out that some of the popular gamma spectra analysis software have shortcomings, which decrease the radiation fingerprint comparison precision. So a new analysis software is developed for solving the problems. In order to display the advantage of developed program, some typical simulative warhead gamma spectra are analyzed respectively by present software and GAMMAVISION and GENNIE2000. Present software can be applied not only in nuclear warheads deep-cuts verification, but also in any radiation measurement field. (authors)

  19. Investigation of gamma spectra analysis

    International Nuclear Information System (INIS)

    Wu Huailong; Liu Suping; Hao Fanhua

    2006-12-01

    During the investigation of radiation fingerprint comparison, it is found out that the popular gamma spectra analysis softwares are faultful, which decrease the precision of radiation fingerprint comparison. So a new analysis software is development for solving the problems. In order to display the advantage of new program, some typical simulative gamma spectra of radiation source are analyzed respectively by our software and GAMMAVISION and GENNIE2000. The software can be applied not only in nuclear warheads deep-cuts verification, but also in any radiation measurement field. (authors)

  20. Molecular structure, Hirshfeld surface analysis, theoretical investigations and nonlinear optical properties of a novel crystalline chalcone derivative: (E)-1-(5-bromothiophen-2-yl)-3-(p-tolyl)prop-2-en-1-one

    Science.gov (United States)

    Pramodh, B.; Lokanath, N. K.; Naveen, S.; Naresh, P.; Ganguly, S.; Panda, J.

    2018-06-01

    In the present work, the crystal structure of a novel chalcone derivative, (E)-1-(5-bromothiophen-2-yl)-3-(p-tolyl) prop-2-en-1-one has been confirmed by X-ray diffraction studies. Hirshfeld surface analysis was carried out to explore the intermolecular interactions. From the Hirshfeld surface analysis it was observed that H⋯H (26.7%) and C⋯H (26.3%) are the major contributors to the intermolecular interactions which stabilizes the crystal structure. The coordinates were optimized using the density functional theory (DFT) calculations using B3LYP hybrid functions with 6-31G(d) basis set. The structural parameters obtained from XRD studies compliment with those calculated using DFT calculations. The HOMO and LUMO energy gap was found to be 4.1778 eV. The molecular electrostatic potential (MEP) was plotted to identify the possible reactions sites of the molecule. Further, non-linear optical (NLO) properties were investigated by calculating hyperpolarizabilities which indicate that the title compound would be a potential candidate for the NLO applications.

  1. A molecular investigation of adsorption onto mineral pigments

    Science.gov (United States)

    Ninness, Brian J.

    Pigment suspensions are important in several processes such as ceramics, paints, inks, and coatings. In the wet state, pigments are combined with a variety of chemical species such as polymers, surfactants, and polyelectrolytes which produce a complex colloidal system. The adsorption, desorption, and redistribution of these species at the pigment-aqueous solution interface can have an impact on the behavior in both the wet state or its final dried state. The goal of this work is to establish a molecular picture of the adsorption properties of these pigmented systems. A novel in situ infrared technique has been developed which allows the detection of adsorbed surface species on pigment particles in an aqueous environment. The technique involves the use of a polymeric binder to anchor the colloidal pigment particles to the surface of an internal reflection element (IRE). The binder only weakly perturbs about 25% of the reactive surface sites (hydroxyl groups) on silica. The reaction of succinic anhydride with an aminosilanized silica surface has been quantified using this technique. The adsorption dynamics of the cationic surfactant cetyltrimethylammonium bromide (C16TAB) at the TiO2-aqueous solution interface has been investigated using Fourier transform infrared-attenuated total reflection spectroscopy (FTIR-ATR) and electrokinetic analysis. At low bulk concentrations, C16TAB is shown to adsorb as isolated islands with a "defective" bilayer structure. Anionic probe molecules are shown to effectively "tune" the adsorbed surfactant microstructure. The results indicate that the structure of the adsorbed surfactant layer, and not the amount of adsorbed surfactant, dictates the subsequent adsorption behavior of the system. Atomic Layer Deposition is used to deposit a TiO2 layer onto the surfaces of silica and kaolin pigments. The process involves the cyclic reaction sequence of the vapors of TiCl4 and H2O. Three complete deposition cycles are needed before the surfaces

  2. Comparative Investigation of Normal Modes and Molecular Dynamics of Hepatitis C NS5B Protein

    International Nuclear Information System (INIS)

    Asafi, M S; Tekpinar, M; Yildirim, A

    2016-01-01

    Understanding dynamics of proteins has many practical implications in terms of finding a cure for many protein related diseases. Normal mode analysis and molecular dynamics methods are widely used physics-based computational methods for investigating dynamics of proteins. In this work, we studied dynamics of Hepatitis C NS5B protein with molecular dynamics and normal mode analysis. Principal components obtained from a 100 nanoseconds molecular dynamics simulation show good overlaps with normal modes calculated with a coarse-grained elastic network model. Coarse-grained normal mode analysis takes at least an order of magnitude shorter time. Encouraged by this good overlaps and short computation times, we analyzed further low frequency normal modes of Hepatitis C NS5B. Motion directions and average spatial fluctuations have been analyzed in detail. Finally, biological implications of these motions in drug design efforts against Hepatitis C infections have been elaborated. (paper)

  3. Molecular investigations of β-thalassemic children in Erbil governorate

    Science.gov (United States)

    Hasan, Ahmad N.; Al-Attar, Mustafa S.

    2017-09-01

    The present work studies the molecular investigation of 40 thalassemic carriers using polymerase chain reaction. Forty thalassemic carriers who were registered and treated at Erbil thalassemic center and twenty apparently healthy children have been included in the present study. Ages of both groups ranged between 1-18 years. Four primers used to detect four different beta thalassemia mutations they were codon 8/9, codon 8, codon 41/42 and IVS-1-5. The two most common mutations detected among thalassemia group were Cd8/9 with 8 cases (20%) and Cd-8 with 6 cases (15%) followed by codon 41/42 with 4 cases (10%) which investigated and detected for the first time in Erbil governorate through the present study and finally IVS-1-5 with 3 cases (7.5%), while no any cases detected among control group.

  4. Theoretical investigations of molecular wires: Electronic spectra and electron transport

    Science.gov (United States)

    Palma, Julio Leopoldo

    The results of theoretical and computational research are presented for two promising molecular wires, the Nanostar dendrimer, and a series of substituted azobenzene derivatives connected to aluminum electrodes. The electronic absorption spectra of the Nanostar (a phenylene-ethynylene dendrimer attached to an ethynylperylene chromophore) were calculated using a sequential Molecular Dynamics/Quantum Mechanics (MD/QM) method to perform an analysis of the temperature dependence of the electronic absorption process. We modeled the Nanostar as a series of connected units, and performed MD simulations for each chromophore at 10 K and 300 K to study how the temperature affected the structures and, consequently, the spectra. The absorption spectra of the Nanostar were computed using an ensemble of 8000 structures for each chromophore. Quantum Mechanical (QM) ZINDO/S calculations were performed for each conformation in the ensemble, including 16 excited states, for a total of 128,000 excitation energies. The spectral intensity was then scaled linearly with the number of conjugated units. Our calculations for both the individual chromophores and the Nanostar, are in good agreement with experiments. We explain in detail the effects of temperature and the consequences for the absorption process. The second part of this thesis presents a study of the effects of chemical substituents on the electron transport properties of the azobenzene molecule, which has been proposed recently as a component of a light-driven molecular switch. This molecule has two stable conformations (cis and trans) in its electronic ground state, with considerable differences in their conductance. The electron transport properties were calculated using first-principles methods combining non-equilibrium Green's function (NEGF) techniques with density functional theory (DFT). For the azobenzene studies, we included electron-donating groups and electron-withdrawing groups in meta- and ortho-positions with

  5. Investigating biofuels through network analysis

    International Nuclear Information System (INIS)

    Curci, Ylenia; Mongeau Ospina, Christian A.

    2016-01-01

    Biofuel policies are motivated by a plethora of political concerns related to energy security, environmental damages, and support of the agricultural sector. In response to this, much scientific work has chiefly focussed on analysing the biofuel domain and on giving policy advice and recommendations. Although innovation has been acknowledged as one of the key factors in sustainable and cost-effective biofuel development, there is an urgent need to investigate technological trajectories in the biofuel sector by starting from consistent data and appropriate methodological tools. To do so, this work proposes a procedure to select patent data unequivocally related to the investigated sector, it uses co-occurrence of technological terms to compute patent similarity and highlights content and interdependencies of biofuels technological trajectories by revealing hidden topics from unstructured patent text fields. The analysis suggests that there is a breaking trend towards modern generation biofuels and that innovators seem to focus increasingly on the ability of alternative energy sources to adapt to the transport/industrial sector. - Highlights: • Innovative effort is devoted to biofuels additives and modern biofuels technologies. • A breaking trend can be observed from the second half of the last decade. • A patent network is identified via text mining techniques that extract latent topics.

  6. Conformation of phylogenetic relationship of Penaeidae shrimp based on morphometric and molecular investigations.

    Science.gov (United States)

    Rajakumaran, P; Vaseeharan, B; Jayakumar, R; Chidambara, R

    2014-01-01

    Understanding of accurate phylogenetic relationship among Penaeidae shrimp is important for academic and fisheries industry. The Morphometric and Randomly amplified polymorphic DNA (RAPD) analysis was used to make the phylogenetic relationsip among 13 Penaeidae shrimp. For morphometric analysis forty variables and total lengths of shrimp were measured for each species, and removed the effect of size variation. The size normalized values obtained was subjected to UPGMA (Unweighted Pair-Group Method with Arithmetic Mean) cluster analysis. For RAPD analysis, the four primers showed reliable differentiation between species, and used correlation coefficient between the DNA banding patterns of 13 Penaeidae species to construct UPGMA dendrogram. Phylogenetic relationship from morphometric and molecular analysis for Penaeidae species found to be congruent. We concluded that as the results from morphometry investigations concur with molecular one, phylogenetic relationship obtained for the studied Penaeidae are considered to be reliable.

  7. Molecular Investigation of Pediatric Portuguese Patients with Sensorineural Hearing Loss

    Directory of Open Access Journals (Sweden)

    Célia Nogueira

    2011-01-01

    Full Text Available The understanding of the molecular genetics in sensorineural hearing loss (SNHL has advanced rapidly during the last decade, but the molecular etiology of hearing impairment in the Portuguese population has not been investigated thoroughly. To provide appropriate genetic testing and counseling to families, we analyzed the whole mitochondrial genome in 95 unrelated children with SNHL (53 nonsyndromic and 42 syndromic and searched for variations in two frequent genes, GJB2 and GJB6, in the non-syndromic patients. Mutations in mtDNA were detected in 4.2% of the cases, including a hitherto undescribed change in the mtDNA-tRNATrp gene (namely, m.5558A>G. We also identified mono- or biallelic GJB2 mutations in 20 of 53 non-syndromic cases and also detected two novel mutations (p.P70R and p.R127QfsX84. Our data further reinforce the notion that genetic heterogeneity is paramount in children with SNHL.

  8. Thermal and molecular investigation of laser tissue welding

    Energy Technology Data Exchange (ETDEWEB)

    Small, W., IV

    1998-06-01

    Despite the growing number of successful animal and human trials, the exact mechanisms of laser tissue welding remain unknown. Furthermore, the effects of laser heating on tissue on the molecular scale are not fully understood. To address these issues, a multi-front attack oil both extrinsic (solder/patch mediated) and intrinsic (laser only) tissue welding was launched using two-color infrared thermometry, computer modeling, weld strength assessment, biochemical assays, and vibrational spectroscopy. The coupling of experimentally measured surface temperatures with the predictive numerical simulations provided insight into the sub-surface dynamics of the laser tissue welding process. Quantification of the acute strength of the welds following the welding procedure enabled comparison among trials during an experiment, with previous experiments, and with other studies in the literature. The acute weld integrity also provided an indication of tile probability of long-term success. Molecular effects induced In the tissue by laser irradiation were investigated by measuring tile concentrations of specific collagen covalent crosslinks and characterizing the Fourier-Transform infrared (FTIR) spectra before and after the laser exposure.

  9. Molecular dynamics investigation of tracer diffusion in a simple liquid

    International Nuclear Information System (INIS)

    Ould-Kaddour, F.; Barrat, J.L.

    1991-05-01

    Extensive Molecular-Dynamics (MD) simulations have been carried out for a model trace-solvent system made up of 100 solvent molecules and 8 tracer molecules interacting through truncated Lennard-Jones potentials. The influence of the size ratio between solute and solvent, of their mass ratio and of the solvent viscosity on the diffusivity of a small tracer were investigated. Positive deviations from a Stokes-Einstein behaviour are observed, in qualitative agreement with experimental observations. It was also observed that as tracer and solvent become increasingly dissimilar, their respective dynamics becomes decoupled. We suggest that such decouplings can be interpreted by writing their mobility of the tracer as the sum of two terms, the first one arising from a coupling between tracer dynamics and hydrodynamics modes of the solvent, and the second one describing jump motion in a locally nearly frozen environment. (author). 17 refs, 4 figs, 6 tabs

  10. Stability investigations of relaxing molecular gas flows. Results and perspectives

    Science.gov (United States)

    Grigor'ev, Yurii N.; Ershov, Igor V.

    2017-10-01

    This article presents results of systematic investigations of a dissipative effect which manifests itself as the growth of hydrodynamic stability and suppression of turbulence in relaxing molecular gas flows. The effect can be a new way for control stability and laminar turbulent transition in aerodynamic flows. The consideration of suppression of inviscid acoustic waves in 2D shear flows is presented. Nonlinear evolution of large-scale vortices and Kelvin — Helmholtz waves in relaxing shear flows are studied. Critical Reynolds numbers in supersonic Couette flows are calculated analytically and numerically within the framework of both classical linear and nonlinear energy hydrodynamic stability theories. The calculations clearly show that the relaxation process can appreciably delay the laminar-turbulent transition. The aim of this article is to show the new dissipative effect, which can be used for flow control and laminarization.

  11. Thermal and molecular investigation of laser tissue welding

    Science.gov (United States)

    Small, Ward, IV

    Despite the growing number of successful animal and human trials, the exact mechanisms of laser tissue welding remain unknown. Furthermore, the effects of laser heating on tissue on the molecular scale are not fully understood. To address these issues, a multi-front attack on both extrinsic (solder/patch mediated) and intrinsic (laser only) tissue welding was launched using two-color infrared thermometry, computer modeling, weld strength assessment, biochemical assays, and vibrational spectroscopy. The coupling of experimentally measured surface temperatures with the predictive numerical simulations provided insight into the sub surface dynamics of the laser tissue welding process. Quantification of the acute strength of the welds following the welding procedure enabled comparison among trials during an experiment, with previous experiments, and with other studies in the literature. The acute weld integrity also provided an indication of the probability of long-term success. Molecular effects induced in the tissue by laser irradiation were investigated by measuring the concentrations of specific collagen covalent crosslinks and measuring the infrared absorption spectra before and after the laser exposure. This investigation yielded results pertaining to both the methods and mechanisms of laser tissue welding. The combination of two-color infrared thermometry to obtain accurate surface temperatures free from emissivity bias and computer modeling illustrated the importance of including evaporation in the simulations, which effectively serves as an inherent cooling mechanism during laser irradiation. Moreover, the hydration state predicted by the model was useful in assessing the role of electrostatic versus covalent bonding in the fusion. These tools also helped elicit differences between dye- enhanced liquid solders and solid-matrix patches in laser-assisted tissue welding, demonstrating the significance of repeatable energy delivery. Surprisingly, covalent bonds

  12. An Investigation of Molecular Docking and Molecular Dynamic Simulation on Imidazopyridines as B-Raf Kinase Inhibitors

    Directory of Open Access Journals (Sweden)

    Huiding Xie

    2015-11-01

    Full Text Available In the recent cancer treatment, B-Raf kinase is one of key targets. Nowadays, a group of imidazopyridines as B-Raf kinase inhibitors have been reported. In order to investigate the interaction between this group of inhibitors and B-Raf kinase, molecular docking, molecular dynamic (MD simulation and binding free energy (ΔGbind calculation were performed in this work. Molecular docking was carried out to identify the key residues in the binding site, and MD simulations were performed to determine the detail binding mode. The results obtained from MD simulation reveal that the binding site is stable during the MD simulations, and some hydrogen bonds (H-bonds in MD simulations are different from H-bonds in the docking mode. Based on the obtained MD trajectories, ΔGbind was computed by using Molecular Mechanics Generalized Born Surface Area (MM-GBSA, and the obtained energies are consistent with the activities. An energetic analysis reveals that both electrostatic and van der Waals contributions are important to ΔGbind, and the unfavorable polar solvation contribution results in the instability of the inhibitor with the lowest activity. These results are expected to understand the binding between B-Raf and imidazopyridines and provide some useful information to design potential B-Raf inhibitors.

  13. Molecular activation analysis for chemical species studies

    International Nuclear Information System (INIS)

    Chai Zhifang; Mao Xueying; Wang Yuqi; Sun Jingxin; Qian Qingfang; Hou Xiaolin; Zhang Peiqun; Chen Chunying; Feng Weiyu; Ding Wenjun; Li Xiaolin; Li Chunsheng; Dai Xiongxin

    2001-01-01

    The Molecular Activation Analysis (MAA) mainly refers to an activation analysis method that is able to provide information about the chemical species of elements in systems of interest, though its exact definition has remained to be assigned. Its development is strongly stimulated by the urgent need to know the chemical species of elements, because the bulk contents or concentrations are often insignificant for judging biological, environmental or geochemical effects of elements. In this paper, the features, methodology and limitation of MAA were outlined. Further, the up-to-date MAA progress made in our laboratory was introduced as well. (author)

  14. Spectroscopic investigation (FT-IR and FT-Raman), vibrational assignments, HOMO-LUMO analysis and molecular docking study of 1-hydroxy-4,5,8-tris(4-methoxyphenyl) anthraquinone

    Science.gov (United States)

    Renjith, R.; Sheena Mary, Y.; Tresa Varghese, Hema; Yohannan Panicker, C.; Thiemann, Thies; Shereef, Anas; Al-Saadi, Abdulaziz A.

    2015-12-01

    FT-IR and FT-Raman spectra of 1-hydroxy-4,5,8-tris(4-methoxyphenyl)anthraquinone were recorded and analyzed. The vibrational wavenumbers were computed using DFT quantum chemical calculations. The data obtained from wavenumber calculations were used to assign the vibrational bands obtained experimentally. A detailed molecular picture of the title compound and its interactions were obtained from NBO analysis. From the MEP plot it is clear that the negative electrostatic potential regions are mainly localized over carbonyl group. There is some evidence of a region of negative electrostatic potential due to π-electron density of the benzo groups. Molecular docking study shows that methoxy groups attached to the phenyl rings and hydroxyl group are crucial for binding and the title compound might exhibit inhibitory activity against PI3K and may act as an anti-neoplastic agent.

  15. Molecular investigations of a locally acquired case of melioidosis in Southern AZ, USA.

    Directory of Open Access Journals (Sweden)

    David M Engelthaler

    2011-10-01

    Full Text Available Melioidosis is caused by Burkholderia pseudomallei, a Gram-negative bacillus, primarily found in soils in Southeast Asia and northern Australia. A recent case of melioidosis in non-endemic Arizona was determined to be the result of locally acquired infection, as the patient had no travel history to endemic regions and no previous history of disease. Diagnosis of the case was confirmed through multiple microbiologic and molecular techniques. To enhance the epidemiological analysis, we conducted several molecular genotyping procedures, including multi-locus sequence typing, SNP-profiling, and whole genome sequence typing. Each technique has different molecular epidemiologic advantages, all of which provided evidence that the infecting strain was most similar to those found in Southeast Asia, possibly originating in, or around, Malaysia. Advancements in new typing technologies provide genotyping resolution not previously available to public health investigators, allowing for more accurate source identification.

  16. Chemical protection and sensitization to ionizing radiation:molecular investigations

    International Nuclear Information System (INIS)

    Badiello, R.

    1980-01-01

    Chemical radioprotection and radiosensitization are induced by the presence of certain chemical compounds, which reduce or enhance the effect of ionizing radiation on living organisms. Such substances are either naturally present or may be artificially introduced in the living cells. Chemical radioprotectors are interesting for possible application in the health protection of both professionally exposed workers and patients treated by radiation for diagnostic and thereapeutic purposes. Interest in chemical radiosensitization has increased recently because of its potential application in the radiotherapy of tumours. Both radioprotection and radiosensitization occur by means of complicated mechanisms, which at first correspond to very fast reactions. The mechanism of the interaction between such substances and radiation-induced biological radicals has been investigated by means of pulse radiolysis and rapid mixing techniques. Examples of the application of these techniques are given to illustrate how information has been obtained on the molecular basis of radiation chemical modi-fication at the cellular level. In particular some interactions between model systems of biological interest (DNA, DNA components, enzymes, amino acids, etc.) and sulphur-containing radioprotectors (glutathione, cysteine, etc.) and/or electroaffinic radiosensitizers, are described. (H.K.)

  17. Investigation of naphthofuran moiety as potential dual inhibitor against BACE-1 and GSK-3β: molecular dynamics simulations, binding energy, and network analysis to identify first-in-class dual inhibitors against Alzheimer's disease.

    Science.gov (United States)

    Kumar, Akhil; Srivastava, Gaurava; Srivastava, Swati; Verma, Seema; Negi, Arvind S; Sharma, Ashok

    2017-08-01

    BACE-1 and GSK-3β are potential therapeutic drug targets for Alzheimer's disease. Recently, both the targets received attention for designing dual inhibitors for Alzheimer's disease. Until now, only two-scaffold triazinone and curcumin have been reported as BACE-1 and GSK-3β dual inhibitors. Docking, molecular dynamics, clustering, binding energy, and network analysis of triazinone derivatives with BACE-1 and GSK-3β was performed to get molecular insight into the first reported dual inhibitor. Further, we designed and evaluated a naphthofuran series for its ability to inhibit BACE-1 and GSK-3β with the computational approaches. Docking study of naphthofuran series showed a good binding affinity towards both the targets. Molecular dynamics, binding energy, and network analysis were performed to compare their binding with the targets and amino acids responsible for binding. Naphthofuran series derivatives showed good interaction within the active site residues of both of the targets. Hydrogen bond occupancy and binding energy suggested strong binding with the targets. Dual-inhibitor binding was mostly governed by the hydrophobic interactions for both of the targets. Per residue energy decomposition and network analysis identified the key residues involved in the binding and inhibiting BACE-1 and GSK-3β. The results indicated that naphthofuran series derivative 11 may be a promising first-in-class dual inhibitor against BACE-1 and GSK-3β. This naphthofuran series may be further explored to design better dual inhibitors. Graphical abstract Naphthofuran derivative as a dual inhibitor for BACE-1 and GSK-3β.

  18. Molecular identification of blow flies recovered from human cadavers during crime scene investigations in Malaysia.

    Science.gov (United States)

    Kavitha, Rajagopal; Nazni, Wasi Ahmad; Tan, Tian Chye; Lee, Han Lim; Isa, Mohd Noor Mat; Azirun, Mohd Sofian

    2012-12-01

    Forensic entomology applies knowledge about insects associated with decedent in crime scene investigation. It is possible to calculate a minimum postmortem interval (PMI) by determining the age and species of the oldest blow fly larvae feeding on decedent. This study was conducted in Malaysia to identify maggot specimens collected during crime scene investigations. The usefulness of the molecular and morphological approach in species identifications was evaluated in 10 morphologically identified blow fly larvae sampled from 10 different crime scenes in Malaysia. The molecular identification method involved the sequencing of a total length of 2.2 kilo base pairs encompassing the 'barcode' fragments of the mitochondrial cytochrome oxidase I (COI), cytochrome oxidase II (COII) and t-RNA leucine genes. Phylogenetic analyses confirmed the presence of Chrysomya megacephala, Chrysomya rufifacies and Chrysomya nigripes. In addition, one unidentified blow fly species was found based on phylogenetic tree analysis.

  19. Copromicroscopic and molecular investigations on intestinal parasites in kenneled dogs.

    Science.gov (United States)

    Simonato, Giulia; Frangipane di Regalbono, Antonio; Cassini, Rudi; Traversa, Donato; Beraldo, Paola; Tessarin, Cinzia; Pietrobelli, Mario

    2015-05-01

    Intestinal parasites are common in dogs worldwide, and their importance has recently increased for a renewed awareness on the public health relevance that some of them have. In this study, the prevalence of helminths and protozoa was evaluated by microscopy in 318 canine faecal samples collected from eight rescue shelters in the North-eastern Italy; 285 of them were also submitted to the molecular characterization of Giardia duodenalis and Cryptosporidium spp. isolates. An analysis was performed to evaluate the prevalence rates in relation to canine individual data, shelter provenance and anthelmintic treatments. Overall, 52.5% (167/318) of faecal samples were positive for at least one parasite. Trichuris vulpis showed the highest overall prevalence rate (29.2%), followed by G. duodenalis (15.1%), Toxocara canis (9.7%), ancylostomatids (8.2%) and Cystoisospora (5.7%). The prevalence of G. duodenalis, evaluated by real-time PCR, was 57.9% (165/285), and 79 isolates were characterized by nested PCR on the β-giardin gene. The assemblages found were mainly the host-specific genotypes C and D, while only one assemblage was identified as the human-specific genotype B1. Isolates of Cryptosporidium spp., recorded in 3/285 (1.1%) stool samples, were Cryptosporidium parvum based on the characterization of the Cryptosporidium oocyst wall protein (COWP) gene. Although the results describe a relatively limited risk of dog-originating zoonoses, there is the need to improve the quality of shelter practices towards better health managements for safe pet-adoption campaigns and a minimization of the environmental faecal pollution with canine intestinal parasites.

  20. Investigation of hybrid molecular material prepared by ionic liquid ...

    Indian Academy of Sciences (India)

    Wintec

    Near IR spectral region (1000–2500 nm) shows the elimination of water in the compound which ... 1-Butyl 3-methyl imidazolium bromide; molecular material; phosphotungstic acid; near IR. ..... attributable to the first overtone of hydroxyl groups,.

  1. Molecular structure and DFT investigations on new cobalt(II ...

    Indian Academy of Sciences (India)

    tion process was demonstrated.9 Late-transition metals, especially Ni, Pd ..... in table S2 (Supplementary Information). Most of the ... to molecular system because of atomic charges affect ... structure, acidity–basicity behavior and other proper-.

  2. Investigation of the Physical and Molecular Properties of Asphalt Binders Processed with Used Motor Oils

    Directory of Open Access Journals (Sweden)

    Mohyeldin Ragab

    2015-01-01

    Full Text Available In this work we investigated the performance aspects of addition of used motor oils (UMO to neat and crumb rubber modified asphalts (CRMA and related that to the change of molecular size distribution of modified asphalt’s fractions; asphaltenes, saturates, naphthene aromatics, and polar aromatics. Based on the results of temperature sweep viscoelastic tests, addition of crumb rubber modifier (CRM alone or with UMO results in the formation of internal network within the modified asphalt. Based on the results of short and long term aged asphalts, the utilization of combination of UMO and CRM enhanced the aging behavior of asphalt. Bending beam rheometer was utilized to investigate the low temperature behavior of UMO modified asphalts. Based on those tests, the utilization of the UMO and CRM enhanced the low temperature properties of asphalts. Based on the results of the asphalt separation tests and the Gel Permeation Chromatography (GPC analysis, it was found that saturates and naphthene aromatics are the two asphalt fractions that have similar molecular size fractions as those of UMO. However, UMO only shifts the molecular sizes of saturates after interaction with asphalt. Results also show that polar aromatics pose higher molecular size structures than UMO.

  3. Molecular docking and spectroscopic investigations aided by density functional theory of Parkinson's drug 2-(3,4-dihydroxyphenyl)ethylamine

    Science.gov (United States)

    Sherlin, Y. Sheeba; Vijayakumar, T.; Roy, S. D. D.; Jayakumar, V. S.

    2018-05-01

    Molecular geometry of Parkinson's drug 2-(3,4-Dihydroxyphenyl)ethylamine hydrochloride (Dopamine, DA) has been evaluated and compared with experimental XRD data. Molecular docking and vibrational spectral analysis of DA have been carried out using FT-Raman and FT-IR spectra aided by Density Functional Theory at B3LYP/6-311++G(d,p). The present investigation deals with the analysis of structural and spectral features responsible for drug activities, nature of hydrogen bonding interactions of the molecule and the correlation of Parkinson's nature with its molecular structural features.

  4. Molecular Composition Analysis of Distant Targets

    Science.gov (United States)

    Hughes, Gary B.; Lubin, Philip

    2017-01-01

    This document is the Final Report for NASA Innovative Advanced Concepts (NIAC) Phase I Grant 15-NIAC16A-0145, titled Molecular Composition Analysis of Distant Targets. The research was focused on developing a system concept for probing the molecular composition of cold solar system targets, such as Asteroids, Comets, Planets and Moons from a distant vantage, for example from a spacecraft that is orbiting the target (Hughes et al., 2015). The orbiting spacecraft is equipped with a high-power laser, which is run by electricity from photovoltaic panels. The laser is directed at a spot on the target. Materials on the surface of the target are heated by the laser beam, and begin to melt and then evaporate, forming a plume of asteroid molecules in front of the heated spot. The heated spot glows, producing blackbody illumination that is visible from the spacecraft, via a path through the evaporated plume. As the blackbody radiation from the heated spot passes through the plume of evaporated material, molecules in the plume absorb radiation in a manner that is specific to the rotational and vibrational characteristics of the specific molecules. A spectrometer aboard the spacecraft is used to observe absorption lines in the blackbody signal. The pattern of absorption can be used to estimate the molecular composition of materials in the plume, which originated on the target. Focusing on a single spot produces a borehole, and shallow subsurface profiling of the targets bulk composition is possible. At the beginning of the Phase I research, the estimated Technology Readiness Level (TRL) of the system was TRL-1. During the Phase I research, an end-to-end theoretical model of the sensor system was developed from first principles. The model includes laser energy and optical propagation, target heating, melting and evaporation of target material, plume density, thermal radiation from the heated spot, molecular cross section of likely asteroid materials, and estimation of the

  5. Investigating Atmospheric Oxidation with Molecular Dynamics Imaging and Spectroscopy

    Science.gov (United States)

    Merrill, W. G.; Case, A. S.; Keutsch, F. N.

    2013-06-01

    Volatile organic compounds (VOCs) in the Earth's atmosphere constitute trace gas species emitted primarily from the biosphere, and are the subject of inquiry for a variety of air quality and climate studies. Reactions intiated (primarily) by the hydroxyl radical (OH) lead to a myriad of oxygenated species (OVOCs), which in turn are prone to further oxidation. Investigations of the role that VOC oxidation plays in tropospheric chemistry have brought to light two troubling scenarios: (1) VOCs are responsible in part for the production of two EPA-regulated pollutants---tropospheric ozone and organic aerosol---and (2) the mechanistic details of VOC oxidation remain convoluted and poorly understood. The latter issue hampers the implementation of near-explicit atmospheric simulations, and large discrepancies in OH reactivity exist between measurements and models at present. Such discrepancies underscore the need for a more thorough description of VOC oxidation. Time-of-flight measurements and ion-imaging techniques are viable options for resolving some of the mechanistic and energetic details of VOC oxidation. Molecular beam studies have the advantage of foregoing unwanted bimolecular reactions, allowing for the characterization of specific processes which must typically compete with the complex manifold of VOC oxidation pathways. The focus of this work is on the unimolecular channels of organic peroxy radical intermediates, which are necessarily generated during VOC oxidation. Such intermediates may isomerize and decompose into distinct chemical channels, enabling the unambiguous detection of each pathway. For instance, a (1 + 1') resonance enhanced multiphoton ionization (REMPI) scheme may be employed to detect carbon monoxide generated from a particular unimolecular process. A number of more subtle mechanistic details may be explored as well. By varying the mean free path of the peroxy radicals in a flow tube, the role of collisional quenching in these unimolecular

  6. Reactivity of etoricoxib based on computational study of molecular orbitals, molecular electrostatic potential surface and Mulliken charge analysis

    Science.gov (United States)

    Sachdeva, Ritika; Soni, Abhinav; Singh, V. P.; Saini, G. S. S.

    2018-05-01

    Etoricoxib is one of the selective cyclooxygenase inhibitor drug which plays a significant role in the pharmacological management of arthritis and pain. The theoretical investigation of its reactivity is done using Density Functional Theory calculations. Molecular Electrostatic Potential Surface of etoricoxib and its Mulliken atomic charge distribution are used for the prediction of its electrophilic and nucleophilic sites. The detailed analysis of its frontier molecular orbitals is also done.

  7. Molecular Dynamics Investigation of Efficient SO₂ Absorption by ...

    Indian Academy of Sciences (India)

    Ionic liquids are appropriate candidates for the absorption of acid gases such as SO₂. Six anion functionalized ionic liquids with different basicities have been studied for SO₂ absorption capacity by employing quantum chemical calculations and molecular dynamics (MD) simulations. Gas phase quantum calculations ...

  8. Molecular activation analysis for chemical speciation studies

    International Nuclear Information System (INIS)

    Chai-Chifang

    1998-01-01

    The term of Molecular Activation Analysis (MAA) refers to an activation analysis method that is able to provide information about the chemical species of elements in system of interests, though its definition has remained to be assigned. Its development is strongly stimulated by the urgent need to know the chemical species of elements, because the total concentrations are often without any meaning when assessing health or environmental risks of trace elements.In practice, the MAA is a combination of conventional instrumental or radiochemical activation analysis and physical, chemical or biochemical separation techniques. The MAA is able to play a particular role in speciation studies. However, the critical point in the MAA is that it is not permitted to change the primitive chemical species of elements in systems, or the change has to be under control; in the meantime it is not allowed to form the 'new artifact' originally not present in systems. Some practical examples of MAA for chemical species research performed recently in our laboratory will be presented as follows: Chemical species of platinum group elements in sediment; Chemical species of iodine in marine algae; Chemical species of mercury in human tissues; Chemical species of selenium in corn; Chemical species of rare earth elements in natural plant, etc. The merits and limitations of MAA will be described as well. (author)

  9. Synchrotron based mass spectrometry to investigate the molecular properties of mineral-organic associations

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Suet Yi; Kleber, Markus; Takahashi, Lynelle K.; Nico, Peter; Keiluweit, Marco; Ahmed, Musahid

    2013-04-01

    Soil organic matter (OM) is important because its decay drives life processes in the biosphere. Analysis of organic compounds in geological systems is difficult because of their intimate association with mineral surfaces. To date there is no procedure capable of quantitatively separating organic from mineral phases without creating artifacts or mass loss. Therefore, analytical techniques that can (a) generate information about both organic and mineral phases simultaneously and (b) allow the examination of predetermined high-interest regions of the sample as opposed to conventional bulk analytical techniques are valuable. Laser Desorption Synchrotron Postionization (synchrotron-LDPI) mass spectrometry is introduced as a novel analytical tool to characterize the molecular properties of organic compounds in mineral-organic samples from terrestrial systems, and it is demonstrated that when combined with Secondary Ion Mass Spectrometry (SIMS), can provide complementary information on mineral composition. Mass spectrometry along a decomposition gradient in density fractions, verifies the consistency of our results with bulk analytical techniques. We further demonstrate that by changing laser and photoionization energies, variations in molecular stability of organic compounds associated with mineral surfaces can be determined. The combination of synchrotron-LDPI and SIMS shows that the energetic conditions involved in desorption and ionization of organic matter may be a greater determinant of mass spectral signatures than the inherent molecular structure of the organic compounds investigated. The latter has implications for molecular models of natural organic matter that are based on mass spectrometric information.

  10. Investigation of nuclear multifragmentation using molecular dynamics and restructured aggregation

    International Nuclear Information System (INIS)

    Paula, L. de; Nemeth, J.; Ben-Hao, Sa.; Leray, S.; Ngo, C.; Souza, S.R.; Yu-Ming, Zheng; Paula, L. de; Nemeth, J.; Ben-Hao, Sa.; Yu-Ming, Zheng; Ngo, H.

    1991-01-01

    We study the stability of excited 197 Au nuclei with respect to multifragmentation. For that we use a dynamical simulation based on molecular dynamics and restructured aggregation. A particular attention is paid to check the stability of the ground state nuclei generated by the simulation. Four kinds of excitations are considered: heat, compression, rotation and a geometrical instability created when a projectile drills a hole in a 197 Au nucleus

  11. Thermal conductivity of ZnTe investigated by molecular dynamics

    International Nuclear Information System (INIS)

    Wang Hanfu; Chu Weiguo

    2009-01-01

    The thermal conductivity of ZnTe with zinc-blende structure has been computed by equilibrium molecular dynamics method based on Green-Kubo formalism. A Tersoff's potential is adopted in the simulation to model the atomic interactions. The calculations are performed as a function of temperature up to 800 K. The calculated thermal conductivities are in agreement with the experimental values between 150 K and 300 K, while the results above the room temperature are comparable with the Slack's equation.

  12. Experimental investigation of molecular beam injection in HL-1 tokamak

    International Nuclear Information System (INIS)

    Yao Lianghua; Diao Guangyao; Wang Zhanhe; Deng Huichen; Luo Junlin; Duan Xuru; Cui Zhengying

    1993-07-01

    A new method of gas puffing is presented. The molecular beam, formed by high pressure deuterium gas through Larval nozzle and skimmer slit, is injected into the HL-1 vacuum vessel. The deuterium molecular current from the nozzle passing through the skimmer is about 3 x 10 20 /s. At the line average electron density of 5.2 x 10 19 m -3 , the beam velocity is about 100 m/s. As the plasma density and temperature increasing, the influxes of deuterium particles attenuate quickly. When the molecular beam injection (MBI) just returned to normal gas puffing, the D α emission rapidly decreases, meanwhile, the particles move toward plasma center, the electron density is continuously peaking. The line average electron density rising lasts 45 ms. The thermal energy of plasma and confinement time for particles and energy are also increasing. the MBI is a direct and efficient gas fuelling mode, and the injected particles can reach to inside about 8 cm of plasma and q ≅ 2 confinement region. Its efficiency of injection is about 50%. After the MBI, the particle recycling coefficient R on the wall is 0.6 which is 10% lower than that of normal gas puffing

  13. Molecular analysis of childhood primitive neuroectodermal tumors defines markers associated with poor outcome

    DEFF Research Database (Denmark)

    Scheurlen, W G; Schwabe, G C; Joos, S

    1998-01-01

    PURPOSE: The diagnostic and prognostic significance of well-defined molecular markers was investigated in childhood primitive neuroectodermal tumors (PNET). MATERIALS AND METHODS: Using microsatellite analysis, Southern blot analysis, and fluorescence in situ hybridization (FISH), 30 primary tumors......: In our study, amplification of c-myc was a poor-prognosis marker in PNET. LOH of chromosome 17p was associated with metastatic disease. Molecular analysis of primary tumors using these markers may be useful for stratification of children with PNET in future prospective studies. The other aberrations...... investigated were not of significant prognostic value, but may provide an entry point for future large-scale molecular studies....

  14. Molecular analysis of waxy mutants in rice

    International Nuclear Information System (INIS)

    Yatou, O.; Amano, E.

    1990-01-01

    Full text: The 'waxy' gene is a structural gene coding a glycosyl transferase which synthesises amylose in the endosperm tissue. 'Non-waxy' rice cultivars have an active gene and their amylose content is 18-25% depending upon gene performance and modifier genes. In 'waxy' rice, no amylose is found because the enzyme is absent. In mutants induced by gamma rays, neutrons, EI or EMS, amylose content ranged from 0 to 20%, i.e. there are intermediate phenotypes as well. Some of them had the same amount of the enzyme as a 'non-waxy' cultivar, even fully 'waxy' mutants showed a certain amount of the enzyme. This suggests that in mutants there may be no structural change in the enzyme gene but the enzyme produced might be less active. By molecular analysis of the mutants' genes it was found that only two mutants induced by thermal neutrons show structural alterations, the changes in other mutants are either too small to be detected by Southern analysis or are outside the structural gene in question. (author)

  15. Polymer Molecular Weight Analysis by [Superscript 1]H NMR Spectroscopy

    Science.gov (United States)

    Izunobi, Josephat U.; Higginbotham, Clement L.

    2011-01-01

    The measurement and analysis of molecular weight and molecular weight distribution remain matters of fundamental importance for the characterization and physical properties of polymers. Gel permeation chromatography (GPC) is the most routinely used method for the molecular weight determination of polymers whereas matrix-assisted laser…

  16. Investigation of deformation mechanisms of staggered nanocomposites using molecular dynamics

    Science.gov (United States)

    Mathiazhagan, S.; Anup, S.

    2016-08-01

    Biological materials with nanostructure of regularly or stair-wise staggered arrangements of hard platelets reinforced in a soft protein matrix have superior mechanical properties. Applications of these nanostructures to ceramic matrix composites could enhance their toughness. Using molecular dynamics simulations, mechanical behaviour of the bio-inspired nanocomposites is studied. Regularly staggered model shows better flow behaviour compared to stair-wise staggered model due to the symmetrical crack propagation along the interface. Though higher stiffness and strength are obtained for stair-wise staggered models, rapid crack propagation reduces the toughness. Arresting this crack propagation could lead to superior mechanical properties in stair-wise staggered models.

  17. Synthesis, spectroscopic investigations, DFT studies, molecular docking and antimicrobial potential of certain new indole-isatin molecular hybrids: Experimental and theoretical approaches

    Science.gov (United States)

    Almutairi, Maha S.; Zakaria, Azza S.; Ignasius, P. Primsa; Al-Wabli, Reem I.; Joe, Isaac Hubert; Attia, Mohamed I.

    2018-02-01

    Indole-isatin molecular hybrids 5a-i have been synthesized and characterized by different spectroscopic methods to be evaluated as new antimicrobial agents against a panel of Gram positive bacteria, Gram negative bacteria, and moulds. Compound 5h was selected as a representative example of the prepared compounds 5a-i to perform computational investigations. Its vibrational properties have been studied using FT-IR and FT-Raman with the aid of density functional theory approach. The natural bond orbital analysis as well as HOMO and LUMO molecular orbitals investigations of compound 5h were carried out to explore its possible intermolecular delocalization or hyperconjugation and its possible interactions with the target protein. Molecular docking of compound 5h predicted its binding mode with the fungal target protein.

  18. Investigation of deformation mechanisms of staggered nanocomposites using molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Mathiazhagan, S., E-mail: smathi.research@gmail.com; Anup, S., E-mail: anupiist@gmail.com

    2016-08-19

    Biological materials with nanostructure of regularly or stair-wise staggered arrangements of hard platelets reinforced in a soft protein matrix have superior mechanical properties. Applications of these nanostructures to ceramic matrix composites could enhance their toughness. Using molecular dynamics simulations, mechanical behaviour of the bio-inspired nanocomposites is studied. Regularly staggered model shows better flow behaviour compared to stair-wise staggered model due to the symmetrical crack propagation along the interface. Though higher stiffness and strength are obtained for stair-wise staggered models, rapid crack propagation reduces the toughness. Arresting this crack propagation could lead to superior mechanical properties in stair-wise staggered models. - Highlights: • The deformation behaviour of staggered nanocomposites is studied. • Stair-wise staggered model has high stiffness and strength, but low toughness. • Rapid crack growth in overlap region causes this low toughness. • Toughness could be enhanced by arresting interfacial crack in the overlap.

  19. Investigation of deformation mechanisms of staggered nanocomposites using molecular dynamics

    International Nuclear Information System (INIS)

    Mathiazhagan, S.; Anup, S.

    2016-01-01

    Biological materials with nanostructure of regularly or stair-wise staggered arrangements of hard platelets reinforced in a soft protein matrix have superior mechanical properties. Applications of these nanostructures to ceramic matrix composites could enhance their toughness. Using molecular dynamics simulations, mechanical behaviour of the bio-inspired nanocomposites is studied. Regularly staggered model shows better flow behaviour compared to stair-wise staggered model due to the symmetrical crack propagation along the interface. Though higher stiffness and strength are obtained for stair-wise staggered models, rapid crack propagation reduces the toughness. Arresting this crack propagation could lead to superior mechanical properties in stair-wise staggered models. - Highlights: • The deformation behaviour of staggered nanocomposites is studied. • Stair-wise staggered model has high stiffness and strength, but low toughness. • Rapid crack growth in overlap region causes this low toughness. • Toughness could be enhanced by arresting interfacial crack in the overlap.

  20. Investigating Viruses during the Transformation of Molecular Biology.

    Science.gov (United States)

    Moss, Bernard

    2017-03-10

    This Reflections article describes my early work on viral enzymes and the discovery of mRNA capping, how my training in medicine and biochemistry merged as I evolved into a virologist, the development of viruses as vaccine vectors, and how scientific and technological developments during the 1970s and beyond set the stage for the interrogation of nearly every step in the reproductive cycle of vaccinia virus (VACV), a large DNA virus with about 200 genes. The reader may view this article as a work in progress, because I remain actively engaged in research at the National Institutes of Health (NIH) notwithstanding 50 memorable years there. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  1. Entomologic and molecular investigation into Plasmodium vivax transmission in Singapore, 2009.

    Science.gov (United States)

    Ng, Lee-Ching; Lee, Kim-Sung; Tan, Cheong-Huat; Ooi, Peng-Lim; Lam-Phua, Sai-Gek; Lin, Raymond; Pang, Sook-Cheng; Lai, Yee-Ling; Solhan, Suhana; Chan, Pei-Pei; Wong, Kit-Yin; Ho, Swee-Tuan; Vythilingam, Indra

    2010-10-29

    Singapore has been certified malaria free since November 1982 by the World Health Organization and despite occasional local transmission, the country has maintained the standing. In 2009, three clusters of malaria cases were reported in Singapore. Epidemiological, entomological and molecular studies were carried out to investigate the three clusters, namely Mandai-Sungei Kadut, Jurong Island and Sembawang. A total of 29 malaria patients, with no recent travel history, were reported in the three clusters. Molecular analysis based on the msp3α and msp1 genes showed two independent local transmissions: one in Mandai-Sungei Kadut and another in Sembawang. Almost all cases within each cluster were epidemiologically linked. In Jurong Island cluster, epidemiological link remains uncertain, as almost all cases had a unique genetic profile. Only two cases shared a common profile and were found to be linked to the Mandai-Sungei Kadut cluster. Entomological investigation found Anopheles sinensis to be the predominant Anopheline in the two areas where local transmission of P. vivax was confirmed. Anopheles sinensis was found to be attracted to human bait and bites as early as 19:45 hrs. However, all Anopheles mosquitoes caught were negative for sporozoites and oocysts by dissection. Investigation of P. vivax cases from the three cluster areas confirmed the occurrence of local transmission in two areas. Although An. sinensis was the predominant Anopheline found in areas with confirmed transmission, the vector/s responsible for the outbreaks still remains cryptic.

  2. Entomologic and molecular investigation into Plasmodium vivax transmission in Singapore, 2009

    Directory of Open Access Journals (Sweden)

    Solhan Suhana

    2010-10-01

    Full Text Available Abstract Background Singapore has been certified malaria free since November 1982 by the World Health Organization and despite occasional local transmission, the country has maintained the standing. In 2009, three clusters of malaria cases were reported in Singapore. Methods Epidemiological, entomological and molecular studies were carried out to investigate the three clusters, namely Mandai-Sungei Kadut, Jurong Island and Sembawang. Results A total of 29 malaria patients, with no recent travel history, were reported in the three clusters. Molecular analysis based on the msp3α and msp1 genes showed two independent local transmissions: one in Mandai-Sungei Kadut and another in Sembawang. Almost all cases within each cluster were epidemiologically linked. In Jurong Island cluster, epidemiological link remains uncertain, as almost all cases had a unique genetic profile. Only two cases shared a common profile and were found to be linked to the Mandai-Sungei Kadut cluster. Entomological investigation found Anopheles sinensis to be the predominant Anopheline in the two areas where local transmission of P. vivax was confirmed. Anopheles sinensis was found to be attracted to human bait and bites as early as 19:45 hrs. However, all Anopheles mosquitoes caught were negative for sporozoites and oocysts by dissection. Conclusion Investigation of P. vivax cases from the three cluster areas confirmed the occurrence of local transmission in two areas. Although An. sinensis was the predominant Anopheline found in areas with confirmed transmission, the vector/s responsible for the outbreaks still remains cryptic.

  3. Alternative Radioligands for Investigating the Molecular Pharmacology of Melatonin Receptors.

    Science.gov (United States)

    Legros, Céline; Brasseur, Chantal; Delagrange, Philippe; Ducrot, Pierre; Nosjean, Olivier; Boutin, Jean A

    2016-03-01

    Melatonin exerts a variety of physiologic activities that are mainly relayed through the melatonin receptors MT1 and MT2 Low expressions of these receptors in tissues have led to widespread experimental use of the agonist 2-[(125)I]-iodomelatonin as a substitute for melatonin. We describe three iodinated ligands: 2-(2-[(2-iodo-4,5-dimethoxyphenyl)methyl]-4,5-dimethoxy phenyl) (DIV880) and (2-iodo-N-2-[5-methoxy-2-(naphthalen-1-yl)-1H-pyrrolo[3,2-b]pyridine-3-yl])acetamide (S70254), which are specific ligands at MT2 receptors, and N-[2-(5-methoxy-1H-indol-3-yl)ethyl]iodoacetamide (SD6), an analog of 2-[(125)I]-iodomelatonin with slightly different characteristics. Here, we further characterized these new ligands with regards to their molecular pharmacology. We performed binding experiments, saturation assays, association/dissociation rate measurements, and autoradiography using sheep and rat tissues and recombinant cell lines. Our results showed that [(125)I]-S70254 is receptor, and can be used with both cells and tissue. This radioligand can be used in autoradiography. Similarly, DIV880, a partial agonist [43% of melatonin on guanosine 5'-3-O-(thio)triphosphate binding assay], selective for MT2, can be used as a tool to selectively describe the pharmacology of this receptor in tissue samples. The molecular pharmacology of both human melatonin receptors MT1 and MT2, using a series of 24 ligands at these receptors and the new radioligands, did not lead to noticeable variations in the profiles. For the first time, we described radiolabeled tools that are specific for one of the melatonin receptors (MT2). These tools are amenable to binding experiments and to autoradiography using sheep or rat tissues. These specific tools will permit better understanding of the role and implication in physiopathologic processes of the melatonin receptors. Copyright © 2016 by The American Society for Pharmacology and Experimental Therapeutics.

  4. Molecular Analysis Research at Community College of Philadelphia

    Science.gov (United States)

    2015-09-21

    YOUR FORM TO THE ABOVE ADDRESS. Community College of Philadelphia Community College of Philadelphia 1700 Spring Garden Street Philadelphia, PA 19130...Approved for Public Release; Distribution Unlimited Final Report: Molecular Analysis Research at Community College of Philadelphia The views, opinions...Molecular Analysis Research at Community College of Philadelphia Report Title AXIMA Assurance mass spectrometer, Leica DMI-8 fluorescent microscope

  5. Molecular Investigation of the Stem Snap Point in Textile Hemp

    Directory of Open Access Journals (Sweden)

    Marc Behr

    2017-12-01

    Full Text Available Fibre crops are important natural resources, as they sustainably provide bast fibres, an economically-valuable raw material used in the textile and biocomposite sectors. Among fibre crops, textile hemp (Cannabis sativa L. is appreciated for its long and strong gelatinous bast fibres. The stem of fibre crops is a useful system for cell wall-oriented studies, because it shows a strong tissue polarity with a lignified inner core and a cellulosic hypolignified cortex, as well as a basipetal lignification gradient. Along the stem axis of fibre crops, a specific region, denoted snap point, marks the transition from elongation (above it to fibre thickening (below it. After empirically determining the snap point by tilting the plant, we divided the stem segment containing it into three non-overlapping consecutive regions measuring 1 cm each, and carried out targeted RT-qPCR on cell wall-related genes separately, in outer and inner tissues. Different gene clusters can be observed, two of which are the major gene groups, i.e., one group with members expressed at higher levels in the inner tissues, and one group whose genes are more expressed in the cortex. The present results provide a molecular validation that the snap point is characterised by a gradient of events associated with the shift from fibre elongation to thickening.

  6. Molecular Dynamics Investigation of Efficient SO2 Absorption by ...

    Indian Academy of Sciences (India)

    ANIRBAN MONDAL

    J. Chem. Sci. Vol. 129, No. 7, July 2017, pp. 859–872. c Indian Academy of Sciences. ... Ionic liquids are appropriate candidates for the absorption of acid gases such as SO2. Six anion- ... nificant number of task-specific ILs were designed and used to ...... investigation of a pilot-scale jet bubbling reactor for wet flue gas ...

  7. Investigation of the molecular relationship between breast cancer and obesity by candidate gene prioritization methods

    Directory of Open Access Journals (Sweden)

    Saba Garshasbi

    2015-10-01

    Full Text Available Background: Cancer and obesity are two major public health concerns. More than 12 million cases of cancer are reported annually. Many reports confirmed obesity as a risk factor for cancer. The molecular relationship between obesity and breast cancer has not been clear yet. The purpose of this study was to investigate priorities of effective genes in the molecular relationship between obesity and breast cancer. Methods: In this study, computer simulation method was used for prioritizing the genes that involved in the molecular links between obesity and breast cancer in laboratory of systems biology and bioinformatics (LBB, Tehran University, Tehran, Iran, from March to July 2014. In this study, ENDEAVOUR software was used for prioritizing the genes and integrating multiple data sources was used for data analysis. Training genes were selected from effective genes in obesity and/or breast cancer. Two groups of candidate genes were selected. The first group was included the existential genes in 5 common region chromosomes (between obesity and breast cancer and the second group was included the results of genes microarray data analysis of research Creighton, et al (In 2012 on patients with breast cancer. The microarray data were analyzed with GER2 software (R online software on GEO website. Finally, both training and candidate genes were entered in ENDEAVOUR software package. Results: The candidate genes were prioritized to four style and five genes in ten of the first priorities were repeated twice. In other word, the outcome of prioritizing of 72 genes (Product of microarray data analysis and genes of 5 common chromosome regions (Between obesity and breast cancer showed, 5 genes (TNFRSF10B, F2, IGFALS, NTRK3 and HSP90B1 were the priorities in the molecular connection between obesity and breast cancer. Conclusion: There are some common genes between breast cancer and obesity. So, molecular relationship is confirmed. In this study the possible effect

  8. Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas

    NARCIS (Netherlands)

    Liu, Yang; Sethi, Nilay S; Hinoue, Toshinori; Schneider, Barbara G; Cherniack, Andrew D; Sanchez-Vega, Francisco; Seoane, Jose A; Farshidfar, Farshad; Bowlby, Reanne; Islam, Mirazul; Kim, Jaegil; Chatila, Walid; Akbani, Rehan; Kanchi, Rupa S; Rabkin, Charles S; Willis, Joseph E; Wang, Kenneth K; McCall, Shannon J; Mishra, Lopa; Ojesina, Akinyemi I; Bullman, Susan; Pedamallu, Chandra Sekhar; Lazar, Alexander J; Sakai, Ryo; Thorsson, Vésteinn; Bass, Adam J; Laird, Peter W; de Krijger, RR

    2018-01-01

    We analyzed 921 adenocarcinomas of the esophagus, stomach, colon, and rectum to examine shared and distinguishing molecular characteristics of gastrointestinal tract adenocarcinomas (GIACs). Hypermutated tumors were distinct regardless of cancer type and comprised those enriched for

  9. Molecular Composition Analysis of Distant Targets

    Data.gov (United States)

    National Aeronautics and Space Administration — We propose a system capable of probing the molecular composition of cold solar system targets such as asteroids, comets, planets and moons from a distant vantage....

  10. Molecular Investigation of Tularemia Outbreaks, Spain, 1997–2008

    Science.gov (United States)

    Ariza-Miguel, Jaime; Johansson, Anders; Fernández-Natal, María Isabel; Martínez-Nistal, Carmen; Orduña, Antonio; Rodríguez-Ferri, Elías F.; Hernández, Marta

    2014-01-01

    Tularemia outbreaks occurred in northwestern Spain in 1997–1998 and 2007–2008 and affected >1,000 persons. We assessed isolates involved in these outbreaks by using pulsed-field gel electrophoresis with 2 restriction enzymes and multilocus variable number tandem repeat analysis of 16 genomic loci of Francisella tularensis, the cause of this disease. Isolates were divided into 3 pulsotypes by pulsed-field gel electrophoresis and 8 allelic profiles by multilocus variable number tandem repeat analysis. Isolates obtained from the second tularemia outbreak had the same genotypes as isolates obtained from the first outbreak. Both outbreaks were caused by genotypes of genetic subclade B.Br:FTNF002–00, which is widely distributed in countries in central and western Europe. Thus, reemergence of tularemia in Spain was not caused by the reintroduction of exotic strains, but probably by persistence of local reservoirs of infection. PMID:24750848

  11. Molecular analysis of pancreatic cyst fluid changes clinical management.

    Science.gov (United States)

    Arner, David M; Corning, Brooke E; Ahmed, Ali M; Ho, Henry C; Weinbaum, Bradley J; Siddiqui, Uzma; Aslanian, Harry; Adams, Reid B; Bauer, Todd W; Wang, Andrew Y; Shami, Vanessa M; Sauer, Bryan G

    2018-01-01

    DNA molecular analysis has been suggested as a tool to evaluate pancreatic cysts. This study assesses whether the addition of DNA molecular analysis alters clinical management. This is a retrospective review of 46 consecutive patients who underwent EUS-FNA of pancreatic cysts with DNA molecular analysis at two major academic institutions. Cases were presented to two pancreaticobiliary surgeons first without and then with DNA molecular analysis data. The primary outcome was the frequency with which clinical management was altered with the addition of DNA molecular analysis. Forty-six patients with a mean age of 62.0 (±13.4) years and mean cyst size of 3.2 (±2.3) cm were included in the study. Cyst carcinoembryonic antigen (CEA) was available in 30 patients and ranged from 0.4 to 15,927 ng/mL. DNA molecular analysis was described as benign in 23 (50%), statistically indolent in 13 (28%), statistically higher risk in 9 (20%), and indeterminate in 1 (2%). Surgeon #1 changed the management in 13/46 cases (28%) and surgeon #2 changed the management in 12/46 cases (26%) with the addition of DNA molecular analysis. When organized by CEA concentration, those with an intermediate CEA (45-800 ng/mL) or without a CEA concentration had a management changed more frequently (40%) compared to all others (P molecular analysis alters the clinical management of pancreatic cystic lesions most often when CEA levels are intermediate (45-800 ng/mL) or when no CEA concentration is available. Use of DNA molecular analysis can be considered in this cohort. Further study of molecular markers in pancreatic cystic lesions is recommended.

  12. Delineation of Chondroid Lipoma: An Immunohistochemical and Molecular Biological Analysis

    Science.gov (United States)

    de Vreeze, Ronald S. A.; van Coevorden, Frits; Boerrigter, Lucie; Nederlof, Petra M.; Haas, Rick L.; Bras, Johannes; Rosenwald, Andreas; Mentzel, Thomas; de Jong, Daphne

    2011-01-01

    Aims. Chondroid lipoma (CL) is a benign tumor that mimics a variety of soft tissue tumors and is characterized by translocation t(11;16). Here, we analyze CL and its histological mimics. Methods. CL (n = 4) was compared to a variety of histological mimics (n = 83) for morphological aspects and immunohistochemical features including cyclinD1(CCND1). Using FISH analysis, CCND1 and FUS were investigated as potential translocation partners. Results. All CLs were strongly positive for CCND1. One of 4 myoepitheliomas, CCND1, was positive. In well-differentiated lipomatous tumors and in chondrosarcomas, CCND1 was frequently expressed, but all myxoid liposarcomas were negative. FISH analysis did not give support for direct involvement of CCND1 and FUS as translocation partners. Conclusions. Chondroid lipoma is extremely rare and has several and more prevalent histological mimics. The differential diagnosis of chondroid lipomas can be unraveled using immunohistochemical and molecular support. PMID:21559269

  13. Cloning Yeast Actin cDNA Leads to an Investigative Approach for the Molecular Biology Laboratory

    Science.gov (United States)

    Black, Michael W.; Tuan, Alice; Jonasson, Erin

    2008-01-01

    The emergence of molecular tools in multiple disciplines has elevated the importance of undergraduate laboratory courses that train students in molecular biology techniques. Although it would also be desirable to provide students with opportunities to apply these techniques in an investigative manner, this is generally not possible in the…

  14. Pathogenic Leptospira spp. in bats: Molecular investigation in Southern Brazil.

    Science.gov (United States)

    Mayer, Fabiana Quoos; Dos Reis, Emily Marques; Bezerra, André Vinícius Andrade; Cerva, Cristine; Rosa, Júlio; Cibulski, Samuel Paulo; Lima, Francisco Esmaile Sales; Pacheco, Susi Missel; Rodrigues, Rogério Oliveira

    2017-06-01

    The present study aimed to investigate the frequency of pathogenic Leptospira spp. in Brazilian bats and to determine possible risk factors associated to it. Ninety two bats of 12 species were evaluated. Whole genomic DNA from kidneys was extracted and real-time PCR specific to pathogenic Leptospira spp. was applied. Association between the frequency of specimens positive for Leptospira spp. and sex, age, bat species or family, season of collection, geographic localization and feeding habits was evaluated. The results showed that 39.13% of analyzed bats were found positive for Leptospira spp. Nine bat species had at least one positive result. There was no association among the evaluated variables and frequency of pathogenic Leptospira spp. Although the limitations due to lack of Leptospira spp. isolation, leptospiral carriage was demonstrated in bats of different species from southern Brazil, which reinforces the need for surveillance of infectious agents in wild animals. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Spectroscopic and TDDFT investigation on highly selective fluorogenic chemosensor and construction of molecular logic gates

    Energy Technology Data Exchange (ETDEWEB)

    Basheer, Sabeel M [Department of Chemistry, National Institute of Technology, Tiruchirappalli 620 015 (India); Kumar, Saravana Loganathan Ashok [Department of Chemistry, GRT Institute of Engineering Technology, Tiruttani (India); Kumar, Moorthy Saravana [Research and PG Department of Chemistry, Saraswathi Narayanan College, Madurai 625022 (India); Sreekanth, Anandaram, E-mail: sreekanth@nitt.edu [Department of Chemistry, National Institute of Technology, Tiruchirappalli 620 015 (India)

    2017-03-01

    1,5-Bis(2-fluorene)thiocarbohydrazone (FBTC) was designed and synthesized for selective sensing of fluoride and copper ions. The binding constants of FBTC towards fluoride and copper ions have been calculated using the Benesi-Hildebrand equation, and FBTC has more binding affinity towards copper ion than fluoride ion. The {sup 1}H NMR and {sup 13}C NMR titration studies strongly support the deprotonation was taken from the N–H protons followed by the formation of hydrogen bond via N–H{sup …}F. To understand the fluoride ion sensing mechanism, theoretical investigation had been carried out using the density functional theory and time-dependent density functional theory. The theoretical data well reproduced the experimental results. The deprotonation process has a moderate transition barrier (481.55 kcal/mol). The calculated ΔE and ΔG values (− 253.92 and − 192.41 kcal/mol respectively) suggest the feasibility of sensing process. The potential energy curves give the optimized structures of FBTC-F complex in the ground state and excited state, which states the proton transition occurs at the excited state. The excited state proton transition mechanism was further confirmed with natural bond orbital analysis. The reversibility of the sensor was monitored by the alternate addition of F{sup −} and Cu{sup 2+} ions, which was explained with “Read-Erase-Write-Read” behaviour. The multi-ion detection of sensor used to construct the molecular logic gate, such as AND, OR, NOR and INHIBITION logic gates. - Highlight: • Synthesis and characterised the thiosemicarbohydrazone derivative • Experimental evolution of selective fluoride and copper sensing via both colorimetric and spectroscopic studies • The proposed sensing mechanism of fluoride and copper ion were further confirmed with DFT and TD-DFT investigation • Receptor was turned as molecular switches and molecular logic gates.

  16. Implementation of force distribution analysis for molecular dynamics simulations

    Directory of Open Access Journals (Sweden)

    Seifert Christian

    2011-04-01

    Full Text Available Abstract Background The way mechanical stress is distributed inside and propagated by proteins and other biopolymers largely defines their function. Yet, determining the network of interactions propagating internal strain remains a challenge for both, experiment and theory. Based on molecular dynamics simulations, we developed force distribution analysis (FDA, a method that allows visualizing strain propagation in macromolecules. Results To be immediately applicable to a wide range of systems, FDA was implemented as an extension to Gromacs, a commonly used package for molecular simulations. The FDA code comes with an easy-to-use command line interface and can directly be applied to every system built using Gromacs. We provide an additional R-package providing functions for advanced statistical analysis and presentation of the FDA data. Conclusions Using FDA, we were able to explain the origin of mechanical robustness in immunoglobulin domains and silk fibers. By elucidating propagation of internal strain upon ligand binding, we previously also successfully revealed the functionality of a stiff allosteric protein. FDA thus has the potential to be a valuable tool in the investigation and rational design of mechanical properties in proteins and nano-materials.

  17. Molecular marker analysis of 'Shatangju' and 'Wuzishatangju ...

    African Journals Online (AJOL)

    'Wuzishatangju'(Citrus reticulata Blanco) is an excellent cultivar derived from a bud sport of a seedy 'Shatangju' cultivar found in Guangdong Province in the 1980s. In this study, six molecular markers including random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR), simple sequence repeat (SSR) ...

  18. A genetic analysis of segregation distortion revealed by molecular ...

    Indian Academy of Sciences (India)

    Journal of Genetics, Vol. 90, No. ... Segregation analysis was based on 64 molecular markers, including 26 .... FHB of RIL populations was controlled by quantitative trait ... The authors acknowledge financial support by the National Basic.

  19. Phenotypic and molecular genetic analysis of Pyruvate Kinase ...

    African Journals Online (AJOL)

    Phenotypic and molecular genetic analysis of Pyruvate Kinase deficiency in a Tunisian family. Jaouani Mouna, Hamdi Nadia, Chaouch Leila, Kalai Miniar, Mellouli Fethi, Darragi Imen, Boudriga Imen, Chaouachi Dorra, Bejaoui Mohamed, Abbes Salem ...

  20. MOLECULAR ANALYSIS OF HUMAN SPERMATOZOA: POTENTIAL FOR INFERTILITY RESEARCH

    Science.gov (United States)

    Gordon Research Conference: Mammalian Gametogenesis and Embryogenesis New London, CT, July 1-6, 2000Molecular Analysis of Human Spermatozoa: Potential for Infertility ResearchDavid Miller 1, David Dix2, Robert Reid 3, Stephen A Krawetz 3 1Reproductive ...

  1. Molecular investigation of tick-borne pathogens in dogs from Luanda, Angola.

    Science.gov (United States)

    Cardoso, Luís; Oliveira, Ana Cristina; Granada, Sara; Nachum-Biala, Yaarit; Gilad, Matan; Lopes, Ana Patrícia; Sousa, Sérgio Ramalho; Vilhena, Hugo; Baneth, Gad

    2016-05-10

    No molecular data have been available on tick-borne pathogens that infect dogs from Angola. The occurrence of agents from the genera Anaplasma, Babesia, Ehrlichia and Hepatozoon was assessed in 103 domestic dogs from Luanda, by means of the polymerase chain reaction (PCR) and DNA sequence analysis. Forty-six dogs (44.7 %) were positive for at least one pathogen. Twenty-one animals (20.4 %) were found infected with Anaplasma platys, 18 (17.5 %) with Hepatozoon canis, six (5.8 %) with Ehrlichia canis, six (5.8 %) with Babesia vogeli, one (1.0 %) with Babesia gibsoni and one (1.0 %) with an unnamed Babesia sp. The molecular frequency of single infections taken together was 37.9 % and that of co-infections with several combinations of two pathogens accounted for 6.8 % of the animals. This is the first report of A. platys, B. vogeli, B. gibsoni, E. canis and H. canis infections diagnosed by PCR in domestic dogs from Angola. The present study provides evidence that dogs in Luanda are widely exposed to, and at risk of becoming infected with, tick-borne pathogens. Further investigation is needed, including a larger number of animals, canine populations from other cities and provinces of the country, as well as potential vector ticks, aiming at better characterizing and controlling canine vector-borne diseases in Angola.

  2. Conformational changes in acetylcholine binding protein investigated by temperature accelerated molecular dynamics.

    Directory of Open Access Journals (Sweden)

    Zeynab Mohammad Hosseini Naveh

    Full Text Available Despite the large number of studies available on nicotinic acetylcholine receptors, a complete account of the mechanistic aspects of their gating transition in response to ligand binding still remains elusive. As a first step toward dissecting the transition mechanism by accelerated sampling techniques, we study the ligand-induced conformational changes of the acetylcholine binding protein (AChBP, a widely accepted model for the full receptor extracellular domain. Using unbiased Molecular Dynamics (MD and Temperature Accelerated Molecular Dynamics (TAMD simulations we investigate the AChBP transition between the apo and the agonist-bound state. In long standard MD simulations, both conformations of the native protein are stable, while the agonist-bound structure evolves toward the apo one if the orientation of few key sidechains in the orthosteric cavity is modified. Conversely, TAMD simulations initiated from the native conformations are able to produce the spontaneous transition. With respect to the modified conformations, TAMD accelerates the transition by at least a factor 10. The analysis of some specific residue-residue interactions points out that the transition mechanism is based on the disruption/formation of few key hydrogen bonds. Finally, while early events of ligand dissociation are observed already in standard MD, TAMD accelerates the ligand detachment and, at the highest TAMD effective temperature, it is able to produce a complete dissociation path in one AChBP subunit.

  3. Formalizing the definition of meta-analysis in Molecular Ecology.

    Science.gov (United States)

    ArchMiller, Althea A; Bauer, Eric F; Koch, Rebecca E; Wijayawardena, Bhagya K; Anil, Ammu; Kottwitz, Jack J; Munsterman, Amelia S; Wilson, Alan E

    2015-08-01

    Meta-analysis, the statistical synthesis of pertinent literature to develop evidence-based conclusions, is relatively new to the field of molecular ecology, with the first meta-analysis published in the journal Molecular Ecology in 2003 (Slate & Phua 2003). The goal of this article is to formalize the definition of meta-analysis for the authors, editors, reviewers and readers of Molecular Ecology by completing a review of the meta-analyses previously published in this journal. We also provide a brief overview of the many components required for meta-analysis with a more specific discussion of the issues related to the field of molecular ecology, including the use and statistical considerations of Wright's FST and its related analogues as effect sizes in meta-analysis. We performed a literature review to identify articles published as 'meta-analyses' in Molecular Ecology, which were then evaluated by at least two reviewers. We specifically targeted Molecular Ecology publications because as a flagship journal in this field, meta-analyses published in Molecular Ecology have the potential to set the standard for meta-analyses in other journals. We found that while many of these reviewed articles were strong meta-analyses, others failed to follow standard meta-analytical techniques. One of these unsatisfactory meta-analyses was in fact a secondary analysis. Other studies attempted meta-analyses but lacked the fundamental statistics that are considered necessary for an effective and powerful meta-analysis. By drawing attention to the inconsistency of studies labelled as meta-analyses, we emphasize the importance of understanding the components of traditional meta-analyses to fully embrace the strengths of quantitative data synthesis in the field of molecular ecology. © 2015 John Wiley & Sons Ltd.

  4. Molecular analysis of Ku redox regulation

    Directory of Open Access Journals (Sweden)

    Shatilla Andrea

    2009-08-01

    Full Text Available Abstract Background DNA double-strand breaks (DSBs can occur in response to ionizing radiation (IR, radiomimetic agents and from endogenous DNA-damaging reactive oxygen metabolites. Unrepaired or improperly repaired DSBs are potentially the most lethal form of DNA damage and can result in chromosomal translocations and contribute to the development of cancer. The principal mechanism for the repair of DSBs in humans is non-homologous end-joining (NHEJ. Ku is a key member of the NHEJ pathway and plays an important role in the recognition step when it binds to free DNA termini. Ku then stimulates the assembly and activation of other NHEJ components. DNA binding of Ku is regulated by redox conditions and evidence from our laboratory has demonstrated that Ku undergoes structural changes when oxidized that results in a reduction in DNA binding activity. The C-terminal domain and cysteine 493 of Ku80 were investigated for their contribution to redox regulation of Ku. Results We effectively removed the C-terminal domain of Ku80 generating a truncation mutant and co-expressed this variant with wild type Ku70 in an insect cell system to create a Ku70/80ΔC heterodimer. We also generated two single amino acid variants of Cys493, replacing this amino acid with either an alanine (C493A or a serine (C493S, and over-expressed the variant proteins in SF9 insect cells in complex with wild type Ku70. Neither the truncation nor the amino acid substitutions alters protein expression or stability as determined by SDS-PAGE and Western blot analysis. We show that the C493 mutations do not alter the ability of Ku to bind duplex DNA in vitro under reduced conditions while truncation of the Ku80 C-terminus slightly reduced DNA binding affinity. Diamide oxidation of cysteines was shown to inhibit DNA binding similarly for both the wild-type and all variant proteins. Interestingly, differential DNA binding activity following re-reduction was observed for the Ku70/80

  5. Dynamical analysis of highly excited molecular spectra

    Energy Technology Data Exchange (ETDEWEB)

    Kellman, M.E. [Univ. of Oregon, Eugene (United States)

    1993-12-01

    The goal of this program is new methods for analysis of spectra and dynamics of highly excited vibrational states of molecules. In these systems, strong mode coupling and anharmonicity give rise to complicated classical dynamics, and make the simple normal modes analysis unsatisfactory. New methods of spectral analysis, pattern recognition, and assignment are sought using techniques of nonlinear dynamics including bifurcation theory, phase space classification, and quantization of phase space structures. The emphasis is chaotic systems and systems with many degrees of freedom.

  6. Quantum chemical investigations on the molecular structure, FTIR, UV-Vis and HOMO-LUMO analysis of 15-16-epoxy-7b, 9a dihydroxylabdane 13(16), 14-dien-6-one

    Science.gov (United States)

    Uppal, Anshul; Pathania, Kamni; Khajuria, Yugal

    2018-05-01

    The structural, spectroscopic (Fourier Transform Infrared (FT-IR), Ultra-Violet Visible (UV-VIS)) and thermodynamic properties of 15, 16-epoxy-7b, 9a dihydroxylabdane-13(16), 14-dien-6-one were studied by using both experimental techniques and theoretical methods. The FTIR spectrum of the title compound was recorded in the spectral range 4000-400 cm-1. The UV-VIS spectrum was measured in the spectral range 190-800 nm. The quantum chemistry calculations have been performed to compute optimized geometry, molecular parameters, vibrational frequencies along with intensities using Hartree Fock (HF) theory and Density Functional Theory (DFT) with 6-31G basis set. The calculated HOMO-LUMO energies show that the charge transfer occurs within the molecule. The temperature dependence of the thermodynamic properties like heat capacity, entropy and enthalpy of the optimized structure were obtained. Finally, a comparison between the experimental data and the calculated results presented a good agreement.

  7. Molecular dynamics investigation of nanoscale substrate topography and its interaction with liquids

    Science.gov (United States)

    Cordeiro Rodrigues, Jhonatam

    Nanotechnology has been presenting successful applications in several areas. However, experimentation with nanoscale materials is costly and limited in analysis capability. This research investigates the use of molecular dynamics (MD) simulations to model and study nanomaterials and manufacturing processes. MD simulations are employed to reduce cost, optimize design, increase productivity and allow for the investigation of material interactions not yet observable through experimentation. This work investigates the interaction of water with substrates at the nanoscale. The effect of temperature, droplet impingement velocities and size, as well as substrate material, are investigated at the nanoscale. Several substrate topography designs were modeled to reveal their influence on the wettability of the substrate. Nanoscale gold and silicon substrates are more hydrophilic at higher temperatures than at room temperature. The reduction in droplet diameter increases its wettability. High impingement velocity of droplets does not influence final wettability of substrates but induces higher diffusion rates of droplets in a heated environment. Droplets deposited over a gradient of surface exposure presents spontaneous movement. The Leidenfrost effect was investigated at the nanoscale. Droplets of 4 and 10nm in diameter presented behaviors pertinent to the Leidenfrost effect at 373K, significantly lower than at micro scale and of potential impact to the field. Topographical features were manipulated using superhydrophobic coating resulting in micro whiskers. Nanoimprint lithography (NIL) was used to manufacture substrate topographies at the nanoscale. Water droplets were deposited on the substrates and their wettability was measured using droplet contact angles. Lower surface area exposure resulted in higher contact angles. The experimental relationships between surface topography and substrate wettability were used to validate the insights gained from MD simulations for

  8. Coffee husk composting: an investigation of the process using molecular and non-molecular tools.

    Science.gov (United States)

    Shemekite, Fekadu; Gómez-Brandón, María; Franke-Whittle, Ingrid H; Praehauser, Barbara; Insam, Heribert; Assefa, Fassil

    2014-03-01

    Various parameters were measured during a 90-day composting process of coffee husk with cow dung (Pile 1), with fruit/vegetable wastes (Pile 2) and coffee husk alone (Pile 3). Samples were collected on days 0, 32 and 90 for chemical and microbiological analyses. C/N ratios of Piles 1 and 2 decreased significantly over the 90 days. The highest bacterial counts at the start of the process and highest actinobacterial counts at the end of the process (Piles 1 and 2) indicated microbial succession with concomitant production of compost relevant enzymes. Denaturing gradient gel electrophoresis of rDNA and COMPOCHIP microarray analysis indicated distinctive community shifts during the composting process, with day 0 samples clustering separately from the 32 and 90-day samples. This study, using a multi-parameter approach, has revealed differences in quality and species diversity of the three composts. Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.

  9. Coffee husk composting: An investigation of the process using molecular and non-molecular tools

    Science.gov (United States)

    Shemekite, Fekadu; Gómez-Brandón, María; Franke-Whittle, Ingrid H.; Praehauser, Barbara; Insam, Heribert; Assefa, Fassil

    2014-01-01

    Various parameters were measured during a 90-day composting process of coffee husk with cow dung (Pile 1), with fruit/vegetable wastes (Pile 2) and coffee husk alone (Pile 3). Samples were collected on days 0, 32 and 90 for chemical and microbiological analyses. C/N ratios of Piles 1 and 2 decreased significantly over the 90 days. The highest bacterial counts at the start of the process and highest actinobacterial counts at the end of the process (Piles 1 and 2) indicated microbial succession with concomitant production of compost relevant enzymes. Denaturing gradient gel electrophoresis of rDNA and COMPOCHIP microarray analysis indicated distinctive community shifts during the composting process, with day 0 samples clustering separately from the 32 and 90-day samples. This study, using a multi-parameter approach, has revealed differences in quality and species diversity of the three composts. PMID:24369846

  10. Investigation into the use of molecular hydrogen on the growth of gallium nitride via metal-organic molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Billingsley, Daniel; Pritchett, David; Henderson, Walter; Carver, Alexander G.; Burnham, Shawn D.; Doolittle, W.A. [Georgia Institute of Technology, School of Electrical and Computer Engineering, 777 Atlantic Dr., Atlanta, GA 30332 (United States)

    2008-07-01

    Molecular hydrogen (H{sub 2}) has been investigated as a means to improve ammonia nitridation efficiency and attempts to reduce carbon contamination in ammonia-based metal-organic molecular beam epitaxy (MOMBE). A 30% improvement in crystalline quality, inferred from XRD, as well as an increase in subsequent GaN bulk growth rate was observed when bare sapphire was subject to H{sub 2} annealing before nitridation. However, the use of H{sub 2} during GaN homoepitaxy on GaN templates resulted in increased carbon contamination and decreased growth rate of GaN. The results demonstrate promise and proper uses of H{sub 2} during GaN growth under certain conditions. (copyright 2008 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  11. Molecular analysis of the oral microbiota of dental diseases

    OpenAIRE

    Kanasi, Eleni

    2008-01-01

    Traditionally, bacterial culture has been used for bacterial detection, allowing study of living microorganisms. Molecular methods are rapid and allow simultaneous identification of numerous species and uncultivated phylotypes. The objective of this doctoral thesis was to investigate the role of the oral microbiota, including poorly characterized and uncultivated bacteria, in dental caries and periodontitis, by comprehensive molecular, clinical, and statistical methods. The microbiota of 275 ...

  12. Investigation of naproxen drug using mass spectrometry, thermal analyses and semi-empirical molecular orbital calculation

    Directory of Open Access Journals (Sweden)

    M.A. Zayed

    2017-03-01

    Full Text Available Naproxen (C14H14O3 is a non-steroidal anti-inflammatory drug (NSAID. It is important to investigate its structure to know the active groups and weak bonds responsible for medical activity. In the present study, naproxen was investigated by mass spectrometry (MS, thermal analysis (TA measurements (TG/DTG and DTA and confirmed by semi empirical molecular orbital (MO calculation, using PM3 procedure. These calculations included, bond length, bond order, bond strain, partial charge distribution, ionization energy and heat of formation (ΔHf. The mass spectra and thermal analysis fragmentation pathways were proposed and compared to select the most suitable scheme representing the correct fragmentation pathway of the drug in both techniques. The PM3 procedure reveals that the primary cleavage site of the charged molecule is the rupture of the COOH group (lowest bond order and high strain which followed by CH3 loss of the methoxy group. Thermal analysis of the neutral drug reveals a high response to the temperature variation with very fast rate. It decomposed in several sequential steps in the temperature range 80–400 °C. These mass losses appear as two endothermic and one exothermic peaks which required energy values of 255.42, 10.67 and 371.49 J g−1 respectively. The initial thermal ruptures are similar to that obtained by mass spectral fragmentation (COOH rupture. It was followed by the loss of the methyl group and finally by ethylene loss. Therefore, comparison between MS and TA helps in selection of the proper pathway representing its fragmentation. This comparison is successfully confirmed by MO-calculation.

  13. Correlation analysis of the Taurus molecular cloud complex

    International Nuclear Information System (INIS)

    Kleiner, S.C.

    1985-01-01

    Autocorrelation and power spectrum methods were applied to the analysis of the density and velocity structure of the Taurus Complex and Heiles Cloud 2 as traced out by 13 CO J = 1 → 0 molecular line observations obtained with the 14m antenna of the Five College Radio Astronomy Observatory. Statistically significant correlations in the spacing of density fluctuations within the Taurus Complex and Heiles 2 were uncovered. The length scales of the observed correlations correspond in magnitude to the Jeans wavelengths characterizing gravitational instabilities with (i) interstellar atomic hydrogen gas for the case of the Taurus complex, and (ii) molecular hydrogen for Heiles 2. The observed correlations may be the signatures of past and current gravitational instabilities frozen into the structure of the molecular gas. The appendices provide a comprehensive description of the analytical and numerical methods developed for the correlation analysis of molecular clouds

  14. Molecular identification of python species: development and validation of a novel assay for forensic investigations.

    Science.gov (United States)

    Ciavaglia, Sherryn A; Tobe, Shanan S; Donnellan, Stephen C; Henry, Julianne M; Linacre, Adrian M T

    2015-05-01

    Python snake species are often encountered in illegal activities and the question of species identity can be pertinent to such criminal investigations. Morphological identification of species of pythons can be confounded by many issues and molecular examination by DNA analysis can provide an alternative and objective means of identification. Our paper reports on the development and validation of a PCR primer pair that amplifies a segment of the mitochondrial cytochrome b gene that has been suggested previously as a good candidate locus for differentiating python species. We used this DNA region to perform species identification of pythons, even when the template DNA was of poor quality, as might be the case with forensic evidentiary items. Validation tests are presented to demonstrate the characteristics of the assay. Tests involved the cross-species amplification of this marker in non-target species, minimum amount of DNA template required, effects of degradation on product amplification and a blind trial to simulate a casework scenario that provided 100% correct identity. Our results demonstrate that this assay performs reliably and robustly on pythons and can be applied directly to forensic investigations where the presence of a species of python is in question. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  15. Fragrance analysis using molecular and biochemical methods in ...

    African Journals Online (AJOL)

    admin

    Biochemical analysis of aroma was performed with the 1.7% KOH solution and molecular analysis of aroma was carried out with microsatellite markers present on chromosome 8 (BAD2, BADEX7-5, SCUSSR1) to determine the extent of association between trait, marker and chromosome 8. Among these markers, BAD2 ...

  16. Molecular responses and expression analysis of genes in a ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-06-17

    Jun 17, 2009 ... Molecular responses and expression analysis of genes in a xerophytic desert shrub Haloxylon ammodendron .... physiological determination and cDNA-AFLP analysis, three groups of seeds were sowed in pots with sand and .... HaDR27. U. 234. PDR-like ABC transporter. AT1G59870. HaDR28. U. 135.

  17. Interactive analysis of systems biology molecular expression data

    Directory of Open Access Journals (Sweden)

    Prabhakar Sunil

    2008-02-01

    Full Text Available Abstract Background Systems biology aims to understand biological systems on a comprehensive scale, such that the components that make up the whole are connected to one another and work through dependent interactions. Molecular correlations and comparative studies of molecular expression are crucial to establishing interdependent connections in systems biology. The existing software packages provide limited data mining capability. The user must first generate visualization data with a preferred data mining algorithm and then upload the resulting data into the visualization package for graphic visualization of molecular relations. Results Presented is a novel interactive visual data mining application, SysNet that provides an interactive environment for the analysis of high data volume molecular expression information of most any type from biological systems. It integrates interactive graphic visualization and statistical data mining into a single package. SysNet interactively presents intermolecular correlation information with circular and heatmap layouts. It is also applicable to comparative analysis of molecular expression data, such as time course data. Conclusion The SysNet program has been utilized to analyze elemental profile changes in response to an increasing concentration of iron (Fe in growth media (an ionomics dataset. This study case demonstrates that the SysNet software is an effective platform for interactive analysis of molecular expression information in systems biology.

  18. Molecular characterization and expression analysis of chalcone ...

    African Journals Online (AJOL)

    Chalcone synthase (CHS, EC: 2.3.1.74) is a key enzyme in the flavonoid and anthocyanin biosynthesis pathway. In order to investigate the role of CHS in tree peony flower coloration mechanism, we isolated and characterized the CHS gene from Paeonia suffruticosa cv. Yu Ji Yan Zhuang and analyzed its spatial and ...

  19. Molecular Characterization and Expression Analysis of Equine ( Gene in Horse (

    Directory of Open Access Journals (Sweden)

    Ki-Duk Song

    2014-05-01

    Full Text Available The objective of this study was to determine the molecular characteristics of the horse vascular endothelial growth factor alpha gene (VEGFα by constructing a phylogenetic tree, and to investigate gene expression profiles in tissues and blood leukocytes after exercise for development of suitable biomarkers. Using published amino acid sequences of other vertebrate species (human, chimpanzee, mouse, rat, cow, pig, chicken and dog, we constructed a phylogenetic tree which showed that equine VEGFα belonged to the same clade of the pig VEGFα. Analysis for synonymous (Ks and non-synonymous substitution ratios (Ka revealed that the horse VEGFα underwent positive selection. RNA was extracted from blood samples before and after exercise and different tissue samples of three horses. Expression analyses using reverse transcription-polymerase chain reaction (RT-PCR and quantitative-polymerase chain reaction (qPCR showed ubiquitous expression of VEGFα mRNA in skeletal muscle, kidney, thyroid, lung, appendix, colon, spinal cord, and heart tissues. Analysis of differential expression of VEGFα gene in blood leukocytes after exercise indicated a unimodal pattern. These results will be useful in developing biomarkers that can predict the recovery capacity of racing horses.

  20. Structural aspects of the solvation shell of lysine and acetylated lysine: A Car-Parrinello and classical molecular dynamics investigation

    International Nuclear Information System (INIS)

    Carnevale, V.; Raugei, S.

    2009-01-01

    Lysine acetylation is a post-translational modification, which modulates the affinity of protein-protein and/or protein-DNA complexes. Its crucial role as a switch in signaling pathways highlights the relevance of charged chemical groups in determining the interactions between water and biomolecules. A great effort has been recently devoted to assess the reliability of classical molecular dynamics simulations in describing the solvation properties of charged moieties. In the spirit of these investigations, we performed classical and Car-Parrinello molecular dynamics simulations on lysine and acetylated-lysine in aqueous solution. A comparative analysis between the two computational schemes is presented with a focus on the first solvation shell of the charged groups. An accurate structural analysis unveils subtle, yet statistically significant, differences which are discussed in connection to the significant electronic density charge transfer occurring between the solute and the surrounding water molecules.

  1. Molecular Eigensolution Symmetry Analysis and Fine Structure

    Directory of Open Access Journals (Sweden)

    William G. Harter

    2013-01-01

    Full Text Available Spectra of high-symmetry molecules contain fine and superfine level cluster structure related to J-tunneling between hills and valleys on rovibronic energy surfaces (RES. Such graphic visualizations help disentangle multi-level dynamics, selection rules, and state mixing effects including widespread violation of nuclear spin symmetry species. A review of RES analysis compares it to that of potential energy surfaces (PES used in Born-Oppenheimer approximations. Both take advantage of adiabatic coupling in order to visualize Hamiltonian eigensolutions. RES of symmetric and D2 asymmetric top rank-2-tensor Hamiltonians are compared with Oh spherical top rank-4-tensor fine-structure clusters of 6-fold and 8-fold tunneling multiplets. Then extreme 12-fold and 24-fold multiplets are analyzed by RES plots of higher rank tensor Hamiltonians. Such extreme clustering is rare in fundamental bands but prevalent in hot bands, and analysis of its superfine structure requires more efficient labeling and a more powerful group theory. This is introduced using elementary examples involving two groups of order-6 (C6 and D3~C3v, then applied to families of Oh clusters in SF6 spectra and to extreme clusters.

  2. Molecular thermal transistor: Dimension analysis and mechanism

    Science.gov (United States)

    Behnia, S.; Panahinia, R.

    2018-04-01

    Recently, large challenge has been spent to realize high efficient thermal transistors. Outstanding properties of DNA make it as an excellent nano material in future technologies. In this paper, we introduced a high efficient DNA based thermal transistor. The thermal transistor operates when the system shows an increase in the thermal flux despite of decreasing temperature gradient. This is what called as negative differential thermal resistance (NDTR). Based on multifractal analysis, we could distinguish regions with NDTR state from non-NDTR state. Moreover, Based on dimension spectrum of the system, it is detected that NDTR state is accompanied by ballistic transport regime. The generalized correlation sum (analogous to specific heat) shows that an irregular decrease in the specific heat induces an increase in the mean free path (mfp) of phonons. This leads to the occurrence of NDTR.

  3. Investigation of a metal-organic interface. Realization and understanding of a molecular switch

    Energy Technology Data Exchange (ETDEWEB)

    Neucheva, Olga [Forschungszentrum Juelich (DE). Institute of Bio- and Nanosystems (IBN), Functional Nanostructures at Surfaces (IBN-3)

    2010-07-01

    The field of molecular organic electronics is an emerging and very dynamic area. The continued trend to miniaturisation, combined with increasing complexity and cost of production in conventional semiconductor electronics, forces companies to turn their attention to alternatives that promise the next levels of scale at significantly lower cost. After consumer electronic devices based on organic transistors, such as TVs and book readers, have already been presented, molecular electronics is expected to offer the next breakthrough in feature size. Unfortunately, most of the organic/metal interfaces contain intrinsic defects that break the homogeneity of the interface properties. In this thesis, the electronic and structural properties of such defects were examined in order to understand the influence of the inhomogeneities on the quality of the interface layer. However, the main focus of this work was the investigation of the local properties of a single molecule. Taking advantage of the Scanning Tunnelling Microscope's (STM's) ability to act as a local probe, a single molecular switch was realized and studied. Moreover, in close collaboration with theory groups, the underlying mechanism driving the switching process was identified and described. Besides the investigation of the switching process, the ability of the STM to build nanostructures of different shapes from large organic molecules was shown. Knowing the parameters for realization and control of the switching process and for building the molecular corrals, the results of this investigation enable the reconstruction of the studied molecular ensemble and its deployment in electric molecular circuits, constituting a next step towards further miniaturization of electronic devices. (orig.)

  4. Molecular analysis of deep subsurface bacteria

    International Nuclear Information System (INIS)

    Jimenez Baez, L.E.

    1989-09-01

    Deep sediments samples from site C10a, in Appleton, and sites, P24, P28, and P29, at the Savannah River Site (SRS), near Aiken, South Carolina were studied to determine their microbial community composition, DNA homology and mol %G+C. Different geological formations with great variability in hydrogeological parameters were found across the depth profile. Phenotypic identification of deep subsurface bacteria underestimated the bacterial diversity at the three SRS sites, since bacteria with the same phenotype have different DNA composition and less than 70% DNA homology. Total DNA hybridization and mol %G+C analysis of deep sediment bacterial isolates suggested that each formation is comprised of different microbial communities. Depositional environment was more important than site and geological formation on the DNA relatedness between deep subsurface bacteria, since more 70% of bacteria with 20% or more of DNA homology came from the same depositional environments. Based on phenotypic and genotypic tests Pseudomonas spp. and Acinetobacter spp.-like bacteria were identified in 85 million years old sediments. This suggests that these microbial communities might have been adapted during a long period of time to the environmental conditions of the deep subsurface

  5. Molecular cloning, structural analysis and expression of a zinc ...

    African Journals Online (AJOL)

    The results of prokaryotic expression of ZnBP and overexpression of the ZnBP gene in A. thaliana improve our understanding of the function of this gene. Future studies should investigate the molecular mechanisms involved in gland morphogenesis in cotton. Key words: Gossypium hirsutum, pigment gland, zinc binding ...

  6. RAPD-PCR molecular analysis of the threatened Cabrera's vole ...

    African Journals Online (AJOL)

    Optimal management and conservation programs of the threatened Cabrera's vole require investigating potential molecular genetic markers in the genomic background, if the few remaining fragile populations are to ... The results described Cabrera's vole populations as a single genetic unit with slightly restricted gene flow.

  7. A molecular cytogenetic analysis of introgression in Alstroemeria

    NARCIS (Netherlands)

    Kamstra, S.A.

    1999-01-01

    This thesis describes the results of a molecular cytogenetic investigation of the process of introgression in Alstroemeria . The aim of this study was to transfer chromosomes or genes from one Alstroemeria species into another. For this, two

  8. Molecular dynamic analysis of the structure of dendrimers

    Energy Technology Data Exchange (ETDEWEB)

    Canetta, E.; Maino, G. E-mail: maino@bologna.enea.it

    2004-01-01

    We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques.

  9. Molecular dynamic analysis of the structure of dendrimers

    International Nuclear Information System (INIS)

    Canetta, E.; Maino, G.

    2004-01-01

    We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques

  10. Activation analysis by filtered neutrons. Preliminary investigation

    International Nuclear Information System (INIS)

    Skarnemark, G.; Rodinson, T.; Skaalberg, M.; Tokay, R.K.

    1986-01-01

    In order to investigate if measuring sensibility and precision by epithermal neutron activation analysis may be improved, different types of geological and biologic test samples were radiated. The test samples were enclosed in an extra filter of tungsten or sodium in order to reduce the flux of those neutrons that otherwise would induce interfering activity in the sample. The geological test samples consist of granites containing lanthanides which had been crushed in tung- sten carbide grinder. Normally such test samples show a interferins 1 87W-activity. By use of a tungsten filter the activity was reduced by up to 60%, which resulted in a considerable improvement of sensibility and precision of the measurement. The biologic test samples consisted of evaporated urine from patients treated with the cell poison cis-platinol. A reliable method to measure the platinum content has not existed so far. This method, however, enables platinum contents as low as about 0.1 ppm to be determined which is quite adequate. To sum up this preliminary study has demonstrated that activation analysis using filtered neutrons, correctly applied, is a satisfactory method of reducing interferences without complicated and time-consuming chemical separation procedures. (O.S.)

  11. 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.

  12. Analysis of the normal optical, Michel and molecular potentials on ...

    Indian Academy of Sciences (India)

    6. — journal of. June 2016 physics pp. 1275–1286. Analysis of the normal ... the levels are obtained for the three optical potentials to estimate the quality ... The experimental angular distribution data for the 40Ca(6Li, d)44Ti reaction .... analysed using the normal optical, Michel and molecular potentials within the framework.

  13. Molecular characterization and expression analysis of fat mass and ...

    Indian Academy of Sciences (India)

    Keywords. fat mass and obesity-associated gene (FTO); rabbit; mRNA expression patterns; sequence analysis; Oryctolagus cuniculus. ... In this work, the molecular characterization and expression features of rabbit (Oryctolagus cuniculus) FTO cDNA were analysed. The rabbit FTO cDNA with a size of 2158 bp was cloned, ...

  14. Fragrance analysis using molecular and biochemical methods in ...

    African Journals Online (AJOL)

    For molecular and biochemical analysis of aroma, a mapping population comprising 208 recombinant inbred lines (RILs) derived from a diverse cross between CSR10 and Taraori Basmati through Single seed descent (SSD) method was used. RILs are among the best mapping populations, which provide a novel material ...

  15. A Molecular Iodine Spectral Data Set for Rovibronic Analysis

    Science.gov (United States)

    Williamson, J. Charles; Kuntzleman, Thomas S.; Kafader, Rachael A.

    2013-01-01

    A data set of 7,381 molecular iodine vapor rovibronic transitions between the X and B electronic states has been prepared for an advanced undergraduate spectroscopic analysis project. Students apply standard theoretical techniques to these data and determine the values of three X-state constants (image omitted) and four B-state constants (image…

  16. Molecular dynamics investigation on adsorption layer of alcohols at the air/brine interface.

    Science.gov (United States)

    Nguyen, Cuong V; Phan, Chi M; Ang, Ha M; Nakahara, Hiromichi; Shibata, Osamu; Moroi, Yoshikiyo

    2015-01-01

    Alcohols are a significant group of surfactants which have been employed extensively in industry to improve the interfacial effects. Recently, the change in surface potential (ΔV) of two isomeric hexanols, methyl isobutyl carbinol (MIBC) and 1-hexanol, was investigated by using an ionizing (241)Am electrode. It clearly showed the opposite effects between MIBC and 1-hexanol in the interfacial zone: one enhanced the presence of cations, whereas the other enhanced the presence of anions. This study employs molecular dynamics simulation to provide new insights into the interactions between alcohol molecules and ions as well as water at the molecular level. The results qualitatively agreed with the experimental data and verified the significance of MIBC branching structure on the molecular arrangement within the interfacial zone. The results also highlighted the role of the second water layer on the interfacial properties.

  17. Molecular biological methods (DGGE) as a tool to investigate nitrification inhibition in wastewater treatment.

    Science.gov (United States)

    Kreuzinger, N; Farnleitner, A; Wandl, G; Hornek, R; Mach, R

    2003-01-01

    Incomplete nitrification at an activated sludge plant for biological pre-treatment of rendering plant effluents led to a detailed investigation on the origin and solution of this problem. Preliminary studies revealed that an inhibition of ammonia oxidising microorganisms (AOM) by process waters of the rendering plant was responsible for the situation. We were able to show a correlation between the existence of specific AOM and nitrification capacity expressed as oxygen uptake rate for maximal nitrification (OURNmax). Only Nitrosospira sp. was found in the activated sludge of the rendering plant and another industrial wastewater treatment plant with problems in nitrification, while reference plants without nitrification problems showed Nitrosomonas spp. as the predominant ammonia oxidising bacteria. By accompanying engineering investigations and experiments (cross-feeding experiments, operation of a two-stage laboratory plant) with molecular biological methods (DGGE--Denaturing Gradient Gel Electrophoresis) we were able to elaborate an applicable solution for the rendering plant. Laboratory experiments with a two-stage process layout finally provided complete nitrification overcoming the inhibiting nature of process waters from the rendering plant. DGGE analysis of the second stage activated sludge from the laboratory plant showed a shift in population structure from Nitrosospira sp. towards Nitrosomonas spp. simultaneous to the increase of nitrification capacity. Nitrification capacities comparable to full-scale municipal wastewater treatment plants could be maintained for more than two months. As the design of wastewater treatment plants for nitrification is linked to the growth characteristics of Nitrosomonas spp., established criteria can be applied for the redesign of the full-scale plant.

  18. Importance and pitfalls of molecular analysis to parasite epidemiology.

    Science.gov (United States)

    Constantine, Clare C

    2003-08-01

    Molecular tools are increasingly being used to address questions about parasite epidemiology. Parasites represent a diverse group and they might not fit traditional population genetic models. Testing hypotheses depends equally on correct sampling, appropriate tool and/or marker choice, appropriate analysis and careful interpretation. All methods of analysis make assumptions which, if violated, make the results invalid. Some guidelines to avoid common pitfalls are offered here.

  19. Investigation of the molecular conformations of ethanol using electron momentum spectroscopy

    International Nuclear Information System (INIS)

    Ning, C G; Luo, Z H; Huang, Y R; Liu, K; Zhang, S F; Deng, J K; Hajgato, B; Morini, F; Deleuze, M S

    2008-01-01

    The valence electronic structure and momentum-space electron density distributions of ethanol have been investigated with our newly constructed high-resolution electron momentum spectrometer. The measurements are compared to thermally averaged simulations based on Kohn-Sham (B3LYP) orbital densities as well as one-particle Green's function calculations of ionization spectra and Dyson orbital densities, assuming Boltzmann's statistical distribution of the molecular structure over the two energy minima defining the anti and gauche conformers. One-electron ionization energies and momentum distributions in the outer-valence region were found to be highly dependent upon the molecular conformation. Calculated momentum distributions indeed very sensitively reflect the distortions and topological changes that molecular orbitals undergo due to the internal rotation of the hydroxyl group, and thereby exhibit variations which can be traced experimentally. The B3LYP model Kohn-Sham orbital densities are overall in good agreement with the experimental distributions, and closely resemble benchmark ADC(3) Dyson orbital densities. Both approaches fail to quantitatively reproduce the experimental momentum distributions characterizing the highest occupied molecular orbital. Since electron momentum spectroscopy measurements at various electron impact energies indicate that the plane wave impulse approximation is valid, this discrepancy between theory and experiment is tentatively ascribed to thermal disorder, i.e. large-amplitude and thermally induced dynamical distortions of the molecular structure in the gas phase

  20. A bibliometric analysis on tobacco regulation investigators.

    Science.gov (United States)

    Li, Dingcheng; Okamoto, Janet; Liu, Hongfang; Leischow, Scott

    2015-01-01

    To facilitate the implementation of the Family Smoking Prevention and Tobacco Control Act of 2009, the Federal Drug Agency (FDA) Center for Tobacco Products (CTP) has identified research priorities under the umbrella of tobacco regulatory science (TRS). As a newly integrated field, the current boundaries and landscape of TRS research are in need of definition. In this work, we conducted a bibliometric study of TRS research by applying author topic modeling (ATM) on MEDLINE citations published by currently-funded TRS principle investigators (PIs). We compared topics generated with ATM on dataset collected with TRS PIs and topics generated with ATM on dataset collected with a TRS keyword list. It is found that all those topics show a good alignment with FDA's funding protocols. More interestingly, we can see clear interactive relationships among PIs and between PIs and topics. Based on those interactions, we can discover how diverse each PI is, how productive they are, which topics are more popular and what main components each topic involves. Temporal trend analysis of key words shows the significant evaluation in four prime TRS areas. The results show that ATM can efficiently group articles into discriminative categories without any supervision. This indicates that we may incorporate ATM into author identification systems to infer the identity of an author of articles using topics generated by the model. It can also be useful to grantees and funding administrators in suggesting potential collaborators or identifying those that share common research interests for data harmonization or other purposes. The incorporation of temporal analysis can be employed to assess the change over time in TRS as new projects are funded and the extent to which new research reflects the funding priorities of the FDA.

  1. Conformational analysis of oligosaccharides and polysaccharides using molecular dynamics simulations.

    Science.gov (United States)

    Frank, Martin

    2015-01-01

    Complex carbohydrates usually have a large number of rotatable bonds and consequently a large number of theoretically possible conformations can be generated (combinatorial explosion). The application of systematic search methods for conformational analysis of carbohydrates is therefore limited to disaccharides and trisaccharides in a routine analysis. An alternative approach is to use Monte-Carlo methods or (high-temperature) molecular dynamics (MD) simulations to explore the conformational space of complex carbohydrates. This chapter describes how to use MD simulation data to perform a conformational analysis (conformational maps, hydrogen bonds) of oligosaccharides and how to build realistic 3D structures of large polysaccharides using Conformational Analysis Tools (CAT).

  2. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

    Science.gov (United States)

    Kumar, Sudhir; Stecher, Glen; Li, Michael; Knyaz, Christina; Tamura, Koichiro

    2018-06-01

    The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.

  3. Molecular- and nm-scale Investigation of the Structure and Compositional Heterogeneity of Naturally Occurring Ferrihydrite

    Science.gov (United States)

    Cismasu, C.; Michel, F. M.; Stebbins, J. F.; Tcaciuc, A. P.; Brown, G. E.

    2008-12-01

    Ferrihydrite is a hydrated Fe(III) nano-oxide that forms in vast quantities in contaminated acid mine drainage environments. As a result of its high surface area, ferrihydrite is an important environmental sorbent, and plays an essential role in the geochemical cycling of pollutant metal(loid)s in these settings. Despite its environmental relevance, this nanomineral remains one of the least understood environmental solids in terms of its structure (bulk and surface), compositional variations, and the factors affecting its reactivity. Under natural aqueous conditions, ferrihydrite often precipitates in the presence of several inorganic compounds such as aluminum, silica, arsenic, etc., or in the presence of organic matter. These impurities can affect the molecular-level structure of naturally occurring ferrihydrite, thus modifying fundamental properties that are directly correlated with solid-phase stability and surface reactivity. Currently there exists a significant gap in our understanding of the structure of synthetic vs. natural ferrihydrites, due to the inherent difficulties associated to the investigation of these poorly crystalline nanophases. In this study, we combined synchrotron- and laboratory-based techniques to characterize naturally occurring ferrihydrite from an acid mine drainage system situated at the New Idria mercury mine in California. We used high-energy X-ray total scattering and pair distribution function analysis to elucidate quantitative structural details of these samples. We have additionally used scanning transmission X-ray microscopy high resolution imaging (30 nm) to evaluate the spatial relationship of major elements Si, Al, and C within ferrihydrite. Al, Si and C K-edge near- edge X-ray absorption fine structure spectroscopy and 27Al nuclear magnetic resonance spectroscopy were used to obtain short-range structural information. By combining these techniques we attain the highest level of resolution permitted by current analytical

  4. Investigation of the molecular level interactions between mucins and food proteins: Spectroscopic, tribological and rheological studies

    OpenAIRE

    Celebioglu, Hilal Yilmaz; Chronakis, Ioannis S.; Lee, Seunghwan; Guðjónsdóttir, María

    2017-01-01

    The thesis investigated the structure and molecular-level interaction of β-lactoglobulin (BLG) and mucins, representing major components of the dairy products and saliva/digestion systems, respectively. Mucins are long glycoprotein molecules responsible for the gel nature of the mucous layer covers epithelial surfaces throughout the body. A literature review of the interactions of different mucin types and saliva mucins with several food proteins and food protein emulsions, as well as their f...

  5. Molecular Dynamics Investigation of Cl− and Water Transport through a Eukaryotic CLC Transporter

    OpenAIRE

    Cheng, Mary Hongying; Coalson, Rob D.

    2012-01-01

    Early crystal structures of prokaryotic CLC proteins identified three Cl– binding sites: internal (Sint), central (Scen), and external (Sext). A conserved external GLU (GLUex) residue acts as a gate competing for Sext. Recently, the first crystal structure of a eukaryotic transporter, CmCLC, revealed that in this transporter GLUex competes instead for Scen. Here, we use molecular dynamics simulations to investigate Cl– transport through CmCLC. The gating and Cl–/H+ transport cycle are inferre...

  6. Molecular and Genetic Investigation of Tau in Chronic Traumatic Encephalopathy (Log No. 13267017)

    Science.gov (United States)

    2017-10-01

    AWARD NUMBER: W81XWH-14-1-0399 TITLE: Molecular & Genetic Investigation of Tau in Chronic Traumatic Encephalopathy (Log No. 13267017) PRINCIPAL...this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data ...sources, gathering and maintaining the data needed, and completing and reviewing the collection of information. Send comments regarding this burden

  7. Analytical and molecular dynamical investigations of the influence of molecular vibrations upon the (e,2e) electron momentum distributions of furan

    International Nuclear Information System (INIS)

    Morini, F; Deleuze, M S; Watanabe, N; Takahashi, M

    2015-01-01

    The role of molecular vibrations has been theoretically investigated in the electronic ground state on the (e, 2e) valence orbital momentum profiles of furan by means of two complementary approaches. The first one relies upon the principles of Born-Oppenheimer Molecular Dynamics (BOMD), whereas the second one, referred as Harmonic Analytical Quantum Mechanical (HAQM) approach, includes on quantum-mechanical (paper)

  8. Electron transport in dipyridazine and dipyridimine molecular junctions: a first-principles investigation

    Science.gov (United States)

    Parashar, Sweta

    2018-05-01

    We present density functional theory-nonequilibrium Green’s function method for electron transport of dipyridazine and dipyridimine molecular junctions with gold, copper and nickel electrodes. Our investigation reveals that the junctions formed with gold and copper electrodes bridging dipyridazine molecule through thiol anchoring group enhance current as compared to the junctions in which the molecule and electrode were coupled directly. Further, nickel electrode displays weak decrease of current with increase of voltage at about 1.2 V. The result is fully rationalized by means of the distribution of molecular orbitals as well as shift in molecular energy levels and HOMO-LUMO gap with applied bias voltage. Our findings are compared with theoretical and experimental results available for other molecular junctions. Present results predict potential avenues for changing the transport behavior by not only changing the electrodes, but also the position of nitrogen atom and type of anchoring-atom that connect molecule and electrodes, thus extending applications of dipyridazine and dipyridimine molecule in future integrated circuits.

  9. Online molecular image repository and analysis system: A multicenter collaborative open-source infrastructure for molecular imaging research and application.

    Science.gov (United States)

    Rahman, Mahabubur; Watabe, Hiroshi

    2018-05-01

    Molecular imaging serves as an important tool for researchers and clinicians to visualize and investigate complex biochemical phenomena using specialized instruments; these instruments are either used individually or in combination with targeted imaging agents to obtain images related to specific diseases with high sensitivity, specificity, and signal-to-noise ratios. However, molecular imaging, which is a multidisciplinary research field, faces several challenges, including the integration of imaging informatics with bioinformatics and medical informatics, requirement of reliable and robust image analysis algorithms, effective quality control of imaging facilities, and those related to individualized disease mapping, data sharing, software architecture, and knowledge management. As a cost-effective and open-source approach to address these challenges related to molecular imaging, we develop a flexible, transparent, and secure infrastructure, named MIRA, which stands for Molecular Imaging Repository and Analysis, primarily using the Python programming language, and a MySQL relational database system deployed on a Linux server. MIRA is designed with a centralized image archiving infrastructure and information database so that a multicenter collaborative informatics platform can be built. The capability of dealing with metadata, image file format normalization, and storing and viewing different types of documents and multimedia files make MIRA considerably flexible. With features like logging, auditing, commenting, sharing, and searching, MIRA is useful as an Electronic Laboratory Notebook for effective knowledge management. In addition, the centralized approach for MIRA facilitates on-the-fly access to all its features remotely through any web browser. Furthermore, the open-source approach provides the opportunity for sustainable continued development. MIRA offers an infrastructure that can be used as cross-boundary collaborative MI research platform for the rapid

  10. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics

    Directory of Open Access Journals (Sweden)

    von Haeseler Arndt

    2004-06-01

    Full Text Available Abstract Background Most analysis programs for inferring molecular phylogenies are difficult to use, in particular for researchers with little programming experience. Results TREEFINDER is an easy-to-use integrative platform-independent analysis environment for molecular phylogenetics. In this paper the main features of TREEFINDER (version of April 2004 are described. TREEFINDER is written in ANSI C and Java and implements powerful statistical approaches for inferring gene tree and related analyzes. In addition, it provides a user-friendly graphical interface and a phylogenetic programming language. Conclusions TREEFINDER is a versatile framework for analyzing phylogenetic data across different platforms that is suited both for exploratory as well as advanced studies.

  11. Cocoa content influences chocolate molecular profile investigated by MALDI-TOF mass spectrometry.

    Science.gov (United States)

    Bonatto, Cínthia C; Silva, Luciano P

    2015-06-01

    Chocolate authentication is a key aspect of quality control and safety. Matrix-assisted laser desorption ionization time-of flight (MALDI-TOF) mass spectrometry (MS) has been demonstrated to be useful for molecular profiling of cells, tissues, and even food. The present study evaluated if MALDI-TOF MS analysis on low molecular mass profile may classify chocolate samples according to the cocoa content. The molecular profiles of seven processed commercial chocolate samples were compared by using MALDI-TOF MS. Some ions detected exclusively in chocolate samples corresponded to the metabolites of cocoa or other constituents. This method showed the presence of three distinct clusters according to confectionery and sensorial features of the chocolates and was used to establish a mass spectra database. Also, novel chocolate samples were evaluated in order to check the validity of the method and to challenge the database created with the mass spectra of the primary samples. Thus, the method was shown to be reliable for clustering unknown samples into the main chocolate categories. Simple sample preparation of the MALDI-TOF MS approach described will allow the surveillance and monitoring of constituents during the molecular profiling of chocolates. © 2014 Society of Chemical Industry.

  12. Accommodating error analysis in comparison and clustering of molecular fingerprints.

    OpenAIRE

    Salamon, H.; Segal, M. R.; Ponce de Leon, A.; Small, P. M.

    1998-01-01

    Molecular epidemiologic studies of infectious diseases rely on pathogen genotype comparisons, which usually yield patterns comprising sets of DNA fragments (DNA fingerprints). We use a highly developed genotyping system, IS6110-based restriction fragment length polymorphism analysis of Mycobacterium tuberculosis, to develop a computational method that automates comparison of large numbers of fingerprints. Because error in fragment length measurements is proportional to fragment length and is ...

  13. New Diethyl Ammonium Salt of Thiobarbituric Acid Derivative: Synthesis, Molecular Structure Investigations and Docking Studies

    Directory of Open Access Journals (Sweden)

    Assem Barakat

    2015-11-01

    Full Text Available The synthesis of the new diethyl ammonium salt of diethylammonium(E-5-(1,5-bis(4-fluorophenyl-3-oxopent-4-en-1-yl-1,3-diethyl-4,6-dioxo-2-thioxohexaydropyrimidin-5-ide 3 via a regioselective Michael addition of N,N-diethylthiobarbituric acid 1 to dienone 2 is described. In 3, the carboanion of the thiobarbituric moiety is stabilized by the strong intramolecular electron delocalization with the adjacent carbonyl groups and so the reaction proceeds without any cyclization. The molecular structure investigations of 3 were determined by single-crystal X-ray diffraction as well as DFT computations. The theoretically calculated (DFT/B3LYP geometry agrees well with the crystallographic data. The effect of fluorine replacement by chlorine atoms on the molecular structure aspects were investigated using DFT methods. Calculated electronic spectra showed a bathochromic shift of the π-π* transition when fluorine is replaced by chlorine. Charge decomposition analyses were performed to study possible interaction between the different fragments in the studied systems. Molecular docking simulations examining the inhibitory nature of the compound show an anti-diabetic activity with Pa (probability of activity value of 0.229.

  14. Yield and Failure Behavior Investigated for Cross-Linked Phenolic Resins Using Molecular Dynamics

    Science.gov (United States)

    Monk, Joshua D.; Lawson, John W.

    2016-01-01

    Molecular dynamics simulations were conducted to fundamentally evaluate the yield and failure behavior of cross-linked phenolic resins at temperatures below the glass transition. Yield stress was investigated at various temperatures, strain rates, and degrees of cross-linking. The onset of non-linear behavior in the cross-linked phenolic structures was caused by localized irreversible molecular rearrangements through the rotation of methylene linkers followed by the formation or annihilation of neighboring hydrogen bonds. The yield stress results, with respect to temperature and strain rate, could be fit by existing models used to describe yield behavior of amorphous glasses. The degree of cross-linking only indirectly influences the maximum yield stress through its influence on glass transition temperature (Tg), however there is a strong relationship between the degree of cross-linking and the failure mechanism. Low cross-linked samples were able to separate through void formation, whereas the highly cross-linked structures exhibited bond scission.

  15. The interaction between 4-aminoantipyrine and bovine serum albumin: Multiple spectroscopic and molecular docking investigations

    International Nuclear Information System (INIS)

    Teng Yue; Liu Rutao; Li Chao; Xia Qing; Zhang Pengjun

    2011-01-01

    4-Aminoantipyrine (AAP) is widely used in the pharmaceutical industry, in biochemical experiments and in environmental monitoring. AAP as an aromatic pollutant in the environment poses a great threat to human health. To evaluate the toxicity of AAP at the protein level, the effects of AAP on bovine serum albumin (BSA) were investigated by multiple spectroscopic techniques and molecular modeling. After the inner filter effect was eliminated, the experimental results showed that AAP effectively quenched the intrinsic fluorescence of BSA via static quenching. The number of binding sites, the binding constant, the thermodynamic parameters and binding subdomain were measured, and indicated that AAP could spontaneously bind with BSA on subdomain IIIA through electrostatic forces. Molecular docking results revealed that AAP interacted with the Glu 488 and Glu 502 residues of BSA. Furthermore, the conformation of BSA was demonstrably changed in the presence of AAP. The skeletal structure of BSA loosened, exposing internal hydrophobic aromatic ring amino acids and peptide strands to the solution.

  16. Application of atomic absorption in molecular analysis (spectrophotometry)

    International Nuclear Information System (INIS)

    Baliza, S.V.; Soledade, L.E.B.

    1981-01-01

    The apparatus of atomic absorption has been considered by all the experts in chemical analysis as one of the most important equipments in actual utilization in such field. Among its several applications one should emphasize direct and indirect metals analyses using flame, graphite furnace, cold vapor generator,... Besides such known applications, the authors have developed at the R and D Center of CSN a patent pendent method for the utilization of such equipment for molecular analysis, in substitution of a sophisticated and specific apparatus. (Author) [pt

  17. Magnetic effects on the solvent properties investigated by molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Moosavi, Fatemeh, E-mail: moosavibaigi@um.ac.ir; Gholizadeh, Mostafa

    2014-03-15

    This paper investigates how an external constant magnetic field in the Z-direction affects the performance of a solvent. The molecular dynamics simulation comprised common inorganic and organic solvents including water, acetone, acetonitrile, toluene, and n-hexane at the ambient temperature and pressure. A static magnetic field applied in the simulation process is able to reduce the solvent mobility in the solution in order to enhance the solvent–solute reaction. Simulation results show that the diffusivity decreases because of increasing the effective interactions. Besides, magnetic field reduces the volume of the solvent and increases the strength of the hydrogen bonds by maximizing attractive electrostatic and vdW interactions caused by changes in the radial distribution function of the solvents. Hydrogen-bonding characteristics of solvents investigated by molecular dynamics simulations were evidence for the hydrogen bonding strength of O···H that is a more efficient intermolecular hydrogen-bonding in comparison with N···H. - Highlights: • Molecular dynamics simulation technique investigates the effect of magnetic field on transport dynamics inside the solvent bulk. • External constant magnetic field influences on intermolecular interactions, thermophysics, and transport properties of the solvents. • Applying magnetic field strengthened hydrogen bond maximizes attractive electrostatic interactions, charge distribution becomes stronger, and the molecule mobility is demoted. • The low diffusivity of the solvents in the solutions increases the performance of the interactions and promotes the interactions. • On introducing a magnetic field of flux density parallel to the Z-direction, solvent acts as an obstacle to diffusion of solutes.

  18. Accommodating error analysis in comparison and clustering of molecular fingerprints.

    Science.gov (United States)

    Salamon, H; Segal, M R; Ponce de Leon, A; Small, P M

    1998-01-01

    Molecular epidemiologic studies of infectious diseases rely on pathogen genotype comparisons, which usually yield patterns comprising sets of DNA fragments (DNA fingerprints). We use a highly developed genotyping system, IS6110-based restriction fragment length polymorphism analysis of Mycobacterium tuberculosis, to develop a computational method that automates comparison of large numbers of fingerprints. Because error in fragment length measurements is proportional to fragment length and is positively correlated for fragments within a lane, an align-and-count method that compensates for relative scaling of lanes reliably counts matching fragments between lanes. Results of a two-step method we developed to cluster identical fingerprints agree closely with 5 years of computer-assisted visual matching among 1,335 M. tuberculosis fingerprints. Fully documented and validated methods of automated comparison and clustering will greatly expand the scope of molecular epidemiology.

  19. Investigations of the Formation of Molecular Hydrogen on Dust Grain Analogues

    Science.gov (United States)

    Vidali, Gianfranco; Roser, Joseph E.; Manico, Giulio; Pirronello, Valerio

    2002-01-01

    In the last four years we have been working to investigate the formation of molecular hydrogen on surfaces of materials of astrophysical interest, such as silicates, carbonaceous particles and ices, and in conditions approximating the ones present in a variety of astrophysical environments. Our experimental studies - the first of their kind and complemented with computer simulations and theoretical analyses - have given not only hydrogen recombination rates under different ISM conditions, but they have also offered new insights into this fundamental astrophysical problem. Here we summarize our experimental methods and most significant results.

  20. Milestone in the NTB phase investigation and beyond: direct insight into molecular self-assembly.

    Science.gov (United States)

    Ivšić, Trpimir; Vinković, Marijana; Baumeister, Ute; Mikleušević, Ana; Lesac, Andreja

    2014-12-14

    Although liquid-crystalline materials are most widely exploited for flat-panel displays, their ability to self-organize into periodically ordered nanostructures gives rise to a broad variety of additional applications. The recently discovered low-temperature nematic phase (N(TB)) with unusual characteristics generated considerable attention within the scientific community: despite the fact that the molecules from which the phase is composed are not chiral, the helicoidal structure of the phase is strongly implicated. Here we report on combined experimental, computational and spectroscopic studies of the structural aspects influencing formation of the N(TB) phase as well as on the molecular organization within the phase. In an extensive DFT study, the structure-property prerequisite was traced to a "bent-propeller" shape of the molecule. We also demonstrate the first utilization of liquid state NMR for direct analysis of intermolecular interactions within thermotropic liquid-crystalline phases, providing new insight into molecular packing that can lead towards design of novel chiral functional materials. The synergy of experimental, computational and NMR studies suggests a syn-parallel helical molecular organization within the N(TB) phase.

  1. Archives of Astronomical Spectral Observations and Atomic/Molecular Databases for their Analysis

    Directory of Open Access Journals (Sweden)

    Ryabchikova T.

    2015-12-01

    Full Text Available We present a review of open-source data for stellar spectroscopy investigations. It includes lists of the main archives of medium-to-high resolution spectroscopic observations, with brief characteristics of the archive data (spectral range, resolving power, flux units. We also review atomic and molecular databases that contain parameters of spectral lines, cross-sections and reaction rates needed for a detailed analysis of high resolution, high signal-to-noise ratio stellar spectra.

  2. An investigation on non-invasive fungal sinusitis; Molecular identification of etiologic agents

    Directory of Open Access Journals (Sweden)

    Abdolrasoul Mohammadi

    2017-01-01

    Full Text Available Background: Fungal sinusitis is increasing worldwide in the past two decades. It is divided into two types including invasive and noninvasive. Noninvasive types contain allergic fungal sinusitis (AFS and fungus ball. AFS is a hypersensitivity reaction to fungal allergens in the mucosa of the sinonasal tract in atopic individuals. The fungus ball is a different type of noninvasive fungal rhinosinusitis which is delineated as an accumulation of debris and fungal elements inside a paranasal sinus. Fungal sinusitis caused by various fungi such as Aspergillus species, Penicillium, Mucor, Rhizopus, and phaeohyphomycetes. The aim of the present study is to identify fungal species isolated from noninvasive fungal sinusitis by molecular methods. Materials and Methods: During 2015–2016, a total of 100 suspected patients were examined for fungal sinusitis. Functional endoscopic sinus surgery was performed using the Messerklinger technique. Clinical samples were identified by phenotypic and molecular methods. Polymerase chain reaction (PCR sequencing of ITS1-5.8S-ITS2 region and PCR-restriction fragment length polymorphism with Msp I restriction enzyme was performed for molecular identification of molds and yeasts, respectively. Results: Twenty-seven out of 100 suspected cases (27% had fungal sinusitis. Nasal congestion (59% and headache (19% were the most common clinical signs among patients. Fifteen patients (55.5% were male and 12 patients (44.5% were female. Aspergillus flavus was the most prevalent fungal species (26%, followed by Penicillium chrysogenum (18.5% and Candida glabrata species complex (15%. Conclusion: Since clinical manifestations, computed tomography scan, endoscopy, and histopathological findings are very nonspecific in AFS and fungus ball; therefore, molecular investigations are compulsory for precise identification of etiologic agents and appropriate management of these fungal infections.

  3. Investigating the binding behaviour of two avidin-based testosterone binders using molecular recognition force spectroscopy.

    Science.gov (United States)

    Rangl, Martina; Leitner, Michael; Riihimäki, Tiina; Lehtonen, Soili; Hytönen, Vesa P; Gruber, Hermann J; Kulomaa, Markku; Hinterdorfer, Peter; Ebner, Andreas

    2014-02-01

    Molecular recognition force spectroscopy, a biosensing atomic force microscopy technique allows to characterise the dissociation of ligand-receptor complexes at the molecular level. Here, we used molecular recognition force spectroscopy to study the binding capability of recently developed testosterone binders. The two avidin-based proteins called sbAvd-1 and sbAvd-2 are expected to bind both testosterone and biotin but differ in their binding behaviour towards these ligands. To explore the ligand binding and dissociation energy landscape of these proteins, we tethered biotin or testosterone to the atomic force microscopy probe while the testosterone-binding protein was immobilized on the surface. Repeated formation and rupture of the ligand-receptor complex at different pulling velocities allowed determination of the loading rate dependence of the complex-rupturing force. In this way, we obtained the molecular dissociation rate (k(off)) and energy landscape distances (x(β)) of the four possible complexes: sbAvd-1-biotin, sbAvd-1-testosterone, sbAvd-2-biotin and sbAvd-2-testosterone. It was found that the kinetic off-rates for both proteins and both ligands are similar. In contrast, the x(β) values, as well as the probability of complex formations, varied considerably. In addition, competitive binding experiments with biotin and testosterone in solution differ significantly for the two testosterone-binding proteins, implying a decreased cross-reactivity of sbAvd-2. Unravelling the binding behaviour of the investigated testosterone-binding proteins is expected to improve their usability for possible sensing applications. Copyright © 2014 John Wiley & Sons, Ltd.

  4. Investigation of plutonium abundance and age analysis

    Energy Technology Data Exchange (ETDEWEB)

    Huailong, Wu; Jian, Gong; Fanhua, Hao [China Academy of Engineering Physics, Mianyang (China). Inst. of Nuclear Physics and Chemistry

    2007-06-15

    Based on spectra analysis software, all of the plutonium material peak counts are analyzed. Relatively efficiency calibration is done by the non-coupling peaks of {sup 239}Pu. By using the known isotopes half life and yield, the coupling peaks counts are allocated by non-coupling peaks, consequently the atom ratios of each isotope are gotten. The formula between atom ratio and abundance or age is deduced by plutonium material isotopes decay characteristic. And so the abundance and age of plutonium material is gotten. After some re- peat measurements for a plutonium equipment are completed, a comparison between our analysis results and PC-FRAM and the owner's reference results are done. (authors)

  5. Cellular and molecular investigations of the adhesion and mechanics of Listeria monocytogenes

    Science.gov (United States)

    Eskhan, Asma Omar

    Atomic force microscopy has been used to quantify the adherence and mechanical properties of an array of L. monocytogenes strains and their surface biopolymers. First, eight L. monocytogenes strains that represented the two major lineages of the species were compared for their adherence and mechanics at cellular and molecular levels. Our results indicated that strains of lineage' II were characterized by higher adhesion and Young's moduli, longer and more rigid surface biopolymers and lower specific and nonspecific forces when compared to lineage' I strains. Additionally, adherence and mechanical properties of eight L. monocytogenes epidemic and environmental strains were probed. Our results pointed to that environmental and epidemic strains representative of a given lineage were similar in their adherence and mechanical properties when investigated at a cellular level. However, when the molecular properties of the strains were considered, epidemic strains were characterized by higher specific and nonspecific forces, shorter, denser and more flexible biopolymers compared to environmental strains. Second, the role of environmental pH conditions of growth on the adhesion and mechanics of a pathogenic L. monocytogenes EGDe was investigated. Our results pointed to a transition in the adhesion energies for cells cultured at pH 7. In addition, when the types of molecular forces that govern the adhesion were quantified using Poisson statistical approach and using a new proposed method, specific hydrogen-bond energies dominated the bacterial adhesion process. Such a finding is instrumental to researchers designing methods to control bacterial adhesion. Similarly, bacterial cells underwent a transition in their mechanical properties. We have shown that cells cultured at pH 7 were the most rigid compared to those cultured in lower or higher pH conditions of growth. Due to transitions observed in adherence and mechanics when cells were cultured at pH 7, we hypothesized that

  6. Onboard functional and molecular imaging: A design investigation for robotic multipinhole SPECT

    International Nuclear Information System (INIS)

    Bowsher, James; Giles, William; Yin, Fang-Fang; Yan, Susu; Roper, Justin

    2014-01-01

    Purpose: Onboard imaging—currently performed primarily by x-ray transmission modalities—is essential in modern radiation therapy. As radiation therapy moves toward personalized medicine, molecular imaging, which views individual gene expression, may also be important onboard. Nuclear medicine methods, such as single photon emission computed tomography (SPECT), are premier modalities for molecular imaging. The purpose of this study is to investigate a robotic multipinhole approach to onboard SPECT. Methods: Computer-aided design (CAD) studies were performed to assess the feasibility of maneuvering a robotic SPECT system about a patient in position for radiation therapy. In order to obtain fast, high-quality SPECT images, a 49-pinhole SPECT camera was designed which provides high sensitivity to photons emitted from an imaging region of interest. This multipinhole system was investigated by computer-simulation studies. Seventeen hot spots 10 and 7 mm in diameter were placed in the breast region of a supine female phantom. Hot spot activity concentration was six times that of background. For the 49-pinhole camera and a reference, more conventional, broad field-of-view (FOV) SPECT system, projection data were computer simulated for 4-min scans and SPECT images were reconstructed. Hot-spot localization was evaluated using a nonprewhitening forced-choice numerical observer. Results: The CAD simulation studies found that robots could maneuver SPECT cameras about patients in position for radiation therapy. In the imaging studies, most hot spots were apparent in the 49-pinhole images. Average localization errors for 10-mm- and 7-mm-diameter hot spots were 0.4 and 1.7 mm, respectively, for the 49-pinhole system, and 3.1 and 5.7 mm, respectively, for the reference broad-FOV system. Conclusions: A robot could maneuver a multipinhole SPECT system about a patient in position for radiation therapy. The system could provide onboard functional and molecular imaging with 4-min

  7. Onboard functional and molecular imaging: A design investigation for robotic multipinhole SPECT

    Energy Technology Data Exchange (ETDEWEB)

    Bowsher, James, E-mail: james.bowsher@duke.edu; Giles, William; Yin, Fang-Fang [Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina 27710 and Medical Physics Graduate Program, Duke University, Durham, North Carolina 27710 (United States); Yan, Susu [Medical Physics Graduate Program, Duke University, Durham, North Carolina 27710 (United States); Roper, Justin [Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina 27710 (United States)

    2014-01-15

    Purpose: Onboard imaging—currently performed primarily by x-ray transmission modalities—is essential in modern radiation therapy. As radiation therapy moves toward personalized medicine, molecular imaging, which views individual gene expression, may also be important onboard. Nuclear medicine methods, such as single photon emission computed tomography (SPECT), are premier modalities for molecular imaging. The purpose of this study is to investigate a robotic multipinhole approach to onboard SPECT. Methods: Computer-aided design (CAD) studies were performed to assess the feasibility of maneuvering a robotic SPECT system about a patient in position for radiation therapy. In order to obtain fast, high-quality SPECT images, a 49-pinhole SPECT camera was designed which provides high sensitivity to photons emitted from an imaging region of interest. This multipinhole system was investigated by computer-simulation studies. Seventeen hot spots 10 and 7 mm in diameter were placed in the breast region of a supine female phantom. Hot spot activity concentration was six times that of background. For the 49-pinhole camera and a reference, more conventional, broad field-of-view (FOV) SPECT system, projection data were computer simulated for 4-min scans and SPECT images were reconstructed. Hot-spot localization was evaluated using a nonprewhitening forced-choice numerical observer. Results: The CAD simulation studies found that robots could maneuver SPECT cameras about patients in position for radiation therapy. In the imaging studies, most hot spots were apparent in the 49-pinhole images. Average localization errors for 10-mm- and 7-mm-diameter hot spots were 0.4 and 1.7 mm, respectively, for the 49-pinhole system, and 3.1 and 5.7 mm, respectively, for the reference broad-FOV system. Conclusions: A robot could maneuver a multipinhole SPECT system about a patient in position for radiation therapy. The system could provide onboard functional and molecular imaging with 4-min

  8. Mechanistic investigation of Fe(III) oxide reduction by low molecular weight organic sulfur species

    Science.gov (United States)

    Eitel, Eryn M.; Taillefert, Martial

    2017-10-01

    Low molecular weight organic sulfur species, often referred to as thiols, are known to be ubiquitous in aquatic environments and represent important chemical reductants of Fe(III) oxides. Thiols are excellent electron shuttles used during dissimilatory iron reduction, and in this capacity could indirectly affect the redox state of sediments, release adsorbed contaminants via reductive dissolution, and influence the carbon cycle through alteration of bacterial respiration processes. Interestingly, the reduction of Fe(III) oxides by thiols has not been previously investigated in environmentally relevant conditions, likely due to analytical limitations associated with the detection of thiols and their oxidized products. In this study, a novel electrochemical method was developed to simultaneously determine thiol/disulfide pair concentrations in situ during the reduction of ferrihydrite in batch reactors. First order rate laws with respect to initial thiol concentration were confirmed for Fe(III) oxyhydroxide reduction by four common thiols: cysteine, homocysteine, cysteamine, and glutathione. Zero order was determined for both Fe(III) oxyhydroxide and proton concentration at circumneutral pH. A kinetic model detailing the molecular mechanism of the reaction was optimized with proposed intermediate surface structures. Although metal oxide overall reduction rate constants were inversely proportional to the complexity of the thiol structure, the extent of metal reduction increased with structure complexity, indicating that surface complexes play a significant role in the ability of these thiols to reduce iron. Taken together, these results demonstrate the importance of considering the molecular reaction mechanism at the iron oxide surface when investigating the potential for thiols to act as electron shuttles during dissimilatory iron reduction in natural environments.

  9. Spectroscopic and molecular modeling investigation on the binding of a synthesized steroidal amide to protein

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Hua-xin, E-mail: h.x.zhang@yeah.net; Liu, E.

    2014-09-15

    Owing to the various valuable biological activities, steroidal amides have become a hot topic in steroidal pharmaceutical chemistry. In this paper, an anti-tumor steroid derivate (DAAO) was synthesized and identified. The interaction between DAAO and human serum albumin (HSA) was studied by fluorescence spectra, circular dichroism (CD) spectra, molecular modeling and molecular probe techniques. The results suggested that DAAO had reacted with HSA through hydrogen bonds and van der Waals power. The formation of DAAO–HSA complex at ground state led to static quenching of HSA's fluorescence. The number of binding sites, binding constants, enthalpy change (ΔH{sup θ}), Gibbs free energy change (ΔG{sup θ}) and entropy change (ΔS{sup θ}) were calculated at different temperatures based on fluorescence quenching theory and classic equation. Molecular modeling investigation indicated that DAAO was more inclined to absorb on Sudlow's site I in subdomain IIA of HSA molecule on grounds of the lowest energy principle and steric hindrance effect. The binding location was further confirmed by fluorescence probe experiment using warfarin (site I probe) for displacement. Furthermore, the conformational changes of HSA in presence of DAAO were investigated by CD spectra. The results could provide new evidence explaining the relationship between the chemical structure and biological activity and may be useful for understanding the anti-cancer mechanism of steroidal drug. - Highlights: • A designed steroidal amide compound (DAAO) was synthesized by introducing amido bonds into a steroid nucleus. • DAAO binds to Sudlow's site I in HSA through hydrogen bonds and van der Waals power. • The interaction was a spontaneous and exothermic process with modest degree of reversibility. • The secondary structure of HSA and the microenvironment of TRP214 altered. • Amido bond in steroid nucleus (–NH–CO–) plays important role in stabling the structure of

  10. Polyphilic Interactions as Structural Driving Force Investigated by Molecular Dynamics Simulation (Project 7

    Directory of Open Access Journals (Sweden)

    Christopher Peschel

    2017-09-01

    Full Text Available We investigated the effect of fluorinated molecules on dipalmitoylphosphatidylcholine (DPPC bilayers by force-field molecular dynamics simulations. In the first step, we developed all-atom force-field parameters for additive molecules in membranes to enable an accurate description of those systems. On the basis of this force field, we performed extensive simulations of various bilayer systems containing different additives. The additive molecules were chosen to be of different size and shape, and they included small molecules such as perfluorinated alcohols, but also more complex molecules. From these simulations, we investigated the structural and dynamic effects of the additives on the membrane properties, as well as the behavior of the additive molecules themselves. Our results are in good agreement with other theoretical and experimental studies, and they contribute to a microscopic understanding of interactions, which might be used to specifically tune membrane properties by additives in the future.

  11. Molecular Isotopic Distribution Analysis (MIDAs) with adjustable mass accuracy.

    Science.gov (United States)

    Alves, Gelio; Ogurtsov, Aleksey Y; Yu, Yi-Kuo

    2014-01-01

    In this paper, we present Molecular Isotopic Distribution Analysis (MIDAs), a new software tool designed to compute molecular isotopic distributions with adjustable accuracies. MIDAs offers two algorithms, one polynomial-based and one Fourier-transform-based, both of which compute molecular isotopic distributions accurately and efficiently. The polynomial-based algorithm contains few novel aspects, whereas the Fourier-transform-based algorithm consists mainly of improvements to other existing Fourier-transform-based algorithms. We have benchmarked the performance of the two algorithms implemented in MIDAs with that of eight software packages (BRAIN, Emass, Mercury, Mercury5, NeutronCluster, Qmass, JFC, IC) using a consensus set of benchmark molecules. Under the proposed evaluation criteria, MIDAs's algorithms, JFC, and Emass compute with comparable accuracy the coarse-grained (low-resolution) isotopic distributions and are more accurate than the other software packages. For fine-grained isotopic distributions, we compared IC, MIDAs's polynomial algorithm, and MIDAs's Fourier transform algorithm. Among the three, IC and MIDAs's polynomial algorithm compute isotopic distributions that better resemble their corresponding exact fine-grained (high-resolution) isotopic distributions. MIDAs can be accessed freely through a user-friendly web-interface at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/midas/index.html.

  12. Investigating the molecular basis for heterophylly in the aquatic plant Potamogeton octandrus (Potamogetonaceae with comparative transcriptomics

    Directory of Open Access Journals (Sweden)

    Dingxuan He

    2018-02-01

    Full Text Available Many plant species exhibit different leaf morphologies within a single plant, or heterophylly. The molecular mechanisms regulating this phenomenon, however, have remained elusive. In this study, the transcriptomes of submerged and floating leaves of an aquatic heterophyllous plant, Potamogeton octandrus Poir, at different stages of development, were sequenced using high-throughput sequencing (RNA-Seq, in order to aid gene discovery and functional studies of genes involved in heterophylly. A total of 81,103 unigenes were identified in submerged and floating leaves and 6,822 differentially expressed genes (DEGs were identified by comparing samples at differing time points of development. KEGG pathway enrichment analysis categorized these unigenes into 128 pathways. A total of 24,025 differentially expressed genes were involved in carbon metabolic pathways, biosynthesis of amino acids, ribosomal processes, and plant-pathogen interactions. In particular, KEGG pathway enrichment analysis categorized a total of 70 DEGs into plant hormone signal transduction pathways. The high-throughput transcriptomic results presented here highlight the potential for understanding the molecular mechanisms underlying heterophylly, which is still poorly understood. Further, these data provide a framework to better understand heterophyllous leaf development in P. octandrus via targeted studies utilizing gene cloning and functional analyses.

  13. DSC and EPR investigations on effects of cholesterol component on molecular interactions between paclitaxel and phospholipid within lipid bilayer membrane.

    Science.gov (United States)

    Zhao, Lingyun; Feng, Si-Shen; Kocherginsky, Nikolai; Kostetski, Iouri

    2007-06-29

    Differential scanning calorimetry (DSC) and electron paramagnetic resonance spectroscopy (EPR) were applied to investigate effects of cholesterol component on molecular interactions between paclitaxel, which is one of the best antineoplastic agents found from nature, and dipalmitoylphosphatidylcholine (DPPC) within lipid bilayer vesicles (liposomes), which could also be used as a model cell membrane. DSC analysis showed that incorporation of paclitaxel into the DPPC bilayer causes a reduction in the cooperativity of bilayer phase transition, leading to a looser and more flexible bilayer structure. Including cholesterol component in the DPPC/paclitaxel mixed bilayer can facilitate the molecular interaction between paclitaxel and lipid and make the tertiary system more stable. EPR analysis demonstrated that both of paclitaxel and cholesterol have fluidization effect on the DPPC bilayer membranes although cholesterol has more significant effect than paclitaxel does. The reduction kinetics of nitroxides by ascorbic acid showed that paclitaxel can inhibit the reaction by blocking the diffusion of either the ascorbic acid or nitroxide molecules since the reaction is tested to be a first order one. Cholesterol can remarkably increase the reduction reaction speed. This research may provide useful information for optimizing liposomal formulation of the drug as well as for understanding the pharmacology of paclitaxel.

  14. The pathology of familial breast cancer: Immunohistochemistry and molecular analysis

    International Nuclear Information System (INIS)

    Osin, Pinchas P; Lakhani, Sunil R

    1999-01-01

    Extensive studies of BRCA1- and BRCA2-associated breast tumours have been carried out in the few years since the identification of these familial breast cancer predisposing genes. The morphological studies suggest that BRCA1 tumours differ from BRCA2 tumours and from sporadic breast cancers. Recent progress in immunohistochemistry and molecular biology techniques has enabled in-depth investigation of molecular pathology of these tumours. Studies to date have investigated issues such as steroid hormone receptor expression, mutation status of tumour suppressor genes TP53 and c-erbB2, and expression profiles of cell cycle proteins p21, p27 and cyclin D 1 . Despite relative paucity of data, strong evidence of unique biological characteristics of BRCA1-associated breast cancer is accumulating. BRCA1-associated tumours appear to show an increased frequency of TP53 mutations, frequent p53 protein stabilization and absence of imunoreactivity for steroid hormone receptors. Further studies of larger number of samples of both BRCA1- and BRCA2-associated tumours are necessary to clarify and confirm these observations

  15. Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations.

    Science.gov (United States)

    Timko, Jeff; Kuyucak, Serdar

    2012-11-28

    Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K(+) ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K(+) ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K(+) ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K(+) ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.

  16. Molecular activation analysis for organo-halogen contaminants in yogurt

    International Nuclear Information System (INIS)

    Zhang Hong; Chai Zhifang

    2004-01-01

    The concentrations of total halogen (TX), extractable organo-halogen (EOX), extractable persistent organo-halogen (EPOX), organo-chlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs) in 18 different yogurt specimens of 14 brands from Beijing, Tianjin, Shanghai, Guangzhou and Shijiazhuang were determined by epithermal neutron activation analysis (ENAA), molecular activation analysis (MAA) and GC-Mass Spectrometry (GC-MS), respectively. The results indicated that the halogen in yogurt mainly existed as inorganic species and non-extractable organo-halogen compounds. About 1/3 to 1/4 of EOX was EPOX. Further, EOCl and EPOCl were the main organo-halogen species in yogurt. The average concentration of the unknown organo-chlorine was 96% of the EPOCl. HCHs and DDTs were still the main contaminants of OCPs in the yogurt of interest. Also, PCB202, PCB103 and PCB208 were the main contaminants of PCBs. (authors)

  17. Molecular analysis of radiation-induced mutations in vitro

    International Nuclear Information System (INIS)

    Kronenberg, A.

    1996-01-01

    This review will focus on the nature of specific locus mutations detected in mammalian cells exposed in vitro to different types of ionizing radiations. Ionizing radiation has been shown to produce a wide variety of heritable alterations in DNA. These range from single base pair substitutions to stable loss or translocation of large portions of whole chromosomes. Data will be reviewed for certain test systems that reveal different mutation spectra. Techniques for the analysis of molecular alterations include applications of the polymerase chain reaction, some of which may be coupled with DNA sequence analysis, and a variety of hybridization-based techniques. The complexity of large scale rearrangements is approached with cytogenetic techniques including high resolution banding and various applications of the fluorescence in situ hybridization (FISH) technique. Radiation-induced mutant frequencies and mutation spectra are a function of the linkage constraints on the recovery of viable mutants for a given locus and test system. 44 refs

  18. Epidemiological and molecular investigation of a measles outbreak in Punjab, Pakistan, 2013-2015.

    Science.gov (United States)

    Zaidi, Syed Sohail Zahoor; Hameed, Abdul; Ali, Naeem; Rana, Muhammad Suleman; Umair, Massab; Alam, Muhammad Masroor; Aamir, Uzma Bashir; Khurshid, Adnan; Sharif, Salmaan; Shaukat, Shahzad; Angez, Mehar; Mujtaba, Ghulam; Arshad, Yasir; Akthar, Ribqa; Sufian, Mian Muhammad; Mehmood, Nayab

    2018-04-28

    Despite the availability of an effective vaccine, the measles virus continues to cause significant morbidity and mortality in children worldwide. Molecular characterization of wild-type measles strains is an invaluable component of epidemiological studies or surveillance systems that provides important information pertinent to outbreak linkages and transmission pathways. Serum samples and throat swabs were collected from suspected measles cases from the Punjab province of Pakistan (2013-2015) and further tested for measles immunoglobulin M (IgM) through enzyme-linked immunosorbent assay and reverse-transcriptase polymerase chain reaction for molecular characterization. Among the total of 5415 blood samples, 59% tested positive for measles IgM. Males had a higher infection rate (55%) than females (45%), and the highest frequency of positive cases (63%) was found in the age group of 0 to 5 years. Partial sequencing of the nucleoprotein gene showed that 27 strains belonged to the B3 genotype, whereas 2 viruses were identified as D4. On phylogenetic analysis, Pakistani B3 strains were found to be closely related to previously reported indigenous strains and those from neighboring countries of Iran and Qatar. This is the first report on the detection of the measles B3 genotype from Punjab, Pakistan. The current study shows a high burden of measles infections in Punjab province owing to poor routine immunization coverage in major cities. It is imperative that national health authorities adopt strategic steps on an urgent basis for improvement of routine immunization coverage. Molecular epidemiology of the measles viruses circulating in different parts of the country can provide useful data to manage future outbreaks. © 2018 Wiley Periodicals, Inc.

  19. Binding of carvedilol to serum albumins investigated by multi-spectroscopic and molecular modeling methods

    Energy Technology Data Exchange (ETDEWEB)

    Safarnejad, Azam; Shaghaghi, Masoomeh [Department of Chemistry, Payame Noor University, P.O. Box. 19395-3697, Tehran (Iran, Islamic Republic of); Dehghan, Golamreza [Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz (Iran, Islamic Republic of); Soltani, Somaieh, E-mail: soltanisomaieh@gmail.com [Drug applied research center and pharmacy faculty, Tabriz University of Medical Sciences, Tabriz (Iran, Islamic Republic of)

    2016-08-15

    Carvedilol (CAR) binding to human and bovine serum albumins (HSA and BSA) was studied using fluorescence, UV–vis absorption and Fourier transform infrared spectroscopy (FTIR) and molecular docking techniques at different temperatures (288, 298 and 308 K) under physiologic pH. Results obtained from fluorescence data indicated that values of binding sites (n), effective quenching constants (Ka) and binding constants (K{sub b}) decreased under higher temperature and that the quenching mechanism was static. The thermodynamic parameters including enthalpy (ΔH), entropy (ΔS) and Gibb's free energy (ΔG) changes were calculated by the van't Hoff equation and these data showed that hydrogen bonds and Van der Waals contacts were the main binding force in HSA–CAR and BSA–CAR systems. Binding distance (r) between HSA–CAR and BSA–CAR were calculated by the Förster (fluorescence resonance energy transfer (FRET)) method. FTIR absorption studies showed that the secondary structure was changed according to the interaction of HSA/BSA and CAR. Results determined by molecular docking were in agreement with thermodynamic and FRET data and confirmed that the binding mechanism of Carvedilol to HSA and BSA is different. - Highlights: • The quenching mechanism between Carvedilol and HSA /BSA is a static process. • Hydrogen bonds and Van der Waals contacts were stabilized the Carvedilol albumin complexes. • Molecular modeling simulations confirmed the fluorescence spectroscopy and FRET analysis. • According to the binding mechanism differences between HSA and BSA, the results of BSA experiments could not be applied for HSA binding.

  20. Young's moduli of carbon materials investigated by various classical molecular dynamics schemes

    Science.gov (United States)

    Gayk, Florian; Ehrens, Julian; Heitmann, Tjark; Vorndamme, Patrick; Mrugalla, Andreas; Schnack, Jürgen

    2018-05-01

    For many applications classical carbon potentials together with classical molecular dynamics are employed to calculate structures and physical properties of such carbon-based materials where quantum mechanical methods fail either due to the excessive size, irregular structure or long-time dynamics. Although such potentials, as for instance implemented in LAMMPS, yield reasonably accurate bond lengths and angles for several carbon materials such as graphene, it is not clear how accurate they are in terms of mechanical properties such as for instance Young's moduli. We performed large-scale classical molecular dynamics investigations of three carbon-based materials using the various potentials implemented in LAMMPS as well as the EDIP potential of Marks. We show how the Young's moduli vary with classical potentials and compare to experimental results. Since classical descriptions of carbon are bound to be approximations it is not astonishing that different realizations yield differing results. One should therefore carefully check for which observables a certain potential is suited. Our aim is to contribute to such a clarification.

  1. Investigation of the silicon ion density during molecular beam epitaxy growth

    CERN Document Server

    Eifler, G; Ashurov, K; Morozov, S

    2002-01-01

    Ions impinging on a surface during molecular beam epitaxy influence the growth and the properties of the growing layer, for example, suppression of dopant segregation and the generation of crystal defects. The silicon electron gun in the molecular beam epitaxy (MBE) equipment is used as a source for silicon ions. To use the effect of ion bombardment the mechanism of generation and distribution of ions was investigated. A monitoring system was developed and attached at the substrate position in the MBE growth chamber to measure the ion and electron densities towards the substrate. A negative voltage was applied to the substrate to modify the ion energy and density. Furthermore the current caused by charge carriers impinging on the substrate was measured and compared with the results of the monitoring system. The electron and ion densities were measured by varying the emission current of the e-gun achieving silicon growth rates between 0.07 and 0.45 nm/s and by changing the voltage applied to the substrate betw...

  2. Quantum chemical molecular dynamical investigation of alkyl nitrite photo-dissociated on copper surfaces

    International Nuclear Information System (INIS)

    Wang Xiaojing; Wang Wei; Han Peilin; Kubo, Momoji; Miyamoto, Akira

    2008-01-01

    An accelerated quantum chemical molecular dynamical code 'Colors-Excite' was used to investigate the photolysis of alkyl nitrites series, RONO (R=CH 3 and C(CH 3 ) 3 ) on copper surfaces. Our calculations showed that the photo-dissociated processes are associated with the alkyl substituents of RONO when adsorbed on copper surfaces. For R=CH 3 , a two-step photolysis reaction occurred, yielding diverse intermediate products including RO radical, NO, and HNO, consistent with those reported in gas phase. While for R=C(CH 3 ) 3 , only one-step photolysis reaction occurred and gave intermediate products of RO radical and NO. Consequently, pure RO species were achieved to adsorb on metal surfaces by removing the NO species in photolysis reaction. The detailed photo-dissociated behaviors of RONO on copper surfaces with different alkyl substituents which are uncovered by the present simulation can be extended to explain the diverse dissociative mechanism experimentally observed. The quantum chemical molecular dynamical code 'Colors-Excite' is proved to be highly applicable to the photo-dissociations on metal surfaces

  3. Molecular-orbital and structural descriptors in theoretical investigation of electroreduction of nitrodiazoles

    Directory of Open Access Journals (Sweden)

    BRANKO KOLARIC

    2005-07-01

    Full Text Available It is shown how a simple theoretical approach can be used for the investigation of electro-organic reactions.Mononitroimidazoles and mononitropyrazoles were studied by the semiempirical MNDO-PM3 molecular orbital method. The electrochemical reduction potentials of diazoles have been correlated with the energy of the lowest unoccupied molecular orbital (LUMO. It was found that an admirable correlation could be obtained by the introduction of simple structural descriptors as a correction to the energy of the LUMO. The interaction of a molecule with its surrounding depends on electrostatic potential and on steric hindrance. Most of these steric effects are taken into account using two parameters having a very limited set of integer values. The first (b is the position of a ring substituent regarding ring nitrogens, which accounts for the different orientations of dipole moments and for the different shape of the electrostatic potential. The second (structural parameter (t is the type of the ring, which accounts mostly for different modes of electrode approach, and for different charge polarization patterns in two diazole rings. The extended correlation with ELUMO, b and t, is very good, having a regression coefficient r = 0.991. The intrinsic importance of b and t is exemplified by their high statistical weight.

  4. Molecular Dynamics Investigation of Cl− and Water Transport through a Eukaryotic CLC Transporter

    Science.gov (United States)

    Cheng, Mary Hongying; Coalson, Rob D.

    2012-01-01

    Early crystal structures of prokaryotic CLC proteins identified three Cl– binding sites: internal (Sint), central (Scen), and external (Sext). A conserved external GLU (GLUex) residue acts as a gate competing for Sext. Recently, the first crystal structure of a eukaryotic transporter, CmCLC, revealed that in this transporter GLUex competes instead for Scen. Here, we use molecular dynamics simulations to investigate Cl– transport through CmCLC. The gating and Cl–/H+ transport cycle are inferred through comparative molecular dynamics simulations with protonated and deprotonated GLUex in the presence/absence of external potentials. Adaptive biasing force calculations are employed to estimate the potential of mean force profiles associated with transport of a Cl– ion from Sext to Sint, depending on the Cl– occupancy of other sites. Our simulations demonstrate that protonation of GLUex is essential for Cl– transport from Sext to Scen. The Scen site may be occupied by two Cl– ions simultaneously due to a high energy barrier (∼8 Kcal/mol) for a single Cl– ion to translocate from Scen to Sint. Binding two Cl– ions to Scen induces a continuous water wire from Scen to the extracellular solution through the side chain of the GLUex gate. This may initiate deprotonation of GLUex, which then drives the two Cl– ions out of Scen toward the intracellular side via two putative Cl– transport paths. Finally, a conformational cycle is proposed that would account for the exchange stoichiometry. PMID:22455919

  5. Raman investigation of GaP–Si interfaces grown by molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Bondi, A.; Cornet, C.; Boyer, S.; Nguyen Thanh, T.; Létoublon, A.; Pedesseau, L.; Durand, O. [Université Européenne de Bretagne, INSA, FOTON, UMR CNRS 6082, 20 Avenue des Buttes de Coësmes, F-35708 Rennes (France); Moreac, A. [Institut de Physique de Rennes, UMR-CNRS n°6251, Université Rennes1, Campus de Beaulieu — 35042 Rennes cedex (France); Ponchet, A. [CEMES, UPR CNRS 8011, F-31055 Toulouse (France); Le Corre, A. [Université Européenne de Bretagne, INSA, FOTON, UMR CNRS 6082, 20 Avenue des Buttes de Coësmes, F-35708 Rennes (France); Even, J., E-mail: jacky.even@insa.rennes.fr [Université Européenne de Bretagne, INSA, FOTON, UMR CNRS 6082, 20 Avenue des Buttes de Coësmes, F-35708 Rennes (France)

    2013-08-31

    Raman spectroscopy was used to investigate the residual strain in thin GaP layers deposited on Si substrates by molecular beam epitaxy. Different growth conditions were used to obtain a clean GaP–Si interface, including migration enhanced epitaxy. The strain induced Raman shifts of the longitudinal and the transverse optical GaP lattice modes were analyzed. The effects of crystalline defects are discussed, supported by high resolution transmission electron microscopy and X-ray scattering studies. Finally, Raman Spectroscopy reveals the presence of disorder (or surface)-activated optical phonons. This result is discussed in the light of surface morphology analyses. - Highlights: ► GaP thin layers grown by molecular beam epitaxy on Si substrates. ► Strain-induced Raman shifts of the optical GaP modes are analyzed. ► Simulation of optical GaP modes by density functional perturbation theory. ► Comparison with X-ray diffraction and electron and scanning probe microscopy data.

  6. Investigation of arc repressor DNA-binding specificity by comparative molecular dynamics simulations.

    Science.gov (United States)

    Song, Wei; Guo, Jun-Tao

    2015-01-01

    Transcription factors regulate gene expression through binding to specific DNA sequences. How transcription factors achieve high binding specificity is still not well understood. In this paper, we investigated the role of protein flexibility in protein-DNA-binding specificity by comparative molecular dynamics (MD) simulations. Protein flexibility has been considered as a key factor in molecular recognition, which is intrinsically a dynamic process involving fine structural fitting between binding components. In this study, we performed comparative MD simulations on wild-type and F10V mutant P22 Arc repressor in both free and complex conformations. The F10V mutant has lower DNA-binding specificity though both the bound and unbound main-chain structures between the wild-type and F10V mutant Arc are highly similar. We found that the DNA-binding motif of wild-type Arc is structurally more flexible than the F10V mutant in the unbound state, especially for the six DNA base-contacting residues in each dimer. We demonstrated that the flexible side chains of wild-type Arc lead to a higher DNA-binding specificity through forming more hydrogen bonds with DNA bases upon binding. Our simulations also showed a possible conformational selection mechanism for Arc-DNA binding. These results indicate the important roles of protein flexibility and dynamic properties in protein-DNA-binding specificity.

  7. Investigation of molecular markers related to fecundity in local egyptian sheep

    International Nuclear Information System (INIS)

    Hassanin, W.F.E.

    2011-01-01

    The present experimental work aimed to investigate a number of molecular makers that influence fecundity in local Egyptian sheep. In the present study, twenty two (11 twin producing crossbred ewes, 7 single lamb producing crossbred ewes, 2 crossbred rams from twin producing ewes and 2 pure bred rams from twin producing ewes) were tested. They were carefully selected from the records of the Egyptian Nuclear Research Centre. The ewes were selected for their twin production in three repetitive production cycles while the rams were selected for being produced from prolific ewes as above. The presence of the booroola fecundity gene (FecB) (FecB mutation in bone morphogenic protein receptor gene 1B (BMPR1B)) and the Inverdale gene (FecX I ) (FecX I mutation in bone morphogenic receptor gene (BMP15)) using Forced restriction PCR of the FecB and FecX I mutations, 190 base pair (bp) was amplified using specific primer which was forward (5 ' -CCAGAGGACAATAGCAAAGCAAA -3 ' ) and reverse (5 ' -CAAGATGTTTTCATGCCTCATCAACAGGTC -3 ' ) and designed to introduce a point mutation in the resulting PCR products with FecB carrier sheep containing an AvaII restriction site (G|GACC). The FecB DNA test showed that there were no carriers for the FecB mutation in the selected prolific sheep sample. When a specific primer which was forward (5 ' -GAAGTAACCAGTGTTCCCTCCACCCTTTTCT-3 ' ) and reverse (5 ' -CATGATTGGGAGAATTGAGACC-3 ' ) used to test the presence of FecX I mutation no amplification resulted from DNA samples of the twin producing ewes while two amplified DNA fragments of molecular size 154 bp and 120 bp resulted from the single lamb producing females and male sheep under study. Serum samples were collected from sheep under study and tested using totallab 120 computer software analyses for Native protein gel images. Gel images revealed a protein pattern in twin producing ewe samples characterized by the presence of three bands with molecular weights 679.7, 524.3, and 431.1 kd and the

  8. [Molecular cytogenetic analysis of a case with ring chromosome 3 syndrome].

    Science.gov (United States)

    Zhang, Kaihui; Song, Fengling; Zhang, Dongdong; Zhang, Haiyan; Wang, Ying; Dong, Rui; Zhang, Yufeng; Liu, Yi; Gai, Zhongtao

    2016-12-10

    To investigate the genetic cause for a child with developmental delay and congenital heart disease through molecular cytogenetic analysis. G-banded karyotyping and chromosomal microarray analysis (CMA) were performed for the patient and his parents. The proband's karyotype was detected as ring chromosome 3, and a 3q26.3-25.3 deletion encompassing 45 genes has been found with CMA. Testing of both parents was normal. Clinical phenotype of the patient with ring chromosome 3 mainly depends on the involved genes. It is necessary to combine CMA and karyotyping for the diagnosis of ring chromosome, as CMA can provide more accurate information for variations of the genome.

  9. Investigation of impurity defects in α-iron by molecular dynamics method

    International Nuclear Information System (INIS)

    Kevorkyan, Yu.R.

    1986-01-01

    Investigation of the configuration of impurity defects in α-iron by the molecular dynamics method is presented. The Jhonson model potential has been used to calculate the interaction of matrix atoms. The impurity-matrix atom interaction is described by the same form of the potential shifted along the axis of interatomic distances for a definite value. The correspondence between the shift value and change in the radius of the impurity defect is established on the basis of calculation of the relaxation volume. Possible configurations of the impurity - interstitial matrix atom complexes are obtained for the given model of the impurity defect, dimensional boundaries of possible transitions between different configurations are determined. Formation and bound energies, relaxation volumes of impurity defects are calculated

  10. Plastic protein microarray to investigate the molecular pathways of magnetic nanoparticle-induced nanotoxicity

    International Nuclear Information System (INIS)

    Liu Yingshuai; Li Xuelian; Bao Shujuan; Lu Zhisong; Li Changming; Li Qing

    2013-01-01

    Superparamagnetic iron oxide nanoparticles (SPIONs) (about 15 nm) were synthesized via a hydrothermal method and characterized by field emission scanning electron microscopy, transmission electron microscopy, dynamic light scattering, x-ray diffraction, and vibrating sample magnetometer. The molecular pathways of SPIONs-induced nanotoxicity was further investigated by protein microarrays on a plastic substrate from evaluation of cell viability, reactive oxygen species (ROS) generation and cell apoptosis. The experimental results reveal that 50 μg ml −1 or higher levels of SPIONs cause significant loss of cell viability, considerable generation of ROS and cell apoptosis. It is proposed that high level SPIONs could induce cell apoptosis via a mitochondria-mediated intrinsic pathway by activation of caspase 9 and caspase 3, an increase of the Bax/Bcl-2 ratio, and down-regulation of HSP70 and HSP90 survivor factors. (paper)

  11. Plastic protein microarray to investigate the molecular pathways of magnetic nanoparticle-induced nanotoxicity

    Science.gov (United States)

    Liu, Yingshuai; Li, Xuelian; Bao, Shujuan; Lu, Zhisong; Li, Qing; Li, Chang Ming

    2013-05-01

    Superparamagnetic iron oxide nanoparticles (SPIONs) (about 15 nm) were synthesized via a hydrothermal method and characterized by field emission scanning electron microscopy, transmission electron microscopy, dynamic light scattering, x-ray diffraction, and vibrating sample magnetometer. The molecular pathways of SPIONs-induced nanotoxicity was further investigated by protein microarrays on a plastic substrate from evaluation of cell viability, reactive oxygen species (ROS) generation and cell apoptosis. The experimental results reveal that 50 μg ml-1 or higher levels of SPIONs cause significant loss of cell viability, considerable generation of ROS and cell apoptosis. It is proposed that high level SPIONs could induce cell apoptosis via a mitochondria-mediated intrinsic pathway by activation of caspase 9 and caspase 3, an increase of the Bax/Bcl-2 ratio, and down-regulation of HSP70 and HSP90 survivor factors.

  12. Investigation of the molecular level interactions between mucins and food proteins: Spectroscopic, tribological and rheological studies

    DEFF Research Database (Denmark)

    Celebioglu, Hilal Yilmaz

    The thesis investigated the structure and molecular-level interaction of β-lactoglobulin (BLG) and mucins, representing major components of the dairy products and saliva/digestion systems, respectively. Mucins are long glycoprotein molecules responsible for the gel nature of the mucous layer covers...... epithelial surfaces throughout the body. A literature review of the interactions of different mucin types and saliva mucins with several food proteins and food protein emulsions, as well as their functional properties related to the food oral processing is presented at the first chapter of the thesis (Paper...... V). Most of the studies suggest an electrostatic attraction between positively charged food proteins with negatively charged moieties of mucins (mainly on glycosylated region of mucins). The structural changes occurring during the interaction between BLG, the major whey protein, and bovine...

  13. Investigations of transport properties of molten sodium fluoride using molecular dynamics simulations

    International Nuclear Information System (INIS)

    Chattaraj, D.; Dash, Smruti

    2013-01-01

    The thermal conductivity and coefficient of shear viscosity of molten sodium fluoride were calculated using Green-Kubo equilibrium molecular dynamics (EMD) simulation. The Green-Kubo method is an equilibrium technique based on the fluctuation-dissipation theorem of statistical thermodynamics. The canonical ensemble (N, V, T) was used in the MD simulation to obtain the transport properties of molten NaF. In this simulation, several state points were investigated using the Born-Meyer-Huggins-Tosi-Fumi interionic potential model. The electrostatic interactions present in this ionic fluid were calculated through the Ewald method. The results obtained in this study were found to be in good agreement with the reported experimental data. (author)

  14. Molecular Level Investigation of Staphylococci’s Resistance Mechanisms to Antibiotics

    Directory of Open Access Journals (Sweden)

    Lavinia Lorena PRUTEANU

    2017-09-01

    Full Text Available Polymerase chain reaction (PCR techniques development allows elaboration of many assays for identification of bacteria’s resistance mechanisms to antibiotics. Following this idea, the results of molecular level investigation of bacteria’s resistance mechanisms to antibiotics may give many opportunities to find more rapid methods for identifying the genes which are responsible for antibiotic resistance induction. The aim of this study was to investigate antibiotic resistance genes in Staphylococcus bacteria on molecular level. As classes of antibiotics it was used macrolides-lincosamides-streptogramin B (MLSB and beta-lactams. In the proposed study the bacterial strains are represented by 50 isolates of Staphylococcus. The bacterial strains were analyzed using polymerase chain reaction to identify the nuc, tuf, tst, sea, pathogenic activity genes. After this, the bacteria were tested for ermA, ermB, ermC genes and for mecA, femA which are involved in resistance to macrolides, lincosamides, streptogramin B and to beta-lactams, respectively. The presence or the absence of these genes confirms that tested strains are resistant to specific antibiotic or not. Bacteria pathogenic activity was emphasized by genes as follows: sea (enterotoxin which was found at all isolates, tst (toxic shock toxin gene was not detected in any of isolates and tuf gene (elongation factor was obtained with one pair of primers. Resistance to beta-lactams was evidenced by the presence of mecA in all isolates and femA in some strains. Each of ermC, ermA and ermB, macrolides-lincosamides-streptogramin B resistance genes, were detected.

  15. Molecular analysis of precursor lesions in familial pancreatic cancer.

    Directory of Open Access Journals (Sweden)

    Tatjana Crnogorac-Jurcevic

    Full Text Available With less than a 5% survival rate pancreatic adenocarcinoma (PDAC is almost uniformly lethal. In order to make a significant impact on survival of patients with this malignancy, it is necessary to diagnose the disease early, when curative surgery is still possible. Detailed knowledge of the natural history of the disease and molecular events leading to its progression is therefore critical.We have analysed the precursor lesions, PanINs, from prophylactic pancreatectomy specimens of patients from four different kindreds with high risk of familial pancreatic cancer who were treated for histologically proven PanIN-2/3. Thus, the material was procured before pancreatic cancer has developed, rather than from PanINs in a tissue field that already contains cancer. Genome-wide transcriptional profiling using such unique specimens was performed. Bulk frozen sections displaying the most extensive but not microdissected PanIN-2/3 lesions were used in order to obtain the holistic view of both the precursor lesions and their microenvironment. A panel of 76 commonly dysregulated genes that underlie neoplastic progression from normal pancreas to PanINs and PDAC were identified. In addition to shared genes some differences between the PanINs of individual families as well as between the PanINs and PDACs were also seen. This was particularly pronounced in the stromal and immune responses.Our comprehensive analysis of precursor lesions without the invasive component provides the definitive molecular proof that PanIN lesions beget cancer from a molecular standpoint. We demonstrate the need for accumulation of transcriptomic changes during the progression of PanIN to PDAC, both in the epithelium and in the surrounding stroma. An identified 76-gene signature of PDAC progression presents a rich candidate pool for the development of early diagnostic and/or surveillance markers as well as potential novel preventive/therapeutic targets for both familial and sporadic

  16. Gene Expression Profiling as a Tool to Investigate the Molecular Machinery Activated during Hippocampal Neurodegeneration Induced by Trimethyltin (TMT Administration

    Directory of Open Access Journals (Sweden)

    Maria Concetta Geloso

    2013-08-01

    Full Text Available Trimethyltin (TMT is an organotin compound exhibiting neurotoxicant effects selectively localized in the limbic system and especially marked in the hippocampus, in both experimental animal models and accidentally exposed humans. TMT administration causes selective neuronal death involving either the granular neurons of the dentate gyrus or the pyramidal cells of the Cornu Ammonis, with a different pattern of localization depending on the different species studied or the dosage schedule. TMT is broadly used to realize experimental models of hippocampal neurodegeneration associated with cognitive impairment and temporal lobe epilepsy, though the molecular mechanisms underlying the associated selective neuronal death are still not conclusively clarified. Experimental evidence indicates that TMT-induced neurodegeneration is a complex event involving different pathogenetic mechanisms, probably acting differently in animal and cell models, which include neuroinflammation, intracellular calcium overload, and oxidative stress. Microarray-based, genome-wide expression analysis has been used to investigate the molecular scenario occurring in the TMT-injured brain in different in vivo and in vitro models, producing an overwhelming amount of data. The aim of this review is to discuss and rationalize the state-of-the-art on TMT-associated genome wide expression profiles in order to identify comparable and reproducible data that may allow focusing on significantly involved pathways.

  17. An investigation on the mechanism of sublimed DHB matrix on molecular ion yields in SIMS imaging of brain tissue.

    Science.gov (United States)

    Dowlatshahi Pour, Masoumeh; Malmberg, Per; Ewing, Andrew

    2016-05-01

    We have characterized the use of sublimation to deposit matrix-assisted laser desorption/ionization (MALDI) matrices in secondary ion mass spectrometry (SIMS) analysis, i.e. matrix-enhanced SIMS (ME-SIMS), a common surface modification method to enhance sensitivity for larger molecules and to increase the production of intact molecular ions. We use sublimation to apply a thin layer of a conventional MALDI matrix, 2,5-dihydroxybenzoic acid (DHB), onto rat brain cerebellum tissue to show how this technique can be used to enhance molecular yields in SIMS while still retaining a lateral resolution around 2 μm and also to investigate the mechanism of this enhancement. The results here illustrate that cholesterol, which is a dominant lipid species in the brain, is decreased on the tissue surface after deposition of matrix, particularly in white matter. The decrease of cholesterol is followed by an increased ion yield of several other lipid species. Depth profiling of the sublimed rat brain reveals that the lipid species are de facto extracted by the DHB matrix and concentrated in the top most layers of the sublimed matrix. This extraction/concentration of lipids directly leads to an increase of higher mass lipid ion yield. It is also possible that the decrease of cholesterol decreases the potential suppression of ion yield caused by cholesterol migration to the tissue surface. This result provides us with significant insights into the possible mechanisms involved when using sublimation to deposit this matrix in ME-SIMS.

  18. Nutritional Proteomics: Investigating molecular mechanisms underlying the health beneficial effect of functional foods

    Directory of Open Access Journals (Sweden)

    Yusuke Kawashima

    2013-07-01

    Full Text Available ABSTRACTObjective: We introduce a new technical and conceptual term “nutritional proteomics” by identifying and quantifying the proteins and their changes in a certain organ or tissue dependent on the food intake by utilizing a mass spectrometry-based proteomics technique.Purpose: Food intake is essentially important for every life on earth to sustain the physical as well as mental functions. The outcome of food intake will be manifested in the health state and its dysfunction. The molecular information about the protein expression change caused by diets will assist us to understand the significance of functional foods. We wish to develop nutritional proteomics to promote a new area in functional food studies for a better understanding of the role of functional foods in health and disease.Methods: We chose two classes of food ingredients to show the feasibility of nutritional proteomics, omega-3 polyunsaturated fatty acids and omega-6 polyunsaturated fatty acids both of which are involved in the inflammation/anti-inflammation axis. Each class of the polyunsaturated fatty acids was mixed in mouse chow respectively. The liver tissue of mice fed with omega-3 diet or omega-3 diet was analyzed by the state-of-the-art shotgun proteomics using nano-HPLC-ESI-MS/MS. The data were analyzed by the number of differentially expressed proteins that were guaranteed by 1% false discovery rate for protein identification and by the statistical significance of variance evaluated by p-value in two-tailed distribution analysis better than 0.05 (n=4. The differential pattern of protein expression was characterized with Gene Ontology designation.Results: The data analysis of the shotgun nutritional proteomics identified 2,810 proteins that are validated with 1% FDR. Among these 2,810 proteins, 125 were characterized with statistical significance of variance (p<0.05; n=4 between the omega-3 diet and the omega-6 diet by twotailed distribution analysis. The results

  19. Genetic diversity analysis of common beans based on molecular markers

    Directory of Open Access Journals (Sweden)

    Homar R. Gill-Langarica

    Full Text Available A core collection of the common bean (Phaseolus vulgaris L., representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each, as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP +3/+3 primer combinations and seven simple sequence repeats (SSR loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA and molecular variance (AMOVA analyses. AFLP analysis produced 530 bands (88.5% polymorphic while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus. AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

  20. Genetic diversity analysis of common beans based on molecular markers

    Directory of Open Access Journals (Sweden)

    Homar R. Gill-Langarica

    2011-01-01

    Full Text Available A core collection of the common bean (Phaseolus vulgaris L., representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each, as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP +3/+3 primer combinations and seven simple sequence repeats (SSR loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA and molecular variance (AMOVA analyses. AFLP analysis produced 530 bands (88.5% polymorphic while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus. AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

  1. Genetic diversity of popcorn genotypes using molecular analysis.

    Science.gov (United States)

    Resh, F S; Scapim, C A; Mangolin, C A; Machado, M F P S; do Amaral, A T; Ramos, H C C; Vivas, M

    2015-08-19

    In this study, we analyzed dominant molecular markers to estimate the genetic divergence of 26 popcorn genotypes and evaluate whether using various dissimilarity coefficients with these dominant markers influences the results of cluster analysis. Fifteen random amplification of polymorphic DNA primers produced 157 amplified fragments, of which 65 were monomorphic and 92 were polymorphic. To calculate the genetic distances among the 26 genotypes, the complements of the Jaccard, Dice, and Rogers and Tanimoto similarity coefficients were used. A matrix of Dij values (dissimilarity matrix) was constructed, from which the genetic distances among genotypes were represented in a more simplified manner as a dendrogram generated using the unweighted pair-group method with arithmetic average. Clusters determined by molecular analysis generally did not group material from the same parental origin together. The largest genetic distance was between varieties 17 (UNB-2) and 18 (PA-091). In the identification of genotypes with the smallest genetic distance, the 3 coefficients showed no agreement. The 3 dissimilarity coefficients showed no major differences among their grouping patterns because agreement in determining the genotypes with large, medium, and small genetic distances was high. The largest genetic distances were observed for the Rogers and Tanimoto dissimilarity coefficient (0.74), followed by the Jaccard coefficient (0.65) and the Dice coefficient (0.48). The 3 coefficients showed similar estimations for the cophenetic correlation coefficient. Correlations among the matrices generated using the 3 coefficients were positive and had high magnitudes, reflecting strong agreement among the results obtained using the 3 evaluated dissimilarity coefficients.

  2. Genetic diversity analysis of common beans based on molecular markers.

    Science.gov (United States)

    Gill-Langarica, Homar R; Muruaga-Martínez, José S; Vargas-Vázquez, M L Patricia; Rosales-Serna, Rigoberto; Mayek-Pérez, Netzahualcoyotl

    2011-10-01

    A core collection of the common bean (Phaseolus vulgaris L.), representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico) Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

  3. A network-based biomarker approach for molecular investigation and diagnosis of lung cancer

    Directory of Open Access Journals (Sweden)

    Chen Bor-Sen

    2011-01-01

    Full Text Available Abstract Background Lung cancer is the leading cause of cancer deaths worldwide. Many studies have investigated the carcinogenic process and identified the biomarkers for signature classification. However, based on the research dedicated to this field, there is no highly sensitive network-based method for carcinogenesis characterization and diagnosis from the systems perspective. Methods In this study, a systems biology approach integrating microarray gene expression profiles and protein-protein interaction information was proposed to develop a network-based biomarker for molecular investigation into the network mechanism of lung carcinogenesis and diagnosis of lung cancer. The network-based biomarker consists of two protein association networks constructed for cancer samples and non-cancer samples. Results Based on the network-based biomarker, a total of 40 significant proteins in lung carcinogenesis were identified with carcinogenesis relevance values (CRVs. In addition, the network-based biomarker, acting as the screening test, proved to be effective in diagnosing smokers with signs of lung cancer. Conclusions A network-based biomarker using constructed protein association networks is a useful tool to highlight the pathways and mechanisms of the lung carcinogenic process and, more importantly, provides potential therapeutic targets to combat cancer.

  4. Investigation of the complex reaction coordinate of acid catalyzed amide hydrolysis from molecular dynamics simulations

    International Nuclear Information System (INIS)

    Zahn, Dirk

    2004-01-01

    The rate-determining step of acid catalyzed peptide hydrolysis is the nucleophilic attack of a water molecule to the carbon atom of the amide group. Therein the addition of the hydroxyl group to the amide carbon atom involves the association of a water molecule transferring one of its protons to an adjacent water molecule. The protonation of the amide nitrogen atom follows as a separate reaction step. Since the nucleophilic attack involves the breaking and formation of several bonds, the underlying reaction coordinate is rather complex. We investigate this reaction step from path sampling Car-Parrinello molecular dynamics simulations. This approach does not require the predefinition of reaction coordinates and is thus particularly suited for investigating reaction mechanisms. From our simulations the most relevant components of the reaction coordinate are elaborated. Though the C···O distance of the oxygen atom of the water molecule performing the nucleophilic attack and the corresponding amide carbon atom is a descriptor of the reaction progress, a complete picture of the reaction coordinate must include all three molecules taking part in the reaction. Moreover, the proton transfer is found to depend on favorable solvent configurations. Thus, also the arrangement of non-reacting, i.e. solvent water molecules needs to be considered in the reaction coordinate

  5. Low energy Cu clusters slow deposition on a Fe (001) surface investigated by molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Shixu [School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); Laboratory of Advanced Nuclear Materials, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Gong, Hengfeng [School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); Division of Nuclear Materials Science and Engineering, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800 (China); Chen, Xuanzhi [School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); Li, Gongping, E-mail: ligp@lzu.edu.cn [School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); Wang, Zhiguang, E-mail: zhgwang@impcas.ac.cn [Laboratory of Advanced Nuclear Materials, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China)

    2014-09-30

    Highlights: • We study the deposition of low energy Cu clusters on Fe (001) surface by molecular dynamics. • The interaction between low energy cluster and substrate can be divided to the landing and the thermal diffusion phases. • The phenomenon of contact epitaxy of cluster occurred. • The thermal diffusion of cluster atoms was analyzed. - Abstract: The slow deposition of low energy Cu clusters on a Fe (001) surface was investigated by molecular dynamics simulation. A many-body potential based on Finnis–Sinclair model was used to describe the interactions among atoms. Three clusters comprising of 13, 55 and 147 atoms, respectively, were deposited with incident energies ranging from 0.0 to 1.0 eV/atom at various substrate temperatures (0, 300 and 800 K). The rearrangement and the diffusion of cluster can occur, only when the cluster atoms are activated and obtained enough migration energy. The interaction between low energy cluster and substrate can be divided to the landing and the thermal diffusion phases. In the former, the migration energy originates from the latent heat of binding energy for the soft deposition regime and primarily comes from the incident energy of cluster for the energetic cluster deposition regime. In the latter, the thermal vibration would result in some cluster atoms activated again at medium and high substrate temperatures. Also, the effects of incident energy, cluster size and substrate temperature on the interaction potential energy between cluster and substrate, the final deposition morphology of cluster, the spreading index and the structure parameter of cluster are analyzed.

  6. Investigation of the silicon ion density during molecular beam epitaxy growth

    Science.gov (United States)

    Eifler, G.; Kasper, E.; Ashurov, Kh.; Morozov, S.

    2002-05-01

    Ions impinging on a surface during molecular beam epitaxy influence the growth and the properties of the growing layer, for example, suppression of dopant segregation and the generation of crystal defects. The silicon electron gun in the molecular beam epitaxy (MBE) equipment is used as a source for silicon ions. To use the effect of ion bombardment the mechanism of generation and distribution of ions was investigated. A monitoring system was developed and attached at the substrate position in the MBE growth chamber to measure the ion and electron densities towards the substrate. A negative voltage was applied to the substrate to modify the ion energy and density. Furthermore the current caused by charge carriers impinging on the substrate was measured and compared with the results of the monitoring system. The electron and ion densities were measured by varying the emission current of the e-gun achieving silicon growth rates between 0.07 and 0.45 nm/s and by changing the voltage applied to the substrate between 0 to -1000 V. The dependencies of ion and electron densities were shown and discussed within the framework of a simple model. The charged carrier densities measured with the monitoring system enable to separate the ion part of the substrate current and show its correlation to the generation rate. Comparing the ion density on the whole substrate and in the center gives a hint to the ion beam focusing effect. The maximum ion and electron current densities obtained were 0.40 and 0.61 μA/cm2, respectively.

  7. Linking healthcare associated norovirus outbreaks: a molecular epidemiologic method for investigating transmission

    Directory of Open Access Journals (Sweden)

    Andrews Nick

    2006-07-01

    Full Text Available Abstract Background Noroviruses are highly infectious pathogens that cause gastroenteritis in the community and in semi-closed institutions such as hospitals. During outbreaks, multiple units within a hospital are often affected, and a major question for control programs is: are the affected units part of the same outbreak or are they unrelated transmission events? In practice, investigators often assume a transmission link based on epidemiological observations, rather than a systematic approach to tracing transmission. Here, we present a combined molecular and statistical method for assessing: 1 whether observed clusters provide evidence of local transmission and 2 the probability that anecdotally|linked outbreaks truly shared a transmission event. Methods 76 healthcare associated outbreaks were observed in an active and prospective surveillance scheme of 15 hospitals in the county of Avon, England from April 2002 to March 2003. Viral RNA from 64 out of 76 specimens from distinct outbreaks was amplified by reverse transcription-PCR and was sequenced in the polymerase (ORF 1 and capsid (ORF 2 regions. The genetic diversity, at the nucleotide level, was analysed in relation to the epidemiological patterns. Results Two out of four genetic and epidemiological clusters of outbreaks were unlikely to have occurred by chance alone, thus suggesting local transmission. There was anecdotal epidemiological evidence of a transmission link among 5 outbreaks pairs. By combining this epidemiological observation with viral sequence data, the evidence of a link remained convincing in 3 of these pairs. These results are sensitive to prior beliefs of the strength of epidemiological evidence especially when the outbreak strains are common in the background population. Conclusion The evidence suggests that transmission between hospitals units does occur. Using the proposed criteria, certain hypothesized transmission links between outbreaks were supported while

  8. Molecular dynamics investigations of BioH protein substrate specificity for biotin synthesis.

    Science.gov (United States)

    Xue, Qiao; Cui, Ying-Lu; Zheng, Qing-Chuan; Zhang, Hong-Xing

    2016-05-01

    BioH, an enzyme of biotin synthesis, plays an important role in fatty acid synthesis which assembles the pimelate moiety. Pimeloyl-acyl carrier protein (ACP) methyl ester, which is long known to be a biotin precursor, is the physiological substrate of BioH. Azelayl methyl ester, which has a longer chain than pimeloyl methyl ester, conjugated to ACP is also indeed accepted by BioH with very low rate of hydrolysis. To date, the substrate specificity for BioH and the molecular origin for the experimentally observed rate changes of hydrolysis by the chain elongation have remained elusive. To this end, we have investigated chain elongation effects on the structures by using the fully atomistic molecular dynamics simulations combined with binding free energy calculations. The results indicate that the substrate specificity is determined by BioH together with ACP. The added two methylenes would increase the structural flexibility by protein motions at the interface of ACP and BioH, instead of making steric clashes with the side chains of the BioH hydrophobic cavity. On the other hand, the slower hydrolysis of azelayl substrate is suggested to be associated with the loose of contacts between BioH and ACP, and with the lost electrostatic interactions of two ionic/hydrogen bonding networks at the interface of the two proteins. The present study provides important insights into the structure-function relationships of the complex of BioH with pimeloyl-ACP methyl ester, which could contribute to further understanding about the mechanism of the biotin synthetic pathway, including the catalytic role of BioH.

  9. Experimental, molecular docking investigations and bioavailability study on the inclusion complexes of finasteride and cyclodextrins

    Directory of Open Access Journals (Sweden)

    Mady FM

    2017-06-01

    Full Text Available Fatma M Mady,1,2 Usama Farghaly Aly2 1Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Taibah University, Medina, Saudi Arabia; 2Department of Pharmaceutics, Faculty of Pharmacy, Minia University, Minia, Egypt Abstract: Finasteride (FIN is a Class II candidate of the Biopharmaceutics Classification System (BCS. The lipophilic cavity of cyclodextrins (CyDs enables it to construct a non-covalent inclusion complex with different insoluble drugs. Only β-cyclodextrin (β-CyD and hydroxypropyl-β-CyD (HP-β-CyD have been previously examined with FIN. This study aimed to investigate the consistence of FIN with different kinds of β-CyDs, including dimethyl-β-cyclodextrin (DM-β-CyD, carboxymethyl-β-cyclodextrin (CM-β-CyD, HP-β-CyD, sulfobutyl ether-β-cyclodextrin (SBE-β-CyD, and β-CyD, by the coprecipitation method. The resultant inclusion systems were characterized by differential scanning calorimetry, infrared spectroscopy, X-ray diffractometry, and dissolution studies. Moreover, molecular docking for the selected inclusion systems was carried out to explore the suitable arrangements of FIN in the cavity of β-CyD or its derivatives. The results suggested that the DM-β-CyD inclusion system gave the higher complexation efficiency for improvement in solubility of FIN and hence enhancement of its bioavailability. Pharmacokinetic parameters displayed a higher absorption rate and higher area under the curve of the FIN/DM-β-CyD inclusion complex when compared with the drug alone, which indicates an improvement in the absorption and bioavailability of FIN in the DM-β-CyD inclusion system. Keywords: finasteride, cyclodextrins, molecular docking, pharmacokinetics, bioavailability

  10. Investigating the relative influences of molecular dimensions and binding energies on diffusivities of guest species inside nanoporous crystalline materials

    NARCIS (Netherlands)

    Krishna, R.; van Baten, J.M.

    2012-01-01

    The primary objective of this article is to investigate the relative influences of molecular dimensions and adsorption binding energies on unary diffusivities of guest species inside nanoporous crystalline materials such as zeolites and metal-organic frameworks (MOFs). The investigations are based

  11. Investigating the influence of effective parameters on molecular characteristics of bovine serum albumin nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Rohiwal, S.S.; Satvekar, R.K.; Tiwari, A.P.; Raut, A.V.; Kumbhar, S.G.; Pawar, S.H., E-mail: pawar_s_h@yahoo.com

    2015-04-15

    Graphical abstract: The physiochemical properties of nanoparticles provide the basic aspects about the conformational transitions which could have a strong bearing on the bioavailability for bioactive molecules such as peptides and hormones. - Highlights: • Synthesis and surface and structural properties of Bovine Serum Albumin nanoparticles (BSANPs). • Study of conformational transitions of BSANPs by spectroscopic techniques. • Studies on the effect of pH and protein concentration on formulation of BSANPs. - Abstract: The protein nanoparticles formulation is a challenging task as they are prone to undergo conformational transitions while processing which may affect bioavailability for bioactive compounds. Herein, a modified desolvation method is employed to prepare Bovine Serum Albumin nanoparticles, with controllable particle size ranging from 100 to 300 nm and low polydispersity index. The factors influencing the size and structure of BSA NPs viz. protein concentration, pH and the conditions for purification are well investigated. The structure of BSA NPs is altered due to processing, and may affect the effective binding ability with drugs and bioactive compounds. With that aims, investigations of molecular characteristics of BSA NPs are carried out in detail by using spectroscopic techniques. UV–visible absorption and Fourier Transform Infrared demonstrate the alteration in protein structure of BSA NPs whereas the FT-Raman spectroscopy investigates changes in the secondary and tertiary structures of the protein. The conformational changes of BSA NPs are observed by change in fluorescence intensity and emission maximum wavelength of tryptophan residue by fluorescence spectroscopy. The field emission scanning electron and atomic force microscopy micrographs confirm the size and semi-spherical morphology of the BSA NPs. The effect of concentration and pH on particle size distribution is studied by particle size analyzer.

  12. Detailed investigation on the effect of wall spring stiffness on velocity profile in molecular dynamics simulation

    International Nuclear Information System (INIS)

    Namvar, S; Karimian, S M H

    2012-01-01

    In this paper, motion of 576 monatomic argon molecules is studied in a channel with two 2-layered wall molecules. The effect of wall spring stiffness (K) on maximum value of velocity profile is investigated in the channel. It was observed that for K −2 , there is a decrease in the maximum value of velocity profile with an increase in K. This observation has been already reported by Sofos et al. To investigate a wider range of spring stiffness, in this paper the value of K was increased to more than 500εσ −2 . In this range of wall spring stiffness the behavior of maximum value of velocity profile changed; it increased with an increase in K. In a separate simulation the external force applied to the molecules was also increased and the same non-monotonic behavior of maximum value of velocity was observed. To clarify the reason of this behavior, the concepts of original and effective wall are introduced and through several test it is inferred that the mentioned concepts are not successful to demonstrate the reason of such behavior. It is suggested to obtain non-dimensional parameters governing the simulation in order to investigate the effect of every involved parameter on such a behavior. It is finally concluded that while wall spring stiffness affects the maximum velocity magnitude within the flow, the interaction of the two has not been clearly shown yet. The behavior of the maximum velocity is non-monotonic with the change of K. This is why no specific criterion has been reported for suitable value of wall spring stiffness in molecular dynamics simulation.

  13. Molecular investigation of evaporation of biodroplets containing single-strand DNA on graphene surface.

    Science.gov (United States)

    Akbari, Fahimeh; Foroutan, Masumeh

    2018-02-14

    In this study, the water droplet behaviour of four different types of single-strand DNA with homogeneous base sequence on a graphene substrate during evaporation of the droplet was investigated using molecular dynamics (MD) simulation. The simulation results indicated that the evaporation depended on the DNA sequence. The observed changes can be divided into four parts: (i) vaporization mode, (ii) evaporation flux, (iii) mechanism of single-strand placement on the surface, and (iv) consideration of remaining single strands after evaporation. Our simulation observations indicated different evaporation modes for thymine biodroplets as compared to those for other biodroplets. The evaporation of the thymine biodroplets occurred with an increase in the contact angle, while that of the other biodroplets occur in a constant contact angle mode. Moreover, thymine biodroplets generate the lowest contact line compared to other single strands, and it is always placed far away from the centre of the droplets during evaporation. Investigating variations in the evaporation flux shows that thymine has the highest evaporation flux and guanine has the lowest. Moreover, during initial evaporation, the flux of evaporation increases at the triple point of the biodroplets containing thymine single strands, while it decreases in the other biodroplets. The following observation was obtained from the study of the placement of single strands on the substrate: guanine and thymine interacted slower than other single strands during evaporation with graphene, adenine single strand had a higher folding during evaporation, and guanine single strand showed the lowest end-to-end distance. The investigation of single-strand DNA after evaporation shows that adenine produces the most stable structure at the end of evaporation. In addition, cytosine is the most stretched single-strand DNA due to its lack of internal π-π stacking and hydrogen bonding. Therefore, cytosine single strand is more

  14. Complete Chloroplast Genomes of Papaver rhoeas and Papaver orientale: Molecular Structures, Comparative Analysis, and Phylogenetic Analysis

    Directory of Open Access Journals (Sweden)

    Jianguo Zhou

    2018-02-01

    Full Text Available Papaver rhoeas L. and P. orientale L., which belong to the family Papaveraceae, are used as ornamental and medicinal plants. The chloroplast genome has been used for molecular markers, evolutionary biology, and barcoding identification. In this study, the complete chloroplast genome sequences of P. rhoeas and P. orientale are reported. Results show that the complete chloroplast genomes of P. rhoeas and P. orientale have typical quadripartite structures, which are comprised of circular 152,905 and 152,799-bp-long molecules, respectively. A total of 130 genes were identified in each genome, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Sequence divergence analysis of four species from Papaveraceae indicated that the most divergent regions are found in the non-coding spacers with minimal differences among three Papaver species. These differences include the ycf1 gene and intergenic regions, such as rpoB-trnC, trnD-trnT, petA-psbJ, psbE-petL, and ccsA-ndhD. These regions are hypervariable regions, which can be used as specific DNA barcodes. This finding suggested that the chloroplast genome could be used as a powerful tool to resolve the phylogenetic positions and relationships of Papaveraceae. These results offer valuable information for future research in the identification of Papaver species and will benefit further investigations of these species.

  15. Thermal behaviour of molecular sieves (SAPO-11/AIPO-11 type) investigated by synchrotron radiation X-ray diffraction (SRXD)

    International Nuclear Information System (INIS)

    Neissendorfer, F.; Jahn, E.; Gusenko, S.N.; Sheromov, M.A.

    1991-01-01

    The structure of molecular sieves is important for a successful application as a catalyzer. The final structure of the synthetic product depends on the technological steps. This process was investigated by in-situ Synchrotron radiation X-ray diffraction. Structural changes in the molecular sieves exist not only during the heating process but also during the following cooling process. (author) 3 figs., 2 refs

  16. Investigating the molecular mechanisms of organophosphate and pyrethroid resistance in the fall armyworm Spodoptera frugiperda.

    Directory of Open Access Journals (Sweden)

    Renato A Carvalho

    Full Text Available The fall armyworm Spodoptera frugiperda is an economically important pest of small grain crops that occurs in all maize growing regions of the Americas. The intensive use of chemical pesticides for its control has led to the selection of resistant populations, however, to date, the molecular mechanisms underlying resistance have not been characterised. In this study the mechanisms involved in the resistance of two S. frugiperda strains collected in Brazil to chlorpyrifos (OP strain or lambda-cyhalothrin (PYR strain were investigated using molecular and genomic approaches. To examine the possible role of target-site insensitivity the genes encoding the organophosphate (acetylcholinesterase, AChE and pyrethroid (voltage-gated sodium channel, VGSC target-site proteins were PCR amplified. Sequencing of the S. frugiperda ace-1 gene identified several nucleotide changes in the OP strain when compared to a susceptible reference strain (SUS. These result in three amino acid substitutions, A201S, G227A and F290V, that have all been shown previously to confer organophosphate resistance in several other insect species. Sequencing of the gene encoding the VGSC in the PYR strain, identified mutations that result in three amino acid substitutions, T929I, L932F and L1014F, all of which have been shown previously to confer knockdown/super knockdown-type resistance in several arthropod species. To investigate the possible role of metabolic detoxification in the resistant phenotype of the OP and PYR stains all EST sequences available for S. frugiperda were used to design a gene-expression microarray. This was then used to compare gene expression in the resistant strains with the susceptible reference strain. Members of several gene families, previously implicated in metabolic resistance in other insects were found to be overexpressed in the resistant strains including glutathione S-transferases, cytochrome P450s and carboxylesterases. Taken together these results

  17. Investigating the molecular mechanisms of organophosphate and pyrethroid resistance in the fall armyworm Spodoptera frugiperda.

    Science.gov (United States)

    Carvalho, Renato A; Omoto, Celso; Field, Linda M; Williamson, Martin S; Bass, Chris

    2013-01-01

    The fall armyworm Spodoptera frugiperda is an economically important pest of small grain crops that occurs in all maize growing regions of the Americas. The intensive use of chemical pesticides for its control has led to the selection of resistant populations, however, to date, the molecular mechanisms underlying resistance have not been characterised. In this study the mechanisms involved in the resistance of two S. frugiperda strains collected in Brazil to chlorpyrifos (OP strain) or lambda-cyhalothrin (PYR strain) were investigated using molecular and genomic approaches. To examine the possible role of target-site insensitivity the genes encoding the organophosphate (acetylcholinesterase, AChE) and pyrethroid (voltage-gated sodium channel, VGSC) target-site proteins were PCR amplified. Sequencing of the S. frugiperda ace-1 gene identified several nucleotide changes in the OP strain when compared to a susceptible reference strain (SUS). These result in three amino acid substitutions, A201S, G227A and F290V, that have all been shown previously to confer organophosphate resistance in several other insect species. Sequencing of the gene encoding the VGSC in the PYR strain, identified mutations that result in three amino acid substitutions, T929I, L932F and L1014F, all of which have been shown previously to confer knockdown/super knockdown-type resistance in several arthropod species. To investigate the possible role of metabolic detoxification in the resistant phenotype of the OP and PYR stains all EST sequences available for S. frugiperda were used to design a gene-expression microarray. This was then used to compare gene expression in the resistant strains with the susceptible reference strain. Members of several gene families, previously implicated in metabolic resistance in other insects were found to be overexpressed in the resistant strains including glutathione S-transferases, cytochrome P450s and carboxylesterases. Taken together these results provide

  18. Investigating Molecular Inheritance of Carbon in Star-forming Regions along a Galactic Gradient

    KAUST Repository

    Smith, Rachel L.

    2015-04-01

    Observations of CO isotopologues taken at high spectral resolution toward young stellar objects (YSOs) are valuable tools for investigating protoplanetary chemical reservoirs, and enable robust comparisons between YSOs and solar system material (meteorites and the Sun). Investigating a range of YSO environments also helps parameterize variations in the distribution and evolution of carbon-based molecules, furthering an understanding of prebiotic chemistry. We have begun a wide survey of massive YSOs using Keck-NIRSPEC at high spectral resolution (R=25,000). Fundamental and first-overtone near-IR CO rovibrational absorption spectra have thus far been obtained toward 14 massive, luminous YSOs at Galactocentric radii (RGC) ranging from ~4.5 to 9.7 kpc. From these data we can obtain precise [12CO]/[13CO] gas-phase abundance ratios along a Galactic gradient, and [12CO]/[13CO]Gas can be further evaluated against published [12CO2]/[13CO2]Ice and [12CO]/[13CO]Ice because all observations are in absorption, a robust study of molecular inheritance is possible by virtue of comparing 12C/13C along the same lines-of-sight. Initial results for cold CO gas at RGC ~ 6.1 kpc and 9.4 kpc reveal [12C16O]/[13C16O] of 59+/‑8 and 74+/‑3, respectively, roughly following an expected 12C/13C Galactic gradient. Thus far, we find [12CO]/[13CO] in the cold CO gas to be lower than [12CO2]/[13CO2]Ice, suggesting that CO2 may not originate from CO reservoirs as often assumed. While very high-resolution observations of CO gas toward low-mass YSOs observed with VLT-CRIRES show significant heterogeneity in [12CO]/[13CO] at RGC ~ 8 kpc, this dispersion is not found for the massive YSOs. Both the low-mass and massive YSOs have higher [12CO]/[13CO] in warm vs. cold gas, and both show signatures suggesting possible interplay between CO ice and gas reservoirs. Overall, our results indicate that carbon isotopic evolution in massive YSO environments may follow different paths compared to low-mass YSOs

  19. Investigating Molecular Inheritance of Carbon in Star-forming Regions along a Galactic Gradient

    KAUST Repository

    Smith, Rachel L.; Blake, Geoffrey; Boogert, Adwin; Pontoppidan, Klaus Martin; Lockwood, Alexandra C.

    2015-01-01

    Observations of CO isotopologues taken at high spectral resolution toward young stellar objects (YSOs) are valuable tools for investigating protoplanetary chemical reservoirs, and enable robust comparisons between YSOs and solar system material (meteorites and the Sun). Investigating a range of YSO environments also helps parameterize variations in the distribution and evolution of carbon-based molecules, furthering an understanding of prebiotic chemistry. We have begun a wide survey of massive YSOs using Keck-NIRSPEC at high spectral resolution (R=25,000). Fundamental and first-overtone near-IR CO rovibrational absorption spectra have thus far been obtained toward 14 massive, luminous YSOs at Galactocentric radii (RGC) ranging from ~4.5 to 9.7 kpc. From these data we can obtain precise [12CO]/[13CO] gas-phase abundance ratios along a Galactic gradient, and [12CO]/[13CO]Gas can be further evaluated against published [12CO2]/[13CO2]Ice and [12CO]/[13CO]Ice because all observations are in absorption, a robust study of molecular inheritance is possible by virtue of comparing 12C/13C along the same lines-of-sight. Initial results for cold CO gas at RGC ~ 6.1 kpc and 9.4 kpc reveal [12C16O]/[13C16O] of 59+/‑8 and 74+/‑3, respectively, roughly following an expected 12C/13C Galactic gradient. Thus far, we find [12CO]/[13CO] in the cold CO gas to be lower than [12CO2]/[13CO2]Ice, suggesting that CO2 may not originate from CO reservoirs as often assumed. While very high-resolution observations of CO gas toward low-mass YSOs observed with VLT-CRIRES show significant heterogeneity in [12CO]/[13CO] at RGC ~ 8 kpc, this dispersion is not found for the massive YSOs. Both the low-mass and massive YSOs have higher [12CO]/[13CO] in warm vs. cold gas, and both show signatures suggesting possible interplay between CO ice and gas reservoirs. Overall, our results indicate that carbon isotopic evolution in massive YSO environments may follow different paths compared to low-mass YSOs

  20. Molecular evolution in court: analysis of a large hepatitis C virus outbreak from an evolving source.

    Science.gov (United States)

    González-Candelas, Fernando; Bracho, María Alma; Wróbel, Borys; Moya, Andrés

    2013-07-19

    Molecular phylogenetic analyses are used increasingly in the epidemiological investigation of outbreaks and transmission cases involving rapidly evolving RNA viruses. Here, we present the results of such an analysis that contributed to the conviction of an anesthetist as being responsible for the infection of 275 of his patients with hepatitis C virus. We obtained sequences of the NS5B and E1-E2 regions in the viral genome for 322 patients suspected to have been infected by the doctor, and for 44 local, unrelated controls. The analysis of 4,184 cloned sequences of the E1-E2 region allowed us to exclude 47 patients from the outbreak. A subset of patients had known dates of infection. We used these data to calibrate a relaxed molecular clock and to determine a rough estimate of the time of infection for each patient. A similar analysis led to an estimate for the time of infection of the source. The date turned out to be 10 years before the detection of the outbreak. The number of patients infected was small at first, but it increased substantially in the months before the detection of the outbreak. We have developed a procedure to integrate molecular phylogenetic reconstructions of rapidly evolving viral populations into a forensic setting adequate for molecular epidemiological analysis of outbreaks and transmission events. We applied this procedure to a large outbreak of hepatitis C virus caused by a single source and the results obtained played a key role in the trial that led to the conviction of the suspected source.

  1. Neuroendocrine and squamous colonic composite carcinoma: Case report with molecular analysis

    Institute of Scientific and Technical Information of China (English)

    Sabrina C Wentz; Cindy Vnencak-Jones; William V Chopp

    2011-01-01

    Composite colorectal carcinomas are rare. There are a modest number of cases in the medical literature, with even fewer cases describing composite carcinoma with neuroendocrine and squamous components. There are to our knowledge no reports of composite carcinoma molecular alterations. We present a case of composite carcinoma of the splenic flexure in a 33 year-old Cau casian male to investigate the presence and prognos tic significance of molecular alterations in rare colonic carcinoma subtypes. Formalin-fixed paraffin-embedded (FFPE) tissue was hematoxylin and eosin- and mucicar-mine-stained according to protocol, and immuno-stained with cytokeratin (CK)7, CK20, CDX2, AE1/AE3, chromo-granin-A and synaptophysin. DNA was extracted from FFPE tissues and molecular analyses were performedaccording to lab-developed methods, followed by capil lary electrophoresis. Hematoxylin and eosin staining showed admixed neuroendocrine and keratinized squa mous cells. Positive nuclear CDX2 expression confirmed intestinal derivation. CK7 and CK20 were negative. Neuroendocrine cells stained positively for synaptophy sin and AE1/AE3 and negatively for chromogranin and mucicarmine. Hepatic metastases showed a similar im munohistochemical profile. Molecular analysis revealed a G13D KRAS mutation. BRAF mutational testing was negative and microsatellite instability was not detected. The patient had rapid disease progression on chemo therapy and died 60 d after presentation. Although the G13D KRAS mutation normally predicts an intermediate outcome, the aggressive tumor behavior suggests other modifying factors in rare types of colonic carcinomas.

  2. Mathematical analysis of compressive/tensile molecular and nuclear structures

    Science.gov (United States)

    Wang, Dayu

    Mathematical analysis in chemistry is a fascinating and critical tool to explain experimental observations. In this dissertation, mathematical methods to present chemical bonding and other structures for many-particle systems are discussed at different levels (molecular, atomic, and nuclear). First, the tetrahedral geometry of single, double, or triple carbon-carbon bonds gives an unsatisfying demonstration of bond lengths, compared to experimental trends. To correct this, Platonic solids and Archimedean solids were evaluated as atoms in covalent carbon or nitrogen bond systems in order to find the best solids for geometric fitting. Pentagonal solids, e.g. the dodecahedron and icosidodecahedron, give the best fit with experimental bond lengths; an ideal pyramidal solid which models covalent bonds was also generated. Second, the macroscopic compression/tension architectural approach was applied to forces at the molecular level, considering atomic interactions as compressive (repulsive) and tensile (attractive) forces. Two particle interactions were considered, followed by a model of the dihydrogen molecule (H2; two protons and two electrons). Dihydrogen was evaluated as two different types of compression/tension structures: a coaxial spring model and a ring model. Using similar methods, covalent diatomic molecules (made up of C, N, O, or F) were evaluated. Finally, the compression/tension model was extended to the nuclear level, based on the observation that nuclei with certain numbers of protons/neutrons (magic numbers) have extra stability compared to other nucleon ratios. A hollow spherical model was developed that combines elements of the classic nuclear shell model and liquid drop model. Nuclear structure and the trend of the "island of stability" for the current and extended periodic table were studied.

  3. Molecular analysis of radiation-induced experimental tumors in mice

    International Nuclear Information System (INIS)

    Niwa, O.; Muto, M.; Suzuki, F.

    1992-01-01

    Molecular analysis was made on mouse tumors induced by radiation and chemicals. Expression of oncogenes was studied in 12 types of 178 mouse tumors. Southern blotting was done on tumors in which overexpression of oncogenes was noted. Amplification of the myc oncogene was found in chemically induced sarcomas, but not those induced by radiations. Radiogenic thymomas were studied in detail. These thymomas were induced in two different ways. The first was thymomas induced by direct irradiation of F1 mice between C57BL/6NxC3H/He. Southern analysis of DNA revealed deletion of specific minisatellite bands in these tumors. DNA from directly induced thymomas induced focus formation when transfected into normal Golden hamster cells. The mouse K-ras oncogene was detected in these transformants. The second type of thymomas was induced by X-irradiation of thymectomized B10.thy1.2 mice in which normal thymus from congenic B10,thy1.1. mice was grafted. Thymomas of the donor origin was analysed by transfection and the transformants by DNA from those indirectly induced thymomas did not contain activated ras oncogenes. (author)

  4. MDAnalysis: a toolkit for the analysis of molecular dynamics simulations.

    Science.gov (United States)

    Michaud-Agrawal, Naveen; Denning, Elizabeth J; Woolf, Thomas B; Beckstein, Oliver

    2011-07-30

    MDAnalysis is an object-oriented library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. It is written in the Python language with some performance-critical code in C. It uses the powerful NumPy package to expose trajectory data as fast and efficient NumPy arrays. It has been tested on systems of millions of particles. Many common file formats of simulation packages including CHARMM, Gromacs, Amber, and NAMD and the Protein Data Bank format can be read and written. Atoms can be selected with a syntax similar to CHARMM's powerful selection commands. MDAnalysis enables both novice and experienced programmers to rapidly write their own analytical tools and access data stored in trajectories in an easily accessible manner that facilitates interactive explorative analysis. MDAnalysis has been tested on and works for most Unix-based platforms such as Linux and Mac OS X. It is freely available under the GNU General Public License from http://mdanalysis.googlecode.com. Copyright © 2011 Wiley Periodicals, Inc.

  5. Short-time maximum entropy method analysis of molecular dynamics simulation: Unimolecular decomposition of formic acid

    Science.gov (United States)

    Takahashi, Osamu; Nomura, Tetsuo; Tabayashi, Kiyohiko; Yamasaki, Katsuyoshi

    2008-07-01

    We performed spectral analysis by using the maximum entropy method instead of the traditional Fourier transform technique to investigate the short-time behavior in molecular systems, such as the energy transfer between vibrational modes and chemical reactions. This procedure was applied to direct ab initio molecular dynamics calculations for the decomposition of formic acid. More reactive trajectories of dehydrolation than those of decarboxylation were obtained for Z-formic acid, which was consistent with the prediction of previous theoretical and experimental studies. Short-time maximum entropy method analyses were performed for typical reactive and non-reactive trajectories. Spectrograms of a reactive trajectory were obtained; these clearly showed the reactant, transient, and product regions, especially for the dehydrolation path.

  6. Experimental and computational study on molecular structure and vibrational analysis of an antihyperglycemic biomolecule: Gliclazide

    Science.gov (United States)

    Karakaya, Mustafa; Kürekçi, Mehmet; Eskiyurt, Buse; Sert, Yusuf; Çırak, Çağrı

    2015-01-01

    In present study, the experimental and theoretical harmonic vibrational frequencies of gliclazide molecule have been investigated. The experimental FT-IR (400-4000 cm-1) and Laser-Raman spectra (100-4000 cm-1) of the molecule in the solid phase were recorded. Theoretical vibrational frequencies and geometric parameters (bond lengths and bond angles) have been calculated using ab initio Hartree Fock (HF), density functional theory (B3LYP hybrid function) methods with 6-311++G(d,p) and 6-31G(d,p) basis sets by Gaussian 09W program. The assignments of the vibrational frequencies were performed by potential energy distribution (PED) analysis by using VEDA 4 program. Theoretical optimized geometric parameters and vibrational frequencies have been compared with the corresponding experimental data, and they have been shown to be in a good agreement with each other. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies have been found.

  7. Molecular mechanics and microcalorimetric investigations of the effects of molecular water on the aggregation of asphaltenes in solutions

    DEFF Research Database (Denmark)

    Murgich, J.; Lira-Galeana, C.; Garcia, Daniel Merino

    2002-01-01

    The interaction of two model asphaltene molecules from the Athabasca sand oil with a water molecule in a toluene solution was studied by means of molecular mechanics calculations. It was found that water forms bridging H bonds between the heteroatoms of asphaltenes with a considerable span...... in energies. The stronger H bond found has energies higher than those corresponding to the stacking of the aromatic areas of the same asphaltene molecules. This shows that the water molecule may generate additional mechanisms of aggregation of asphaltenes in toluene solution, as found experimentally. The H...... by titration calorimetry. A simple dimer dissociation model was used to derive the information about the heat and the constant of dissociation from asphaltenes of Mexico and Alaska obtained from the calorimetric data. The association enthalpies calculated were found to be in excellent agreement with those...

  8. Experimental and molecular docking investigation on metal-organic framework MIL-101(Cr) as a sorbent for vortex assisted dispersive micro-solid-phase extraction of trace 5-nitroimidazole residues in environmental water samples prior to UPLC-MS/MS analysis.

    Science.gov (United States)

    Lu, Nan; Wang, Ting; Zhao, Pan; Zhang, Lianjun; Lun, Xiaowen; Zhang, Xueli; Hou, Xiaohong

    2016-11-01

    In the presented work, metal-organic framework (MOF) material MIL-101(Cr) (MIL, Matérial Institute Lavoisier) was used as a sorbent for vortex assisted dispersive micro-solid-phase extraction (VA-D-μ-SPE) of trace amount of metronidazole (MNZ), ronidazole (RNZ), secnidazole (SNZ), dimetridazole (DMZ), tinidazole (TNZ), and ornidazole (ONZ) in different environmental water samples. Ultra-high-performance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS/MS) was used to quantify the target analytes. The extraction conditions, including type of sorbents, amount of MIL-101(Cr), solution pH, extraction method, extraction time, effect of salt, and elution conditions were investigated. Upon the optimal conditions, the developed method showed an excellent extraction performance with the average recovery ranging from 75.2 to 98.8 %. Good sensitivity levels were achieved with the detection limits of 0.03∼0.06 μg/L and the quantitation limits of 0.09∼0.20 μg/L. The linear ranges were varied from 0.1 to 20 for SNZ and ONZ and from 0.2 to 40 μg/L for MNZ, RNZ, DMZ, and TNZ (r 2  > 0.992), and repeatability of the method was satisfactory with the relative standard deviations (RSD) extraction and determination of 5-nitroimidazoles (5-NDZs) in 12 real water samples, showing the positive findings of MNZ and TNZ ranging from 0.3 to 1.0 μg/L. Furthermore, molecular docking was applied to explain the molecular interactions and free binding energies between MIL-101(Cr) and 5-NDZs, providing a deep insight into the adsorption mechanism. The proposed method exhibited the advantages of simplicity, rapidly, less solvent consumption, ease of operation, higher sensitivity, and lower matrix effect. Graphical abstract Schematic diagram of the extraction process and molecular docking investigation.

  9. Theoretical Investigation on the Molecular Structure, Vibrational and NMR Spectra of N, N, 4-Tri chlorobenzenesulfonamide

    International Nuclear Information System (INIS)

    Cinar, M.

    2008-01-01

    In the present study, the structural properties of N,N,4-Tri chlorobenzenesulfonamide have been studied extensively using Density Functional Theory (DFT) employing B3LYP exchange correlation. The geometry of the molecule was fully optimized, vibrational spectrum was calculated and fundamental vibrations were assigned based on the scaled theoretical wavenumbers. The 1 H and 13 C nuclear magnetic resonance (NMR) chemical shifts of the compound were calculated using the Gauge-Invariant Atomic Orbital (GIAO) method. To investigate the basis set effects, calculations were performed at the 6-31G(d,p), 6-311G(d,p), 6-31++G(d,p) and 6-311++G(d,p) levels. Finally, geometric parameters, vibrational bands and isotropic chemical shifts were compared with available experimental data of compound. The fully optimized geometry of the molecule was found to be consistent with the X-ray crystal structure. The observed and calculated frequencies and chemical shifts were found to be in very good agreement. The computed results appear that the basis set has slight effect on the molecular geometry of N,N,4-Tri chlorobenzenesulfonamide

  10. A molecular dynamics investigation on the crizotinib resistance mechanism of C1156Y mutation in ALK

    International Nuclear Information System (INIS)

    Sun, Hui-Yong; Ji, Feng-Qin

    2012-01-01

    Highlights: ► The study revealed the detailed resistance mechanism of the non-active mutation C1156Y in ALK. ► C1156Y leads to crizotinib displacement and conformational changes in the binding cavity. ► The conformations cause a decline in the vdW and electrostatic energy between crizotinib and ALK. -- Abstract: Crizotinib is an anaplastic lymphoma kinase (ALK) inhibitor that has recently been approved in the US for the treatment of non-small cell lung carcinoma (NSCLC). Despite its outstanding safety and efficacy, several resistant mutations against crizotinib have been detected in the treatment of NSCLC. However, in contrast to the widely accepted mechanism of steric hindrance by mutations at the active site, the mechanism by which the C1156Y non-active site mutation confers resistance against crizotinib remains unclear. In the present study, the resistance mechanism of C1156Y in ALK was investigated using molecular dynamics simulations. The results suggest that despite the non-active site mutation, C1156Y causes the dislocation of crizotinib as well as the indirect conformational changes in the binding cavity, which results in a marked decrease in the van der Waals and electrostatic interactions between crizotinib and ALK. The obtained results provide a detailed explanation of the resistance caused by C1156Y and may give a vital clue for the design of drugs to combat crizotinib resistance.

  11. A molecular dynamics investigation on the crizotinib resistance mechanism of C1156Y mutation in ALK

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Hui-Yong [Shandong University of Technology, Zibo 255049 (China); Ji, Feng-Qin, E-mail: fengqinji@mail.hzau.edu.cn [National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070 (China); Center for Bioinformatics, Huazhong Agricultural University, Wuhan 430070 (China)

    2012-06-29

    Highlights: Black-Right-Pointing-Pointer The study revealed the detailed resistance mechanism of the non-active mutation C1156Y in ALK. Black-Right-Pointing-Pointer C1156Y leads to crizotinib displacement and conformational changes in the binding cavity. Black-Right-Pointing-Pointer The conformations cause a decline in the vdW and electrostatic energy between crizotinib and ALK. -- Abstract: Crizotinib is an anaplastic lymphoma kinase (ALK) inhibitor that has recently been approved in the US for the treatment of non-small cell lung carcinoma (NSCLC). Despite its outstanding safety and efficacy, several resistant mutations against crizotinib have been detected in the treatment of NSCLC. However, in contrast to the widely accepted mechanism of steric hindrance by mutations at the active site, the mechanism by which the C1156Y non-active site mutation confers resistance against crizotinib remains unclear. In the present study, the resistance mechanism of C1156Y in ALK was investigated using molecular dynamics simulations. The results suggest that despite the non-active site mutation, C1156Y causes the dislocation of crizotinib as well as the indirect conformational changes in the binding cavity, which results in a marked decrease in the van der Waals and electrostatic interactions between crizotinib and ALK. The obtained results provide a detailed explanation of the resistance caused by C1156Y and may give a vital clue for the design of drugs to combat crizotinib resistance.

  12. Investigation of Interactions between Thrombin and Ten Phenolic Compounds by Affinity Capillary Electrophoresis and Molecular Docking

    Directory of Open Access Journals (Sweden)

    Qiao-Qiao Li

    2018-01-01

    Full Text Available Thrombin plays a vital role in blood coagulation, which is a key process involved in thrombosis by promoting platelet aggregation and converting fibrinogen to form the fibrin clot. In the receptor concept, drugs produce their therapeutic effects via interactions with the targets. Therefore, investigation of interaction between thrombin and small molecules is important to find out the potential thrombin inhibitor. In this study, affinity capillary electrophoresis (ACE and in silico molecular docking methods were developed to study the interaction between thrombin and ten phenolic compounds (p-hydroxybenzoic acid, protocatechuic acid, vanillic acid, gallic acid, catechin, epicatechin, dihydroquercetin, naringenin, apigenin, and baicalein. The ACE results showed that gallic acids and six flavonoid compounds had relative strong interactions with thrombin. In addition, the docking results indicated that all of optimal conformations of the six flavonoid compounds were positioned into the thrombin activity centre and had interaction with the HIS57 or SER195 which was the key residue to bind thrombin inhibitors such as argatroban. Herein, these six flavonoid compounds might have the potential of thrombin inhibition activity. In addition, the developed method in this study can be further applied to study the interactions of other molecules with thrombin.

  13. Spectroscopic Parameter and Molecular Constant Investigations on Low-Lying States of BeF Radical

    Directory of Open Access Journals (Sweden)

    Jin Feng Sun

    2012-02-01

    Full Text Available The potential energy curves (PECs of X2Σ+, A2Πr and B2Σ+ states of BeF radical have been investigated using the complete active space self-consistent-field (CASSCF method, followed by the highly accurate valence internally contracted multireference configuration interaction (MRCI approach at the correlation-consistent basis sets, cc-pV5Z for Be and aug-cc-pV6Z for F. Based on the PECs of X2Σ+, A2Πr and B2Σ+ states, the spectroscopic parameters (De, Re, ωe, ωeχe, αe and Be have also been determined in the present work. With the PECs determined at the present level of theory, vibrational states have been predicted for each state when the rotational quantum number J equals zero (J = 0. The vibrational levels, inertial rotation and centrifugal distortion constants are determined for the three states, and the classical turning points are also calculated for the X2Σ+ state. Compared with the available experiments and other theories, it can be seen that the present spectroscopic parameter and molecular constant results are more fully in agreement with the experimental findings.

  14. A molecular investigation of soil organic carbon composition across a subalpine catchment

    Science.gov (United States)

    Hsu, Hsiao-Tieh; Lawrence, Corey R.; Winnick, Matthew J.; Bargar, John R.; Maher, Katharine

    2018-01-01

    The dynamics of soil organic carbon (SOC) storage and turnover are a critical component of the global carbon cycle. Mechanistic models seeking to represent these complex dynamics require detailed SOC compositions, which are currently difficult to characterize quantitatively. Here, we address this challenge by using a novel approach that combines Fourier transform infrared spectroscopy (FT-IR) and bulk carbon X-ray absorption spectroscopy (XAS) to determine the abundance of SOC functional groups, using elemental analysis (EA) to constrain the total amount of SOC. We used this SOC functional group abundance (SOC-fga) method to compare variability in SOC compositions as a function of depth across a subalpine watershed (East River, Colorado, USA) and found a large degree of variability in SOC functional group abundances between sites at different elevations. Soils at a lower elevation are predominantly composed of polysaccharides, while soils at a higher elevation have more substantial portions of carbonyl, phenolic, or aromatic carbon. We discuss the potential drivers of differences in SOC composition between these sites, including vegetation inputs, internal processing and losses, and elevation-driven environmental factors. Although numerical models would facilitate the understanding and evaluation of the observed SOC distributions, quantitative and meaningful measurements of SOC molecular compositions are required to guide such models. Comparison among commonly used characterization techniques on shared reference materials is a critical next step for advancing our understanding of the complex processes controlling SOC compositions.

  15. Photometric Analysis and Period Investigation of the EW Type ...

    Indian Academy of Sciences (India)

    Photometric Analysis and Period Investigation of the EW Type. Eclipsing ... binary with the less massive secondary component filling the inner Roche lobe. ..... Cox 2000) assuming that the primary component is a normal main sequence star.

  16. Microscopic, chemical, and molecular-biological investigation of the decayed medieval stained window glasses of two Catalonian churches.

    Science.gov (United States)

    Piñar, Guadalupe; Garcia-Valles, Maite; Gimeno-Torrente, Domingo; Fernandez-Turiel, Jose Luis; Ettenauer, Jörg; Sterflinger, Katja

    2013-10-01

    We investigated the decayed historical church window glasses of two Catalonian churches, both under Mediterranean climate. Glass surfaces were studied by scanning electron microscopy (SEM), energy dispersive spectrometry (EDS), and X-ray diffraction (XRD). Their chemical composition was determined by wavelength-dispersive spectrometry (WDS) microprobe analysis. The biodiversity was investigated by molecular methods: DNA extraction from glass, amplification by PCR targeting the16S rRNA and ITS regions, and fingerprint analyses by denaturing gradient gel electrophoresis (DGGE). Clone libraries containing either PCR fragments of the bacterial 16S rDNA or the fungal ITS regions were screened by DGGE. Clone inserts were sequenced and compared with the EMBL database. Similarity values ranged from 89 to 100% to known bacteria and fungi. Biological activity in both sites was evidenced in the form of orange patinas, bio-pitting, and mineral precipitation. Analyses revealed complex bacterial communities consisting of members of the phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. Fungi showed less diversity than bacteria, and species of the genera Cladosporium and Phoma were dominant. The detected Actinobacteria and fungi may be responsible for the observed bio-pitting phenomenon. Moreover, some of the detected bacteria are known for their mineral precipitation capabilities. Sequence results also showed similarities with bacteria commonly found on deteriorated stone monuments, supporting the idea that medieval stained glass biodeterioration in the Mediterranean area shows a pattern comparable to that on stone.

  17. Molecular typing and epidemiological investigation of clinical populations of Pseudomonas aeruginosa using an oligonucleotide-microarray

    Directory of Open Access Journals (Sweden)

    Ballarini Annalisa

    2012-07-01

    Full Text Available Abstract Background Pseudomonas aeruginosa is an opportunistic pathogen which has the potential to become extremely harmful in the nosocomial environment, especially for cystic fibrosis (CF patients, who are easily affected by chronic lung infections. For epidemiological purposes, discriminating P.aeruginosa isolates is a critical step, to define distribution of clones among hospital departments, to predict occurring microevolution events and to correlate clones to their source. A collection of 182 P. aeruginosa clinical strains isolated within Italian hospitals from patients with chronic infections, i.e. cystic fibrosis (CF patients, and with acute infections were genotyped. Molecular typing was performed with the ArrayTube (AT multimarker microarray (Alere Technologies GmbH, Jena, Germany, a cost-effective, time-saving and standardized method, which addresses genes from both the core and accessory P.aeruginosa genome. Pulsed-field gel electrophoresis (PFGE and multilocus sequence typing (MLST were employed as reference genotyping techniques to estimate the ArrayTube resolution power. Results 41 AT-genotypes were identified within our collection, among which 14 were novel and 27 had been previously described in publicly available AT-databases. Almost 30% of the genotypes belonged to a main cluster of clones. 4B9A, EC2A, 3C2A were mostly associated to CF-patients whereas F469, 2C1A, 6C22 to non CF. An investigation on co-infections events revealed that almost 40% of CF patients were colonized by more than one genotype, whereas less than 4% were observed in non CF patients. The presence of the exoU gene correlated with non-CF patients within the intensive care unit (ICU whereas the pKLC102-like island appeared to be prevalent in the CF centre. The congruence between the ArrayTube typing and PFGE or MLST was 0.077 and 0.559 (Adjusted Rand coefficient, respectively. AT typing of this Italian collection could be easily integrated with the global P

  18. Development of PNTDs synthesized from monomers with different molecular length and analysis of molecular damages by heavy ion

    International Nuclear Information System (INIS)

    Kawashima, Hajime; Kodaira, Satoshi; Ihara, Daisuke; Yasuda, Nakahiro; Kusumoto, Tamon; Mori, Yutaka; Yamauchi, Tomoya; Kobayashi, Keiichi; Benton, Eric

    2017-01-01

    Our interests for years lay to investigate the reason why CR-39 polymer has such high sensitivity as plastic nuclear track detector (PNTD) on chemical structural aspects. We developed three PNTDs from three diacrylate compounds as monomers bearing different molecular length as well as different numbers of internal ether bonds. The polymer products obtained were colorless and transparent with 3-D molecular structures as CR-39 and different lattice structures each other. Our purpose of the current study was to investigate structural damages caused in newly prepared PNTDs and CR-39 by irradiation of Nitrogen ion (6 MeV/n, fluence of 5 x 10 11 cm -2 ). The structural damage by irradiation was analyzed by the magnitude of the relative absorbance of specific functional groups such as ester, C=O, ether and C-H bonds by means of FT-IR (ATR) method. The correlation between the relative absorbance and the molecular length of the monomers were discussed. (author)

  19. [Molecular, genetic and physiological analysis of photoinhibition and photosynthetic

    Energy Technology Data Exchange (ETDEWEB)

    1992-01-01

    A major goal of this project is to use a combined molecular genetic, biochemical and physiological approach to understand the relationship between photosynthetic performance and the structure of the multifunctional D1 reaction center protein of Photosystem II encoded by the chloroplast psbA gene. Relative to other chloroplast proteins, turover of D1 is rapid and highly light dependent and de novo synthesis of D1 is required for a plant's recovery from short term exposure to irradiances which induce photoinhibitory damage. These observations have led to models for a damage/repair cycle of PSII involving the targeted degradation and replacement of photodamaged D1. To investigate the effects of perturbing the D1 cycle on photosynthesis and autotrophic growth under high and low irradiance, we have examined the consequences of site-specific mutations of the psbA and 16S rRNA genes affecting synthesis, maturation and function/stability of the D1 protein introduced into the chloroplast genome of wildtype strain of the green alga Chlamydomonas reinhardtii using biolistic transformation.

  20. PROGRAMA DE CALIDAD PARA LAS INVESTIGACIONES BÁSICAS DEL CENTRO DE INMUNOLOGÍA MOLECULAR / PROGRAM OF QUALITY FOR THE BASIC INVESTIGATIONS OF THE CENTER OF MOLECULAR IMMUNOLOGY

    Directory of Open Access Journals (Sweden)

    Dainerys Infante-Santana

    2011-09-01

    Full Text Available

    El artículo describe el Programa de calidad para las investigaciones del Centro de Inmunología Molecular. Este programa incorpora el cumplimiento de las Buenas Prácticas de Laboratorio con una gestión basada en el comportamiento, el análisis de los riesgos, el enfoque a procesos y la evaluación a través de indicadores. La aplicación del nuevo programa de calidad en el proceso de la actividad científica, permitió disminuir los incumplimientos de las mencionadas prácticas, mejorar los indicadores de productividad científica y lograr una mayor cultura de calidad en el área de investigaciones del Centro de Inmunología Molecular.

    Abstract

    The paper describes the Program of quality for the investigations of the Center of Molecular Immunology. This program incorporates the execution of the Good Practices of Laboratory with a behaviour-based management, the analysis of the risks, the process approach and the assessment through indicators. The application of the new quality program in the process of the scientific activity, allowed to decrease the nonfulfillments of the above mentioned practices, to improve the scientific productivity indicators and to achieve a greater quality culture in the area of investigations of the Center of Molecular Immunology.

  1. Investigation of Sorption and Diffusion Mechanisms, and Preliminary Economic Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Bhave, Ramesh R. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Jubin, Robert Thomas [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Spencer, Barry B. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Nair, Sankar [Georgia Inst. of Technology, Atlanta, GA (United States)

    2017-02-01

    This report describes the synthesis and evaluation of molecular sieve zeolite membranes to separate and concentrate tritiated water (HTO) from dilute HTO-bearing aqueous streams. Several monovalent and divalent cation exchanged silico alumino phosphate (SAPO-34) molecular sieve zeolite membranes were synthesized on disk supports and characterized with gas and vapor permeation measurements. The pervaporation process performance was evaluated for the separation and concentration of tritiated water. Experiments were performed using tritiated water feed solution containing tritium at the high end of the range (1 mCi/mL) anticipated in a nuclear fuel processing system that includes both acid and water streams recycling. The tritium concentration was about 0.1 ppm. The permeate was recovered under vacuum. The HTO/H2O selectivity and separation factor calculated from the measured tritium concentrations ranged from 0.99 to 1.23, and 0.83-0.98, respectively. Although the membrane performance for HTO separation was lower than expected, several encouraging observations including molecular sieving and high vapor permeance are reported. Additionally, several new approaches are proposed, such as tuning the sorption and diffusion properties offered by small pore LTA zeolite materials, and cation exchanged aluminosilicates with high metal loading. It is hypothesized that substantially improved preferential transport of tritium (HTO) resulting in a more concentrated permeate can be achieved. Preliminary economic analysis for the membrane-based process to concentrate tritiated water is also discussed.

  2. Sex Change in Clownfish: Molecular Insights from Transcriptome Analysis

    KAUST Repository

    Casas, Laura

    2016-10-17

    Sequential hermaphroditism is a unique reproductive strategy among teleosts that is displayed mainly in fish species living in the coral reef environment. The reproductive biology of hermaphrodites has long been intriguing; however, very little is known about the molecular pathways underlying their sex change. Here, we provide the first de novo transcriptome analyses of a hermaphrodite teleost´s undergoing sex change in its natural environment. Our study has examined relative gene expression across multiple groups—rather than just two contrasting conditions— and has allowed us to explore the differential expression patterns throughout the whole process. Our analysis has highlighted the rapid and complex genomic response of the brain associated with sex change, which is subsequently transmitted to the gonads, identifying a large number of candidate genes, some well-known and some novel, involved in the process. The present study provides strong evidence of the importance of the sex steroidogenic machinery during sex change in clownfish, with the aromatase gene playing a central role, both in the brain and the gonad. This work constitutes the first genome-wide study in a social sex-changing species and provides insights into the genetic mechanism governing social sex change and gonadal restructuring in protandrous hermaphrodites.

  3. Molecular genetic analysis of phosphomannomutase genes in Triticum monococcum

    Institute of Scientific and Technical Information of China (English)

    Chunmei; Yu; Xinyan; Liu; Qian; Zhang; Xinyu; He; Wan; Huai; Baohua; Wang; Yunying; Cao; Rong; Zhou

    2015-01-01

    In higher plants, phosphomannomutase(PMM) is essential for synthesizing the antioxidant ascorbic acid through the Smirnoff–Wheeler pathway. Previously, we characterized six PMM genes(Ta PMM-A1, A2, B1, B2, D1 and D2) in common wheat(Triticum aestivum, AABBDD).Here, we report a molecular genetic analysis of PMM genes in Triticum monococcum(AmAm), a diploid wheat species whose Amgenome is closely related to the A genome of common wheat. Two distinct PMM genes, Tm PMM-1 and Tm PMM-2, were found in T. monococcum. The coding region of Tm PMM-1 was intact and highly conserved. In contrast, two main Tm PMM-2 alleles were identified, with Tm PMM-2a possessing an intact coding sequence and Tm PMM-2b being a pseudogene. The transcript level of Tm PMM-2a was much higher than that of Tm PMM-2b, and a bacterially expressed Tm PMM-2a recombinant protein displayed relatively high PMM activity. In general, the total transcript level of PMM was substantially higher in accessions carrying Tm PMM-1 and Tm PMM-2a than those harboring Tm PMM-1 and Tm PMM-2b. However, total PMM protein and activity levels did not differ drastically between the two genotypes. This work provides new information on PMM genes in T. monococcum and expands our understanding on Triticeae PMM genes, which may aid further functional and applied studies of PMM in crop plants.

  4. Gene hunting: molecular analysis of the chicken genome

    NARCIS (Netherlands)

    Crooijmans, R.P.M.A.

    2000-01-01

    This dissertation describes the development of molecular tools to identify genes that are involved in production and health traits in poultry. To unravel the chicken genome, fluorescent molecular markers (microsatellite markers) were developed and optimized to perform high throughput

  5. Genetic divergence through joint analysis of morphoagronomic and molecular characters in accessions of Jatropha curcas.

    Science.gov (United States)

    Pestana-Caldas, C N; Silva, S A; Machado, E L; de Souza, D R; Cerqueira-Pereira, E C; Silva, M S

    2016-10-05

    The aim of this study was to investigate the genetic divergence between accessions of Jatropha curcas through joint analysis of morphoagronomic and molecular characters. To this end, we investigated 11 morphoagronomic characters and performed molecular genotyping, using 23 inter-simple sequence repeat (ISSR) primers in 46 accessions of J. curcas. We calculated the contribution of each character on divergence using analysis of variance. The grouping among accessions was performed using the Ward-MLM (modified location model) method, using morphoagronomic and molecular data, whereas the cophenetic correlation was obtained based on Gower's algorithm. There were significant differences in all growth-related characteristics: number of primary and secondary branches per plant, plant height, and stem diameter. For characters related to grain production, differences were found for number of fruit clusters per plant and number of inflorescence clusters per plant and average number of seeds per fruit. The greatest phenotypic variation was found in plant height (59.67- 222.33 cm), whereas the smallest variation was found in average number of seeds per fruit (0-2.90), followed by the number of fruit clusters per plant (0-8.67). In total, 94 polymorphic ISSR fragments were obtained. The genotypic grouping identified six groups, indicating that there is genetic divergence among the accessions. The most promising crossings for future hybridization were identified among accessions UFRB60 and UFVJC45, and UFRB61 and UFVJC18. In conclusion, the joint analysis of morphoagronomic characters and ISSR markers is an efficient method to assess the genetic divergence in J. curcas.

  6. Sequence analysis of serum albumins reveals the molecular evolution of ligand recognition properties.

    Science.gov (United States)

    Fanali, Gabriella; Ascenzi, Paolo; Bernardi, Giorgio; Fasano, Mauro

    2012-01-01

    Serum albumin (SA) is a circulating protein providing a depot and carrier for many endogenous and exogenous compounds. At least seven major binding sites have been identified by structural and functional investigations mainly in human SA. SA is conserved in vertebrates, with at least 49 entries in protein sequence databases. The multiple sequence analysis of this set of entries leads to the definition of a cladistic tree for the molecular evolution of SA orthologs in vertebrates, thus showing the clustering of the considered species, with lamprey SAs (Lethenteron japonicum and Petromyzon marinus) in a separate outgroup. Sequence analysis aimed at searching conserved domains revealed that most SA sequences are made up by three repeated domains (about 600 residues), as extensively characterized for human SA. On the contrary, lamprey SAs are giant proteins (about 1400 residues) comprising seven repeated domains. The phylogenetic analysis of the SA family reveals a stringent correlation with the taxonomic classification of the species available in sequence databases. A focused inspection of the sequences of ligand binding sites in SA revealed that in all sites most residues involved in ligand binding are conserved, although the versatility towards different ligands could be peculiar of higher organisms. Moreover, the analysis of molecular links between the different sites suggests that allosteric modulation mechanisms could be restricted to higher vertebrates.

  7. Integrative network analysis unveils convergent molecular pathways in Parkinson's disease and diabetes.

    Science.gov (United States)

    Santiago, Jose A; Potashkin, Judith A

    2013-01-01

    Shared dysregulated pathways may contribute to Parkinson's disease and type 2 diabetes, chronic diseases that afflict millions of people worldwide. Despite the evidence provided by epidemiological and gene profiling studies, the molecular and functional networks implicated in both diseases, have not been fully explored. In this study, we used an integrated network approach to investigate the extent to which Parkinson's disease and type 2 diabetes are linked at the molecular level. Using a random walk algorithm within the human functional linkage network we identified a molecular cluster of 478 neighboring genes closely associated with confirmed Parkinson's disease and type 2 diabetes genes. Biological and functional analysis identified the protein serine-threonine kinase activity, MAPK cascade, activation of the immune response, and insulin receptor and lipid signaling as convergent pathways. Integration of results from microarrays studies identified a blood signature comprising seven genes whose expression is dysregulated in Parkinson's disease and type 2 diabetes. Among this group of genes, is the amyloid precursor protein (APP), previously associated with neurodegeneration and insulin regulation. Quantification of RNA from whole blood of 192 samples from two independent clinical trials, the Harvard Biomarker Study (HBS) and the Prognostic Biomarker Study (PROBE), revealed that expression of APP is significantly upregulated in Parkinson's disease patients compared to healthy controls. Assessment of biomarker performance revealed that expression of APP could distinguish Parkinson's disease from healthy individuals with a diagnostic accuracy of 80% in both cohorts of patients. These results provide the first evidence that Parkinson's disease and diabetes are strongly linked at the molecular level and that shared molecular networks provide an additional source for identifying highly sensitive biomarkers. Further, these results suggest for the first time that

  8. Integrative network analysis unveils convergent molecular pathways in Parkinson's disease and diabetes.

    Directory of Open Access Journals (Sweden)

    Jose A Santiago

    Full Text Available Shared dysregulated pathways may contribute to Parkinson's disease and type 2 diabetes, chronic diseases that afflict millions of people worldwide. Despite the evidence provided by epidemiological and gene profiling studies, the molecular and functional networks implicated in both diseases, have not been fully explored. In this study, we used an integrated network approach to investigate the extent to which Parkinson's disease and type 2 diabetes are linked at the molecular level.Using a random walk algorithm within the human functional linkage network we identified a molecular cluster of 478 neighboring genes closely associated with confirmed Parkinson's disease and type 2 diabetes genes. Biological and functional analysis identified the protein serine-threonine kinase activity, MAPK cascade, activation of the immune response, and insulin receptor and lipid signaling as convergent pathways. Integration of results from microarrays studies identified a blood signature comprising seven genes whose expression is dysregulated in Parkinson's disease and type 2 diabetes. Among this group of genes, is the amyloid precursor protein (APP, previously associated with neurodegeneration and insulin regulation. Quantification of RNA from whole blood of 192 samples from two independent clinical trials, the Harvard Biomarker Study (HBS and the Prognostic Biomarker Study (PROBE, revealed that expression of APP is significantly upregulated in Parkinson's disease patients compared to healthy controls. Assessment of biomarker performance revealed that expression of APP could distinguish Parkinson's disease from healthy individuals with a diagnostic accuracy of 80% in both cohorts of patients.These results provide the first evidence that Parkinson's disease and diabetes are strongly linked at the molecular level and that shared molecular networks provide an additional source for identifying highly sensitive biomarkers. Further, these results suggest for the first

  9. Molecular and biopharmaceutical investigation of alginate-inulin synbiotic coencapsulation of probiotic to target the colon.

    Science.gov (United States)

    Atia, Abdelbasset; Gomma, Ahmed I; Fliss, Ismail; Beyssac, Eric; Garrait, Ghislain; Subirade, Muriel

    2017-03-01

    Colon targeting, as a site-specific delivery for oral formulation, remains a major challenge, especially for sensitive bioactive components such as therapeutic forms of phages, live attenuated virus and prebiotics-probiotics association. Synbiotics could be used to protect encapsulated probiotics during the gastrointestinal tract and control their release in the colon. To achieve these goals, effective prebiotics, such as inulin, could be combined with alginate - the most exploited polymer used for probiotic encapsulation - in the form of beads. This work aimed to study the biopharmaceutical behaviour of alginate beads (A) and inulin-alginate beads of different inulin concentrations (5 or 20%) in 2% alginate (AI5, AI20). Beads were loaded with three probiotic strains (Pediococcus acidilactici Ul5, Lactobacillus reuteri and Lactobacillus salivarius). Dissolution of beads was studied by USP4 under conditions simulating the gastrointestinal condition. The survival rates of the bacterial strains were measured by a specific qPCR bacterial count. Mucoadhesiveness of beads was studied by an ex vivo method using intestinal mucosa. To understand the behaviour of each formulation, the ultrastructure of the polymeric network was studied using scanning electron microscopy (SEM). Molecular interactions between alginate and inulin were studied by Fourier transform infra-red spectroscopy (FTIR). Dissolution results suggested that the presence of inulin in beads provided more protection for the tested bacterial strains against the acidic pH. AI5 was the most effective formulation to deliver probiotics to the colon simulation conditions. FTIR and SEM investigations explained the differences in behaviour of each formula. The developed symbiotic form provided a promising matrix for the development of colonic controlled release systems.

  10. Investigation of the Behavior of Ethylene Molecular Films Using High Resolution Adsorption Isotherms and Neutron Scattering

    International Nuclear Information System (INIS)

    Barbour, Andi M.; Telling, Mark T.; Larese, John Z.

    2010-01-01

    The wetting behavior of ethylene adsorbed on MgO(100) was investigated from 83-135 K using high resolution volumetric adsorption isotherms. The results are compared to ethylene adsorption on graphite, a prototype adsorption system, in an effort to gain further insight into the forces that drive the observed film growth. Layering transitions for ethylene on MgO(100) are observed below the bulk triple point of ethylene (T = 104.0 K). The formation of three discrete adlayers is observed on the MgO(100) surface; onset of the second and third layers occurs at 79.2 ± 1.3 K and 98.3 ± 0.9 K, respectively. Thermodynamic quantities such as differential enthalpy and entropy, heat of adsorption, and isosteric heat of adsorption are determined and compared to the previously published values for ethylene on graphite. The average area occupied by a ethylene molecule on MgO(100) is 22.6 ± 1.1 (angstrom) 2 molecule -1 . The locations of two phase transitions are identified (i.e., layer critical temperatures at T c2 (n=1) at 108.6 ± 1.7 K and T c2 (n=2) at 116.5 ± 1.2 K) and a phase diagram is proposed. Preliminary neutron diffraction measurements reveal evidence of a monolayer solid with a lattice constant of ∼4.2 (angstrom). High resolution INS measurements show that the onset to dynamical motion and monolayer melting take place at 35 K and 65 K, respectively. The data reported here exhibit a striking similarity to ethylene on graphite which suggests that molecule-molecule interactions play an important role in determining the physical properties and growth of molecularly thin ethylene films.

  11. Investigation and molecular docking studies of Bassianolide from Lecanicillium lecanii against Plutella xylostella (Lepidoptera: Plutellidae).

    Science.gov (United States)

    Ravindran, Keppanan; Sivaramakrishnan, Sivaperumal; Hussain, Mubasher; Dash, Chandra Kanta; Bamisile, Bamisope Steve; Qasim, Muhammad; Liande, Wang

    2018-04-01

    Entomopathogenic fungi are rich sources of bioactive secondary metabolites that possess insecticidal properties. The present study reported a novel approach for the identification of insecticidal compounds produced by Lecanicillium lecanii 09 and to assess their toxicity against the diamondback moth Plutella xylostella L. The cyclic peptides groups of toxic substances were separated from L. lecanii 09 through submerged liquid state fermentation. The most abundant toxic metabolite, Bassianolide was purified by high-performance liquid chromatography (HPLC) and its molecular weight and purity were determined by Liquid chromatography - mass spectroscopy (LC-MS), Fourier transformed infrared spectroscopy (FT-IR), and H 1 nuclear magnetic resonance (NMR) respectively. Subsequently, the toxicity of bassianolide was tested against third instar larvae of P. xylostella at three different concentrations (0.01, 0.1, 0.5 mg/ml). The results showed that higher concentration of 0.5 mg/ml had significant maximum mortality at 120 hour post inoculation. Furthermore, we investigated the ligand-target interaction of secondary metabolite binding with target insect immune receptor proteins and predicted the role of toxicity against insect host. This is the first study to report the infection process and the interaction of fungal mediated cyclicdepsipeptide compound (bassianolide) from L. lecanii 09 against the insect host P. xylostella. This novel approach provides a potential impact on biological control using natural toxic compound which acts as good inhibitor on pest insect and prevents toxicity hazards, pollution as well as ecocidal effects killing several beneficial insects. Copyright © 2018 Elsevier Inc. All rights reserved.

  12. 2D IR spectra of cyanide in water investigated by molecular dynamics simulations

    Science.gov (United States)

    Lee, Myung Won; Carr, Joshua K.; Göllner, Michael; Hamm, Peter; Meuwly, Markus

    2013-01-01

    Using classical molecular dynamics simulations, the 2D infrared (IR) spectroscopy of CN− solvated in D2O is investigated. Depending on the force field parametrizations, most of which are based on multipolar interactions for the CN− molecule, the frequency-frequency correlation function and observables computed from it differ. Most notably, models based on multipoles for CN− and TIP3P for water yield quantitatively correct results when compared with experiments. Furthermore, the recent finding that T 1 times are sensitive to the van der Waals ranges on the CN− is confirmed in the present study. For the linear IR spectrum, the best model reproduces the full widths at half maximum almost quantitatively (13.0 cm−1 vs. 14.9 cm−1) if the rotational contribution to the linewidth is included. Without the rotational contribution, the lines are too narrow by about a factor of two, which agrees with Raman and IR experiments. The computed and experimental tilt angles (or nodal slopes) α as a function of the 2D IR waiting time compare favorably with the measured ones and the frequency fluctuation correlation function is invariably found to contain three time scales: a sub-ps, 1 ps, and one on the 10-ps time scale. These time scales are discussed in terms of the structural dynamics of the surrounding solvent and it is found that the longest time scale (≈10 ps) most likely corresponds to solvent exchange between the first and second solvation shell, in agreement with interpretations from nuclear magnetic resonance measurements.

  13. Phase sensitive molecular dynamics of self-assembly glycolipid thin films: A dielectric spectroscopy investigation

    Science.gov (United States)

    Velayutham, T. S.; Ng, B. K.; Gan, W. C.; Majid, W. H. Abd.; Hashim, R.; Zahid, N. I.; Chaiprapa, Jitrin

    2014-08-01

    Glycolipid, found commonly in membranes, is also a liquid crystal material which can self-assemble without the presence of a solvent. Here, the dielectric and conductivity properties of three synthetic glycolipid thin films in different thermotropic liquid crystal phases were investigated over a frequency and temperature range of (10-2-106 Hz) and (303-463 K), respectively. The observed relaxation processes distinguish between the different phases (smectic A, columnar/hexagonal, and bicontinuous cubic Q) and the glycolipid molecular structures. Large dielectric responses were observed in the columnar and bicontinuous cubic phases of the longer branched alkyl chain glycolipids. Glycolipids with the shortest branched alkyl chain experience the most restricted self-assembly dynamic process over the broad temperature range studied compared to the longer ones. A high frequency dielectric absorption (Process I) was observed in all samples. This is related to the dynamics of the hydrogen bond network from the sugar group. An additional low-frequency mechanism (Process II) with a large dielectric strength was observed due to the internal dynamics of the self-assembly organization. Phase sensitive domain heterogeneity in the bicontinuous cubic phase was related to the diffusion of charge carriers. The microscopic features of charge hopping were modelled using the random walk scheme, and two charge carrier hopping lengths were estimated for two glycolipid systems. For Process I, the hopping length is comparable to the hydrogen bond and is related to the dynamics of the hydrogen bond network. Additionally, that for Process II is comparable to the bilayer spacing, hence confirming that this low-frequency mechanism is associated with the internal dynamics within the phase.

  14. Investigating the Fundamentals of Molecular Depth Profiling Using Strong-field Photoionization of Sputtered Neutrals

    Science.gov (United States)

    Willingham, D.; Brenes, D. A.; Winograd, N.; Wucher, A.

    2010-01-01

    Molecular depth profiles of model organic thin films were performed using a 40 keV C60+ cluster ion source in concert with TOF-SIMS. Strong-field photoionization of intact neutral molecules sputtered by 40 keV C60+ primary ions was used to analyze changes in the chemical environment of the guanine thin films as a function of ion fluence. Direct comparison of the secondary ion and neutral components of the molecular depth profiles yields valuable information about chemical damage accumulation as well as changes in the molecular ionization probability. An analytical protocol based on the erosion dynamics model is developed and evaluated using guanine and trehalose molecular secondary ion signals with and without comparable laser photoionization data. PMID:26269660

  15. Molecular epidemiological investigation of Brucella melitensis circulating in Mongolia by MLVA16.

    Science.gov (United States)

    Kang, Sung-Il; Her, Moon; Erdenebaataar, Janchivdorj; Vanaabaatar, Batbaatar; Cho, Hyorim; Sung, So-Ra; Lee, Jin Ju; Jung, Suk Chan; Park, Yong Ho; Kim, Ji-Yeon

    2017-02-01

    Mongolia has a high incidence of brucellosis in human and animals due to livestock husbandry. To investigate the genetic characteristics of Mongolian B. melitensis, an MLVA (multi-locus variable-number tandem-repeat analysis)-16 assay was performed with 94 B. melitensis isolates. They were identified as B. melitensis biovar (bv.) 1 (67), 3 (10) and Rev. 1 vaccine strains (17) using a classical biotyping and multiplex PCR. In genotyping, three human isolates were grouped at 2 genotypes with sheep isolates, and it implies that B. melitensis are cross-infected between human and livestock. In the parsimony analysis, Mongolian B. melitensis isolates had high genetic similarity with Chinese strains, likely due to the geographical proximity, clustered distinctively as compared with other foreign isolates. B. melitensis Rev. 1 vaccine strains were divided into 4 genotypes with 92% similarity. In the analysis of Rev.1 strains, the risk of mutation of vaccine strain might not be overlooked. Animal quarantines should be strengthened to prevent the spread of Brucella species among adjacent countries. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Investigation of mechanisms and molecular epidemiology of linezolid nonsusceptible Enterococcus faecalis isolated from a teaching hospital in China.

    Science.gov (United States)

    Li, Bin; Ma, Chuan-Ling; Yu, Xiao; Sun, Yao; Li, Mei-Mei; Ye, Jian-Zhong; Zhang, Ya-Pei; Wu, Qing; Zhou, Tie-Li

    2016-08-01

    The epidemiological and molecular characteristics of eight linezolid nonsusceptible Enterococcus faecalis isolated from a teaching hospital in China (January to July 2014) were investigated. The target site modifications and cfr gene associated with linezolid resistance were not found. Results of the epidemiological investigation indicated that linezolid resistance possibly occurred on several independent occasions and was often not related to linezolid administration. Copyright © 2015. Published by Elsevier B.V.

  17. High excitation rovibrational molecular analysis in warm environments

    Science.gov (United States)

    Zhang, Ziwei; Stancil, Phillip C.; Cumbee, Renata; Ferland, Gary J.

    2017-06-01

    Inspired by advances in infrared observation (e.g., Spitzer, Herschel and ALMA), we investigate rovibrational emission CO and SiO in warm astrophysical environments. With recent innovation in collisional rate coefficients and rescaling methods, we are able to construct more comprehensive collisional data with high rovibrational states (vibration up to v=5 and rotation up to J=40) and multiple colliders (H2, H and He). These comprehensive data sets are used in spectral simulations with the radiative transfer codes RADEX and Cloudy. We obtained line ratio diagnostic plots and line spectra for both near- and far-infrared emission lines over a broad range of density and temperature for the case of a uniform medium. Considering the importance of both molecules in probing conditions and activities of UV-irradiated interstellar gas, we model rovibrational emission in photodissociation region (PDR) and AGB star envelopes (such as VY Canis Majoris, IK Tau and IRC +10216) with Cloudy. Rotational diagrams, energy distribution diagrams, and spectra are produced to examine relative state abundances, line emission intensity, and other properties. With these diverse models, we expect to have a better understanding of PDRs and expand our scope in the chemical architecture and evolution of AGB stars and other UV-irradiated regions. The soon to be launched James Webb Space Telescope (JWST) will provide high resolution observations at near- to mid-infrared wavelengths, which opens a new window to study molecular vibrational emission calling for more detailed chemical modeling and comprehensive laboratory astrophysics data on more molecules. This work was partially supported by NASA grants NNX12AF42G and NNX15AI61G. We thank Benhui Yang, Kyle Walker, Robert Forrey, and N. Balakrishnan for collaborating on the collisional data adopted in the current work.

  18. Molecular analysis of radiation injury in rat taste buds

    International Nuclear Information System (INIS)

    Nakagawa, K.; Abe, K.

    2003-01-01

    Full text: A critical adverse effect of radiation therapy for head and neck cancer is the resulting decreased sense of taste, which greatly impairs patients' quality of life. Irradiation of the head and neck area decreases the sense of taste within one or two weeks and recovery takes about one month. Although taste bud cells are intimately involved in these manifestations, few basic studies in this area have been reported. Here, we investigate the injury and recovery process of taste bud tissue after irradiation, at the molecular and cellular levels. Rat tongues were selectively irradiated once with 15 Gy of 6 MV X-rays. Immediately thereafter and at periods up to 30 days samples were collected for HE staining, BrdU labelling, p21 and p53 immunohistochemistry, and TUNEL staining. Six days after irradiation, morphologically-identified taste bud cells, as well as the surrounding epithelial tissue, were no longer visible. Immature bud cells reappeared ten days after irradiation, and looked morphologically normal at 13 to 15 days.BrdU labelling revealed DNA synthesis arrest in of epithelial cells 10 days after irradiation. Cells in the basal layer expressed p21 four hours after irradiation. Prior to that, it, p53 accumulation was observed in the nucleus. Expression of p21 was no longer detectable by on the sixth day or later, and DNA synthesis resumed around the eighth day. No apoptosis was detected at any time. The disappearance and reappearance of taste bud cells after a single 15-Gy irradiation dose can be explained by temporary cell cycle arrest in taste bud stem cells, which is regulated by p21

  19. Molecular analysis of the bacterial diversity in uranium mill tailings

    International Nuclear Information System (INIS)

    Geissler, A.

    2003-04-01

    A culture-independent molecular approach has been applied to investigate the bacterial diversity in three uranium contaminated sites. The three analysed soil samples have been collected from the uranium waste pile Haberland near Johanngeorgenstadt (Germany), from the uranium mill tailings in Gunnison, Colorado (USA) and from the uranium mill tailings in Shiprock, New Mexico (USA). The 16S rDNA fragments which has been isolated through direct lysis of the whole-DNA were amplified by the use of the universal primers 16S 43f and 16S 1404r and cloned. With restriction fragment length polymorphismus (RFLP) were the clones screened and one representative of all RFLP types that occurred more than once in the clone library was sequenced and analysed. In spite of the contamination a considerable diversity and significant differences in the composition of the natural bacterial communities in these three sites have been found. In the sample collected from the waste pile Haberland near Johanngeorgenstadt α-Proteobacteria and representatives of the Holophaga/Acidobacterium were numerically predominant. The distribution of bacteria in the sample collected from uranium mill tailings Gunnison was very similar to those found in the Haberland waste pile, but there were found besides α-Proteobacteria and representatives of Holophaga/Acidobacterium a lot of γ-Proteobacteria. The structure of the bacterial community in the sample collected from the uranium mill tailings Shiprock was significantly different. Only some representatives of the Holophaga/Acidobacterium and α-Proteobacteria were represented. Large populations of Bacilli, γ-Proteobacteria and green non sulfur bacteria were dominant in this sample. (orig.)

  20. How does the plasmonic enhancement of molecular absorption depend on the energy gap between molecular excitation and plasmon modes: a mixed TDDFT/FDTD investigation.

    Science.gov (United States)

    Sun, Jin; Li, Guang; Liang, WanZhen

    2015-07-14

    A real-time time-dependent density functional theory coupled with the classical electrodynamics finite difference time domain technique is employed to systematically investigate the optical properties of hybrid systems composed of silver nanoparticles (NPs) and organic adsorbates. The results demonstrate that the molecular absorption spectra throughout the whole energy range can be enhanced by the surface plasmon resonance of Ag NPs; however, the absorption enhancement ratio (AER) for each absorption band differs significantly from the others, leading to the quite different spectral profiles of the hybrid complexes in contrast to those of isolated molecules or sole NPs. Detailed investigations reveal that the AER is sensitive to the energy gap between the molecular excitation and plasmon modes. As anticipated, two separate absorption bands, corresponding to the isolated molecules and sole NPs, have been observed at a large energy gap. When the energy gap approaches zero, the molecular excitation strongly couples with the plasmon mode to form the hybrid exciton band, which possesses the significantly enhanced absorption intensity, a red-shifted peak position, a surprising strongly asymmetric shape of the absorption band, and the nonlinear Fano effect. Furthermore, the dependence of surface localized fields and the scattering response functions (SRFs) on the geometrical parameters of NPs, the NP-molecule separation distance, and the external-field polarizations has also been depicted.

  1. The molecular turn in psychiatry: a philosophical analysis.

    Science.gov (United States)

    Rudnick, Abraham

    2002-06-01

    Biological psychiatry has been dominated by a psychopharmacologically-driven neurotransmitter dysfunction paradigm. The objective of this paper is to explore a reductionist assumption underlying this paradigm, and to suggest an improvement on it. The methods used are conceptual analysis with a comparative approach, particularly using illustrations from the history of both biological psychiatry and molecular biology. The results are that complete reduction to physicochemical explanations is not fruitful, at least in the initial stages of research in the medical and life sciences, and that an appropriate (non-reducible) integrative principle--addressing a property of the whole system under study--is required for each domain of research. This is illustrated in Pauling's use of a topological integrative principle for the discovery of the functioning of proteins and in Watson and Crick's use of the notion of a genetic code as an integrative principle for the discovery of the structure of genes. The neurotransmitter dysfunction paradigm addresses single molecules and their neural pathways, yet their interactions within the CNS as a whole seem most pertinent to mental disorders such as schizophrenia. The lack within biological psychiatry of an integrative principle addressing a property of the CNS as a whole may be responsible for the empirical failure of orthomolecular psychiatry, as well as for the central role that serendipity has played in the study of mental disorders, which is dominated by the neurotransmitter paradigm. The conclusion is that research in biological psychiatry may benefit from using, at least initially, some integrative principle(s) addressing a property of the CNS as a whole, such as connectionism or a hierarchical notion.

  2. microsatellite analysis of the correlation between molecular and ...

    African Journals Online (AJOL)

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    3Northeast Normal University, Laboratory of Plant Molecular Epigenetics, Changchun China, Zip 130024 ... grounds. Furthermore, recent evidences that the environment can influence the ..... Forty Coffee Varieties Assessed by RAPD. Markers ...

  3. Analysis of Time Reversible Born-Oppenheimer Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Lin Lin

    2013-12-01

    Full Text Available We analyze the time reversible Born-Oppenheimer molecular dynamics (TRBOMD scheme, which preserves the time reversibility of the Born-Oppenheimer molecular dynamics even with non-convergent self-consistent field iteration. In the linear response regime, we derive the stability condition, as well as the accuracy of TRBOMD for computing physical properties, such as the phonon frequency obtained from the molecular dynamics simulation. We connect and compare TRBOMD with Car-Parrinello molecular dynamics in terms of accuracy and stability. We further discuss the accuracy of TRBOMD beyond the linear response regime for non-equilibrium dynamics of nuclei. Our results are demonstrated through numerical experiments using a simplified one-dimensional model for Kohn-Sham density functional theory.

  4. Investigating the composition of organic aerosol resulting from cyclohexene ozonolysis: low molecular weight and heterogeneous reaction products

    Directory of Open Access Journals (Sweden)

    J. F. Hamilton

    2006-01-01

    Full Text Available The composition of organic aerosol formed from the gas phase ozonolysis of cyclohexene has been investigated in a smog chamber experiment. Comprehensive gas chromatography with time of flight mass spectrometric detection was used to determine that dicarboxylic acids and corresponding cyclic anhydrides dominated the small gas phase reaction products found in aerosol sampled during the first hour after initial aerosol formation. Structural analysis of larger more polar molecules was performed using liquid chromatography with ion trap tandem mass spectrometry. This indicated that the majority of identified organic mass was in dimer form, built up from combinations of the most abundant small acid molecules, with frequent indication of the inclusion of adipic acid. Trimers and tetramers potentially formed via similar acid combinations were also observed in lower abundances. Tandem mass spectral data indicated dimers with either acid anhydride or ester functionalities as the linkage between monomers. High-resolution mass spectrometry identified the molecular formulae of the most abundant dimer species to be C10H16O6, C11H18O6, C10H14O8 and C11H16O8 and could be used in some cases to reduce uncertainty in exact chemical structure determination by tandem MS.

  5. Molecular dynamics investigation of the physisorption and interfacial characteristics of NBR chains on carbon nanotubes with different characteristics

    Directory of Open Access Journals (Sweden)

    Kun Li

    2017-07-01

    Full Text Available The present study investigates the physisorption and interfacial interactions between multiwalled carbon nanotubes (MWNTs with different characteristics, including different numbers of walls and different functional groups, and acrylonitrile-butadiene rubber (NBR polymer chains based on molecular dynamics simulations performed using modeled MWNT/NBR compound systems. The effects of the initial orientation of NBR chains and their relative distances to nanotubes, number of nanotube layers, and the surface functional groups of nanotubes on nanotube/polymer interactions are examined. Analysis is conducted according to the final configuration obtained in conjunction with the binding energy (Eb, radius of gyration (Rg and end-to-end distance (h. The results show that the final conformations of NBR chains adsorbed on MWNT surfaces is associated with the initial relative angle of the NBR chains and their distance from the nanotubes. For non-functionalized MWNTs, Eb is almost directly proportional to Rg under equivalent parameters. Moreover, it is observed that functional groups hinder the wrapping of NBR chains on the MWNT surfaces. This indicates that functional groups do not always benefit the macro-mechanical properties of the composites. Moreover, the type of the major interaction force has been dramatically changed into electrostatic force from vdW force because of functionalization.

  6. Molecular dynamics investigation of the physisorption and interfacial characteristics of NBR chains on carbon nanotubes with different characteristics

    Science.gov (United States)

    Li, Kun; Gu, Boqin

    2017-07-01

    The present study investigates the physisorption and interfacial interactions between multiwalled carbon nanotubes (MWNTs) with different characteristics, including different numbers of walls and different functional groups, and acrylonitrile-butadiene rubber (NBR) polymer chains based on molecular dynamics simulations performed using modeled MWNT/NBR compound systems. The effects of the initial orientation of NBR chains and their relative distances to nanotubes, number of nanotube layers, and the surface functional groups of nanotubes on nanotube/polymer interactions are examined. Analysis is conducted according to the final configuration obtained in conjunction with the binding energy (Eb), radius of gyration (Rg) and end-to-end distance (h). The results show that the final conformations of NBR chains adsorbed on MWNT surfaces is associated with the initial relative angle of the NBR chains and their distance from the nanotubes. For non-functionalized MWNTs, Eb is almost directly proportional to Rg under equivalent parameters. Moreover, it is observed that functional groups hinder the wrapping of NBR chains on the MWNT surfaces. This indicates that functional groups do not always benefit the macro-mechanical properties of the composites. Moreover, the type of the major interaction force has been dramatically changed into electrostatic force from vdW force because of functionalization.

  7. The origin of the cooperativity in the streptavidin-biotin system: A computational investigation through molecular dynamics simulations

    Science.gov (United States)

    Liu, Fengjiao; Zhang, John Z. H.; Mei, Ye

    2016-06-01

    Previous experimental study measuring the binding affinities of biotin to the wild type streptavidin (WT) and three mutants (S45A, D128A and S45A/D128A double mutant) has shown that the loss of binding affinity from the double mutation is larger than the direct sum of those from two single mutations. The origin of this cooperativity has been investigated in this work through molecular dynamics simulations and the end-state free energy method using the polarized protein-specific charge. The results show that this cooperativity comes from both the enthalpy and entropy contributions. The former contribution mainly comes from the alternations of solvation free energy. Decomposition analysis shows that the mutated residues nearly have no contributions to the cooperativity. Instead, N49 and S88, which are located at the entry of the binding pocket and interact with the carboxyl group of biotin, make the dominant contribution among all the residues in the first binding shell around biotin.

  8. Molecular characterization of two microalgal strains in Egypt and investigation of the antimicrobial activity of their extracts

    Directory of Open Access Journals (Sweden)

    El Semary, NA.

    2013-01-01

    Full Text Available The emergence of new pathogens and the increasing drug-resistance of recognized ones pose a difficult challenge. One way that this challenge is being addressed is through the discovery of new cost-effective drug resources in the form of bioactive compounds. Algae represent a promising source of bioactive compounds in this regard. In the present research, we used molecular and phylogenetic analysis to isolate and identify two microalgal strains. We found that one strain belonged to the phylum chrysophyta and the other to the cyanobacteria. We also investigated the antimicrobial activity of some of the lipophilic extracts of the two microalgal strains. Several fractions showed high individual antimicrobial bioactivity against multidrug-resistant Salmonella sp., Citrobacter sp., Aspergillus niger and Aspergillus flavus. Fraction III from Poterioochromonas malhamensis showed the highest level of activity against two multidrug-resistant bacterial pathogens. The inhibition zone diameter was 1.4 cm for Salmonella and 1.4 cm for Citrobacter. Meanwhile, another lipophilic fraction from the cyanobacterium Synechocystis salina showed broad-spectrum bioactivity (inhibition zone diameter of 0.9 cm for Aspergillus niger, 1 cm for Citrobacter and 0.9 cm for Salmonella. One lipophilic fraction from Aphanizomenon showed antifungal bioactivity against Aspergillus niger and Aspergillus flavus, where the inhibition zone diameter was 1.1 cm and 1.0 cm, respectively. The study highlights the antimicrobial bioactivity of extracts from local microalgae and emphasizes the importance of carrying out screening programs for those microorganisms.

  9. Application of forensic image analysis in accident investigations.

    Science.gov (United States)

    Verolme, Ellen; Mieremet, Arjan

    2017-09-01

    Forensic investigations are primarily meant to obtain objective answers that can be used for criminal prosecution. Accident analyses are usually performed to learn from incidents and to prevent similar events from occurring in the future. Although the primary goal may be different, the steps in which information is gathered, interpreted and weighed are similar in both types of investigations, implying that forensic techniques can be of use in accident investigations as well. The use in accident investigations usually means that more information can be obtained from the available information than when used in criminal investigations, since the latter require a higher evidence level. In this paper, we demonstrate the applicability of forensic techniques for accident investigations by presenting a number of cases from one specific field of expertise: image analysis. With the rapid spread of digital devices and new media, a wealth of image material and other digital information has become available for accident investigators. We show that much information can be distilled from footage by using forensic image analysis techniques. These applications show that image analysis provides information that is crucial for obtaining the sequence of events and the two- and three-dimensional geometry of an accident. Since accident investigation focuses primarily on learning from accidents and prevention of future accidents, and less on the blame that is crucial for criminal investigations, the field of application of these forensic tools may be broader than would be the case in purely legal sense. This is an important notion for future accident investigations. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Genetic diversity in cultivated carioca common beans based on molecular marker analysis

    Directory of Open Access Journals (Sweden)

    Juliana Morini Küpper Cardoso Perseguini

    2011-01-01

    Full Text Available A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats - SSRs and amplified fragment length polymorphisms - AFLPs for assessing the genetic diversity of carioca beans. The amount of information provided by Roger's modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm.

  11. A molecular phylogenetic analysis of the Scarabaeinae (dung beetles).

    Science.gov (United States)

    Monaghan, Michael T; Inward, Daegan J G; Hunt, Toby; Vogler, Alfried P

    2007-11-01

    The dung beetles (Scarabaeinae) include ca. 5000 species and exhibit a diverse array of morphologies and behaviors. This variation presumably reflects the adaptation to a diversity of food types and the different strategies used to avoid competition for vertebrate dung, which is the primary breeding environment for most species. The current classification gives great weight to the major behavioral types, separating the ball rollers and the tunnelers, but existing phylogenetic studies have been based on limited taxonomic or biogeographic sampling and have been contradictory. Here, we present a molecular phylogenetic analysis of 214 species of Scarabaeinae, representing all 12 traditionally recognized tribes and six biogeographical regions, using partial gene sequences from one nuclear (28S) and two mitochondrial (cox1, rrnL) genes. Length variation in 28S (588-621 bp) and rrnL (514-523 bp) was subjected to a thorough evaluation of alternative alignments, gap-coding methods, and tree searches using model-based (Bayesian and likelihood), maximum parsimony, and direct optimization analyses. The small-bodied, non-dung-feeding Sarophorus+Coptorhina were basal in all reconstructions. These were closely related to rolling Odontoloma+Dicranocara, suggesting an early acquisition of rolling behavior. Smaller tribes and most genera were monophyletic, while Canthonini and Dichotomiini each consisted of multiple paraphyletic lineages at hierarchical levels equivalent to the smaller tribes. Plasticity of rolling and tunneling was evidenced by a lack of monophyly (S-H test, p > 0.05) and several reversals within clades. The majority of previously unrecognized clades were geographical, including the well-supported Neotropical Phanaeini+Eucraniini, and a large Australian clade of rollers as well as tunneling Coptodactyla and Demarziella. Only three lineages, Gymnopleurini, Copris+Microcopris and Onthophagus, were widespread and therefore appear to be dispersive at a global scale. A

  12. Investigating the computer analysis of eddy current NDT data

    International Nuclear Information System (INIS)

    Brown, R.L.

    1979-01-01

    The objective of this activity was to investigate and develop techniques for computer analysis of eddy current nondestructive testing (NDT) data. A single frequency commercial eddy current tester and a precision mechanical scanner were interfaced with a PDP-11/34 computer to obtain and analyze eddy current data from samples of 316 stainless steel tubing containing known discontinuities. Among the data analysis techniques investigated were: correlation, Fast Fourier Transforms (FFT), clustering, and Adaptive Learning Networks (ALN). The results were considered encouraging. ALN, for example, correctly identified 88% of the defects and non-defects from a group of 153 signal indications

  13. A systematic investigation of the preparation and properties of composite carbon molecular sieves containing inorganic oxides

    Science.gov (United States)

    Foley, Henry C.

    1990-01-01

    The objective of this research is to define the methodology for the preparation and characterization of new carbon-based molecular sieves with composite structures. Carbon molecular sieves have found increasing application in the field of separation and purification of gases. These materials are relatively easy to prepare and their surfaces can be modified to some extent. It is expected that by combining inorganic oxides with the carbonaceous structure one can begin to design composite materials with a wider range of possible chemical and physical properties. In this way, the IOM-CMS materials may confer distinct advantages over pure carbon molecular sieves, not just for separation, but also for catalysis. The most recent results in the design and characterization of these IOM-CMS materials are reviewed and summarized. Directions for further research are also presented.

  14. Molecular and cytogenetic investigation of Y chromosome deletions over three generations facilitated by intracytoplasmic sperm injection.

    Science.gov (United States)

    Minor, Agata; Wong, Edgar Chan; Harmer, Karynn; Ma, Sai

    2007-08-01

    The azoospermic factor (AZF) region is critical for normal spermatogenesis since microdeletions and partial deletions have been associated with infertility. We investigate the diagnostic ability of karyotyping in detecting clinically relevant Y chromosome deletions. The clinical significance of heterochromatin deletions, microdeletions and partial AZFc deletions is also evaluated. A patient with a Yq deletion, affected by severe oligoasthenoteratozoospermia, underwent intracytoplasmic sperm injection (ICSI) which resulted in the birth of a healthy baby boy. The patient, his father and his son underwent Y chromosome microdeletion and partial AZFc deletion screening. We also studied the aneuploidy rate in the sperm of the patient by fluorescent in situ hybridization. AZF microdeletions were absent in the family. However, microdeletion analysis confirmed that the Yq deletion was limited to the heterochromatin. We found a partial AZFc gr/gr deletion in all three family members. We observed an increased rate of sex chromosome aneuploidy in the infertile patient. Cytogenetic analysis was misleading in identifying the Yq breakpoint. Infertility observed in the patient was associated with the gr/gr partial deletion. However, because of the incomplete penetrance of gr/gr deletions, the consequence of the vertical transmission of the deletion through ICSI remains unknown. Copyright (c) 2007 John Wiley & Sons, Ltd.

  15. A Molecular Investigation of Soil Organic Carbon Composition, Variability, and Spatial Distribution Across an Alpine Catchment

    Science.gov (United States)

    Hsu, H. T.; Lawrence, C. R.; Winnick, M.; Druhan, J. L.; Williams, K. H.; Maher, K.; Rainaldi, G. R.; McCormick, M. E.

    2016-12-01

    The cycling of carbon through soils is one of the least understood aspects of the global carbon cycle and represents a key uncertainty in the prediction of land-surface response to global warming. Thus, there is an urgent need for advanced characterization of soil organic carbon (SOC) to develop and evaluate a new generation of soil carbon models. We hypothesize that shifts in SOC composition and spatial distribution as a function of soil depth can be used to constrain rates of transformation between the litter layer and the deeper subsoil (extending to a depth of approximately 1 m). To evaluate the composition and distribution of SOC, we collected soil samples from East River, a shale-dominated watershed near Crested Butte, CO, and characterized relative changes in SOC species as a function of depth using elemental analysis (EA), Fourier transform infrared spectroscopy (FT-IR) and bulk C X-ray absorption spectroscopy (XAS). Our results show that total organic carbon (TOC) decreases with depth, and high total inorganic carbon (TIC) content was found in deeper soils (after 75 cm), a characteristic of the bedrock (shale). The distribution of aliphatic C relative to the parent material generally decreases with depth and that polysaccharide can be a substantial component of SOC at various depths. On the other hand, the relative distribution of aromatic C, traditionally viewed as recalcitrant, only makes up a very small part of SOC regardless of depth. These observations confirm that molecular structure is not the only determinant of SOC turnover rate. To study other contributors to SOC decomposition, we studied changes in the spatial correlation of SOC and minerals using X-ray fluorescence spectroscopy (XRF) and scanning transmission X-ray microscopy (STXM). We found that aromatics mostly locate on the surface of small soil aggregates (1-10 μm). Polysaccharides and proteins, both viewed as labile traditionally, are more evenly distributed over the interior of the

  16. Classical and quantum analysis of a hetero-triatomic molecular Bose-Einstein condensate model

    International Nuclear Information System (INIS)

    Tonel, A.P.; Kuhn, C.C.N.; Foerster, A.; Santos, G.; Roditi, I.; Santos, Z.V.T.

    2014-11-01

    We investigate an integrable Hamiltonian modelling a hetero-triatomic-molecular Bose-Einstein condensate. This model describes a mixture of two species of atoms in different proportions, which can combine to form a triatomic molecule. Beginning with a classical analysis, we determine the fixed points of the system. Bifurcations of these points separate the parameter space into different regions. Three distinct scenarios are found, varying with the atomic population imbalance. This result suggests the ground state properties of the quantum model exhibits a sensitivity on the atomic population imbalance, which is confirmed by a quantum analysis using different approaches, such as the ground-state expectation values, the behaviour of the quantum dynamics, the energy gap and the ground state fidelity. (author)

  17. Potentiometric investigations of molecular heteroconjugation equilibria of substituted phenol+n-butylamine systems in dimethyl sulfoxide

    International Nuclear Information System (INIS)

    Czaja, MaIgorzata; Baginska, Katarzyna; Kozak, Anna; Makowski, Mariusz; Chmurzynski, Lech

    2005-01-01

    Molecular heteroconjugation constants, K BHA DMSO and K AHB DMSO , expressed as their logarithms, have been determined by potentiometric titration for eleven substituted phenol+n-butylamine systems in a polar protophilic aprotic solvent, dimethyl sulfoxide (DMSO). An increasing tendency towards molecular heteroconjugation in these systems without proton transfer has been found with increasing pK a DMSO (HA), i.e., with decreasing phenol acidity. Moreover, a linear correlation has been established between the determined lgK BHA DMSO values and pK a DMSO (HA). Furthermore, overall stability constants, lgK o DMSO , could be correlated linearly with pK a DMSO (HA) values

  18. A Theoretical Investigation on Rectifying Performance of a Single Motor Molecular Device

    International Nuclear Information System (INIS)

    Lei Hui; Tan Xun-Qiong

    2015-01-01

    We report ab initio calculations of the transport behavior of a phenyl substituted molecular motor. The calculated results show that the transport behavior of the device is sensitive to the rotation degree of the rotor part. When the rotor part is parallel with the stator part, a better rectifying performance can be found in the current-voltage curve. However, when the rotor part revolves to vertical with the stator part, the currents in the positive bias region decrease slightly. More importantly, the rectifying performance disappears. Thus this offers us a new method to modulate the rectifying behavior in molecular devices. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  19. Doses in radiation accidents investigated by chromosome aberration analysis

    International Nuclear Information System (INIS)

    Lloyd, D.C.; Purrott, R.J.; Prosser, J.S.; White, A.D.; Dolphin, G.W.; Reeder, E.J.; Martin, L.C.; Priseman, S.J.; Gray, S.A.

    1979-01-01

    Results from cytogenetic investigations into 63 cases of suspected over-exposure to radiation during 1978 are reviewed. This report is the eighth in an annual series which together contain data on 390 studies. Results from all investigations have been pooled for general analysis. Brief accounts are given, in an appendix, of the circumstances behind the past year's investigations and, where possible, physical estimates of dose have been included for comparison. One case is described in more detail. It concerns a young man who deliberately irradiated himself with several sources of iridium-192 and received a dose of about 1.5 Gy as a fairly uniform whole body exposure. (author)

  20. 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.

  1. Computational and Experimental Investigations of the Molecular Scale Structure and Dynamics of Gologically Important Fluids and Mineral-Fluid Interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Bowers, Geoffrey [Alfred Univ., NY (United States)

    2017-04-05

    United States Department of Energy grant DE-FG02-10ER16128, “Computational and Spectroscopic Investigations of the Molecular Scale Structure and Dynamics of Geologically Important Fluids and Mineral-Fluid Interfaces” (Geoffrey M. Bowers, P.I.) focused on developing a molecular-scale understanding of processes that occur in fluids and at solid-fluid interfaces using the combination of spectroscopic, microscopic, and diffraction studies with molecular dynamics computer modeling. The work is intimately tied to the twin proposal at Michigan State University (DOE DE-FG02-08ER15929; same title: R. James Kirkpatrick, P.I. and A. Ozgur Yazaydin, co-P.I.).

  2. Density functional theory, comparative vibrational spectroscopic studies, highest occupied molecular orbital and lowest unoccupied molecular orbital analysis of Linezolid

    Science.gov (United States)

    Rajalakshmi, K.; Gunasekaran, S.; Kumaresan, S.

    2015-06-01

    The Fourier transform infrared spectra and Fourier transform Raman spectra of Linezolid have been recorded in the regions 4,000-400 and 4,000-100 cm-1, respectively. Utilizing the observed Fourier transform infrared spectra and Fourier transform Raman spectra data, a complete vibrational assignment and analysis of the fundamental modes of the compound have been carried out. The optimum molecular geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities, have been calculated by density functional theory with 6-31G(d,p), 6-311G(d,p) and M06-2X/6-31G(d,p) levels. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. A detailed interpretation of the infrared and Raman spectra of Linezolid is reported. Mulliken's net charges have also been calculated. Ultraviolet-visible spectrum of the title molecule has also been calculated using time-dependent density functional method. Besides, molecular electrostatic potential, highest occupied molecular orbital and lowest unoccupied molecular orbital analysis and several thermodynamic properties have been performed by the density functional theoretical method.

  3. Molecular Analysis of Endolithic Microbial Communities in Volcanic Glasses

    Science.gov (United States)

    di Meo, C. A.; Giovannoni, S.; Fisk, M.

    2002-12-01

    Terrestrial and marine volcanic glasses become mineralogically and chemically altered, and in many cases this alteration has been attributed to microbial activity. We have used molecular techniques to study the resident microbial communities from three different volcanic environments that may be responsible for this crustal alteration. Total microbial DNA was extracted from rhyolite glass of the 7 million year old Rattlesnake Tuff in eastern Oregon. The DNA was amplified using the polymerase chain reaction (PCR) with bacterial primers targeting the 16S rRNA gene. This 16S rDNA was cloned and screened with restriction fragment length polymorphism (RFLP). Out of 89 total clones screened, 46 belonged to 13 different clone families containing two or more members, while 43 clones were unique. Sequences of eight clones representing the most dominant clone families in the library were 92 to 97% similar to soil bacterial species. In a separate study, young pillow basalts (rock- and seawater-associated archaea. The six rock community profiles were quite similar to each other, and the background water communities were also similar, respectively. Both the rock and water communities shared the same dominant peak. To identify the T-RFLP peaks corresponding to the individual members of the rock and seawater communities, clone libraries of the archaeal 16S rDNA for one basalt sample (Dive 3718) and its corresponding background water sample were constructed. The most abundant archaeal genes were closely related to uncultured Group I marine Crenarchaeota that have been previously identified from similar deep-sea habitats. These archaeal genes collectively correspond to the dominant T-RFLP peak present in both the rock and water samples. In a third study, we investigated the microbial community residing in a Hawaiian Scientific Drilling Program core collected near Hilo, Hawaii. Total microbial DNA was extracted from a depth of 1351 m in the drill core (ambient temperature in the

  4. Investigation on the protein-binding properties of icotinib by spectroscopic and molecular modeling method

    Science.gov (United States)

    Zhang, Hua-xin; Xiong, Hang-xing; Li, Li-wei

    2016-05-01

    Icotinib is a highly-selective epidermal growth factor receptor tyrosine kinase inhibitor with preclinical and clinical activity in non-small cell lung cancer, which has been developed as a new targeted anti-tumor drug in China. In this work, the interaction of icotinib and human serum albumin (HSA) were studied by three-dimensional fluorescence spectra, ultraviolet spectra, circular dichroism (CD) spectra, molecular probe and molecular modeling methods. The results showed that icotinib binds to Sudlow's site I in subdomain IIA of HSA molecule, resulting in icotinib-HSA complexes formed at ground state. The number of binding sites, equilibrium constants, and thermodynamic parameters of the reaction were calculated at different temperatures. The negative enthalpy change (ΔHθ) and entropy change (ΔSθ) indicated that the structure of new complexes was stabilized by hydrogen bonds and van der Waals power. The distance between donor and acceptor was calculated according to Förster's non-radiation resonance energy transfer theory. The structural changes of HSA caused by icotinib binding were detected by synchronous spectra and circular dichroism (CD) spectra. Molecular modeling method was employed to unfold full details of the interaction at molecular level, most of which could be supported by experimental results. The study analyzed the probability that serum albumins act as carriers for this new anticarcinogen and provided fundamental information on the process of delivering icotinib to its target tissues, which might be helpful in understanding the mechanism of icotinib in cancer therapy.

  5. Structural investigation of bistrifluron using x-ray crystallography, NMR spectroscopy, and molecular modeling

    CERN Document Server

    Moon, J K; Rhee, S K; Kim, G B; Yun, H S; Chung, B J; Lee, S S; Lim, Y H

    2002-01-01

    A new insecticide, bistrifluron acts as an inhibitor of insect development and interferes with the cuticle formation of insects. Since it shows low acute oral and dermal toxicities, it can be one of potent insecticides. Based on X-ray crystallography, NMR spectroscopy and molecular modeling, the structural studies of bistrifluron have been carried out.

  6. Deep level transient spectroscopic investigation of phosphorus-doped silicon by self-assembled molecular monolayers.

    Science.gov (United States)

    Gao, Xuejiao; Guan, Bin; Mesli, Abdelmadjid; Chen, Kaixiang; Dan, Yaping

    2018-01-09

    It is known that self-assembled molecular monolayer doping technique has the advantages of forming ultra-shallow junctions and introducing minimal defects in semiconductors. In this paper, we report however the formation of carbon-related defects in the molecular monolayer-doped silicon as detected by deep-level transient spectroscopy and low-temperature Hall measurements. The molecular monolayer doping process is performed by modifying silicon substrate with phosphorus-containing molecules and annealing at high temperature. The subsequent rapid thermal annealing drives phosphorus dopants along with carbon contaminants into the silicon substrate, resulting in a dramatic decrease of sheet resistance for the intrinsic silicon substrate. Low-temperature Hall measurements and secondary ion mass spectrometry indicate that phosphorus is the only electrically active dopant after the molecular monolayer doping. However, during this process, at least 20% of the phosphorus dopants are electrically deactivated. The deep-level transient spectroscopy shows that carbon-related defects are responsible for such deactivation.

  7. Current and future molecular approaches to investigate the white pine blister rust pathosystem

    Science.gov (United States)

    B. A. Richardson; A. K. M. Ekramoddoulah; J.-J. Liu; M.-S. Kim; N. B. Klopfenstein

    2010-01-01

    Molecular genetics is proving to be especially useful for addressing a wide variety of research and management questions on the white pine blister rust pathosystem. White pine blister rust, caused by Cronartium ribicola, is an ideal model for studying biogeography, genetics, and evolution because: (1) it involves an introduced pathogen; (2) it includes multiple primary...

  8. A molecular dynamics investigation into the mechanisms of alectinib resistance of three ALK mutants.

    Science.gov (United States)

    He, Muyang; Li, Weikang; Zheng, Qingchuan; Zhang, Hongxing

    2018-01-11

    Alectinib, a highly selective next-genetation anaplastic lymphoma kinase (ALK) inhibitor, has demonstrated promising antitumor activity in patients with ALK-positive non-small cell lung carcinomas (NSCLC). However, the therapeutic benefits of alectinib is inescapably hampered by the development of acquired resistant mutations in ALK. Despite the availability of ample experimental mutagenesis data, the molecular origin and the structural motifs under alectinib binding affinity deficiencies are still ambiguous. Here, molecular dynamics (MD) simulations and molecular mechanics generalized born surface area (MM-GBSA) calculation approaches were employed to elucidate the mechanisms of alectinib resistance induced by the mutations I1171N, V1180L, and L1198F. The MD results reveal that the studied mutations could trigger the dislocation of alectinib as well as conformational changes at the inhibitor binding site, thus induce the interactional changes between alectinib and mutants. The most influenced regions are the ligand binding entrance and the hinge region, which are considered to be the dominant binding motifs accounting for the binding affinity loss in mutants. The "key and lock mechanism" between the ethyl group at position 9 of alectinib and a recognition cavity in the hinge region of ALK is presented to illustrate the major molecular origin of drug resistance. Our results provide mechanistic insight into the effect of ALK mutations resistant to alectinib, which could contribute to further rational design of inhibitors to combat the acquired resistance. © 2018 Wiley Periodicals, Inc.

  9. INVESTIGATIONS INTO MOLECULAR PATHWAYS IN THE POST GENOME ERA: CROSS SPECIES COMPARATIVE GENOMICS APPROACH

    Science.gov (United States)

    Genome sequencing efforts in the past decade were aimed at generating draft sequences of many prokaryotic and eukaryotic model organisms. Successful completion of unicellular eukaryotes, worm, fly and human genome have opened up the new field of molecular biology and function...

  10. Investigation of the Hydroxylation Mechanism of Noncoupled Copper Oxygenases by Ab Initio Molecular Dynamics Simulations

    Czech Academy of Sciences Publication Activity Database

    Meliá, C.; Ferrer, S.; Řezáč, Jan; Parisel, O.; Reinaud, O.; Moliner, V.; de la Lande, A.

    2013-01-01

    Roč. 19, č. 51 (2013), s. 17328-17337 ISSN 0947-6539 Institutional support: RVO:61388963 Keywords : ab initio calculations * copper * electron transfer * enzymes * molecular dynamics * reaction mechanisms Subject RIV: CC - Organic Chemistry Impact factor: 5.696, year: 2013

  11. Teaching Structure-Property Relationships: Investigating Molecular Structure and Boiling Point

    Science.gov (United States)

    Murphy, Peter M.

    2007-01-01

    A concise, well-organized table of the boiling points of 392 organic compounds has facilitated inquiry-based instruction in multiple scientific principles. Many individual or group learning activities can be derived from the tabulated data of molecular structure and boiling point based on the instructor's education objectives and the students'…

  12. Irreversible thermodynamic analysis and application for molecular heat engines

    Science.gov (United States)

    Lucia, Umberto; Açıkkalp, Emin

    2017-09-01

    Is there a link between the macroscopic approach to irreversibility and microscopic behaviour of the systems? Consumption of free energy keeps the system away from a stable equilibrium. Entropy generation results from the redistribution of energy, momentum, mass and charge. This concept represents the essence of the thermodynamic approach to irreversibility. Irreversibility is the result of the interaction between systems and their environment. The aim of this paper is to determine lost works in a molecular engine and compare results with macro (classical) heat engines. Firstly, irreversible thermodynamics are reviewed for macro and molecular cycles. Secondly, irreversible thermodynamics approaches are applied for a quantum heat engine with -1/2 spin system. Finally, lost works are determined for considered system and results show that macro and molecular heat engines obey same limitations. Moreover, a quantum thermodynamic approach is suggested in order to explain the results previously obtained from an atomic viewpoint.

  13. Doses in radiation accidents investigated by chromosome aberration analysis XVI: A review of cases investigated, 1985

    International Nuclear Information System (INIS)

    Lloyd, D.C.; Edwards, A.A.; Prosser, J.S.; Moquet, J.E.; Finnon, P.

    1986-04-01

    During 1985, 28 cases of suspected overexposure to ionising radiation were referred to NRPB for investigation by cytogenetic analysis, and the results are presented in this report. Of the 28 cases, 17 were associated with industrial radiography, 9 from major nuclear organisations and 2 from research, education and health institutions. In 20 cases, no biological indication of overexposure was found. The remaining 8 cases all arose from industrial uses of radiation. The highest overexposure to a sealed source in 1985 ws about 0.4 Gy from an 192 Ir source that became detached from its winding mechanism. Two serious incidents involving unsealed sources are also described; an accidental ingestion of 125 I, for which cytogenetic analysis is of limited relevance, and an inhalation of droplets of tritiated water. The latter also produced a committed dose equivalent of about 0.4 Sv, the estimates from cytogenetic analysis and urine analysis being in good agreement. (author)

  14. The effect of glycosylation on the transferrin structure: A molecular dynamic simulation analysis.

    Science.gov (United States)

    Ghanbari, Z; Housaindokht, M R; Bozorgmehr, M R; Izadyar, M

    2016-09-07

    Transferrins have been defined by the highly cooperative binding of iron and a carbonate anion to form a Fe-CO3-Tf ternary complex. As such, the layout of the binding site residues affects transferrin function significantly; In contrast to N-lobe, C-lobe binding site of the transferrin structure has been less characterized and little research which surveyed the interaction of carbonate with transferrin in the C-lobe binding site has been found. In the present work, molecular dynamic simulation was employed to gain access into the molecular level understanding of carbonate binding site and their interactions in each lobe. Residues responsible for carbonate binding of transferrin structure were pointed out. In addition, native human transferrin is a glycoprotein that two N-linked complex glycan chains located in the C-lobe. Usually, in the molecular dynamic simulation for simplifying, glycan is removed from the protein structure. Here, we explore the effect of glycosylation on the transferrin structure. Glycosylation appears to have an effect on the layout of the binding site residue and transferrin structure. On the other hand, sometimes the entire transferrin formed by separated lobes that it allows the results to be interpreted in a straightforward manner rather than more parameters required for full length protein. But, it should be noted that there are differences between the separated lobe and full length transferrin, hence, a comparative analysis by the molecular dynamic simulation was performed to investigate such structural variations. Results revealed that separation in C-lobe caused a significant structural variation in comparison to N-lobe. Consequently, the separated lobes and the full length one are different, showing the importance of the interlobe communication and the impact of the lobes on each other in the transferrin structure. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Investigating Convergence Patterns for Numerical Methods Using Data Analysis

    Science.gov (United States)

    Gordon, Sheldon P.

    2013-01-01

    The article investigates the patterns that arise in the convergence of numerical methods, particularly those in the errors involved in successive iterations, using data analysis and curve fitting methods. In particular, the results obtained are used to convey a deeper level of understanding of the concepts of linear, quadratic, and cubic…

  16. Molecular tools for carotenogenesis analysis in the zygomycete Mucor circinelloides.

    Science.gov (United States)

    Torres-Martínez, Santiago; Ruiz-Vázquez, Rosa M; Garre, Victoriano; López-García, Sergio; Navarro, Eusebio; Vila, Ana

    2012-01-01

    The carotene producer fungus Mucor circinelloides is the zygomycete more amenable to genetic manipulations by using molecular tools. Since the initial development of an effective procedure of genetic transformation, more than two decades ago, the availability of new molecular approaches such as gene replacement techniques and gene expression inactivation by RNA silencing, in addition to the sequencing of its genome, has made Mucor a valuable organism for the study of a number of processes. Here we describe in detail the main techniques and methods currently used to manipulate M. circinelloides, including transformation, gene replacement, gene silencing, RNAi, and immunoprecipitation.

  17. Large scale aggregate microarray analysis reveals three distinct molecular subclasses of human preeclampsia.

    Science.gov (United States)

    Leavey, Katherine; Bainbridge, Shannon A; Cox, Brian J

    2015-01-01

    Preeclampsia (PE) is a life-threatening hypertensive pathology of pregnancy affecting 3-5% of all pregnancies. To date, PE has no cure, early detection markers, or effective treatments short of the removal of what is thought to be the causative organ, the placenta, which may necessitate a preterm delivery. Additionally, numerous small placental microarray studies attempting to identify "PE-specific" genes have yielded inconsistent results. We therefore hypothesize that preeclampsia is a multifactorial disease encompassing several pathology subclasses, and that large cohort placental gene expression analysis will reveal these groups. To address our hypothesis, we utilized known bioinformatic methods to aggregate 7 microarray data sets across multiple platforms in order to generate a large data set of 173 patient samples, including 77 with preeclampsia. Unsupervised clustering of these patient samples revealed three distinct molecular subclasses of PE. This included a "canonical" PE subclass demonstrating elevated expression of known PE markers and genes associated with poor oxygenation and increased secretion, as well as two other subclasses potentially representing a poor maternal response to pregnancy and an immunological presentation of preeclampsia. Our analysis sheds new light on the heterogeneity of PE patients, and offers up additional avenues for future investigation. Hopefully, our subclassification of preeclampsia based on molecular diversity will finally lead to the development of robust diagnostics and patient-based treatments for this disorder.

  18. Novel insights into systemic autoimmune rheumatic diseases using shared molecular signatures and an integrative analysis.

    Science.gov (United States)

    Hudson, Marie; Bernatsky, Sasha; Colmegna, Ines; Lora, Maximilien; Pastinen, Tomi; Klein Oros, Kathleen; Greenwood, Celia M T

    2017-06-03

    We undertook this study to identify DNA methylation signatures of three systemic autoimmune rheumatic diseases (SARDs), namely rheumatoid arthritis, systemic lupus erythematosus, and systemic sclerosis, compared to healthy controls. Using a careful design to minimize confounding, we restricted our study to subjects with incident disease and performed our analyses on purified CD4 + T cells, key effector cells in SARD. We identified differentially methylated (using the Illumina Infinium HumanMethylation450 BeadChip array) and expressed (using the Illumina TruSeq stranded RNA-seq protocol) sites between cases and controls, and investigated the biological significance of this SARD signature using gene annotation databases. We recruited 13 seropositive rheumatoid arthritis, 19 systemic sclerosis, 12 systemic lupus erythematosus subjects, and 8 healthy controls. We identified 33 genes that were both differentially methylated and expressed (26 over- and 7 under-expressed) in SARD cases versus controls. The most highly overexpressed gene was CD1C (log fold change in expression = 1.85, adjusted P value = 0.009). In functional analysis (Ingenuity Pathway Analysis), the top network identified was lipid metabolism, molecular transport, small molecule biochemistry. The top canonical pathways included the mitochondrial L-carnitine shuttle pathway (P = 5E-03) and PTEN signaling (P = 8E-03). The top upstream regulator was HNF4A (P = 3E-05). This novel SARD signature contributes to ongoing work to further our understanding of the molecular mechanisms underlying SARD and provides novel targets of interest.

  19. In silico investigation of molecular effects caused by missense mutations in creatine transporter protein

    Science.gov (United States)

    Zhang, Zhe; Schwatz, Charles; Alexov, Emil

    2011-03-01

    Creatine transporter (CT) protein, which is encoded by SLC6A8 gene, is essential for taking up the creatine in the cell, which in turn plays a key role in the spatial and temporal maintenance of energy in skeletal and cardiac muscle cells. It was shown that some missense mutations in CT cause mental retardation, while others are harmless non-synonymous single nucleoside polymorphism (nsSNP). Currently fifteen missense mutations in CT are known, among which twelve are disease-causing. Sequence analysis reveals that there is no clear trend distinguishing disease-causing from harmless missense mutations. Because of that, we built 3D model of the CT using highly homologous template and use the model to investigate the effects of mutations of CT stability and hydrogen bond network. It is demonstrated that disease-causing mutations affect the folding free energy and ionization states of titratable group in much greater extend as compared with harmless mutations. Supported by grants from NLM, NIH, grant numbers 1R03LM009748 and 1R03LM009748-S1.

  20. Molecular analysis of cross-bacterial contamination detected in ...

    African Journals Online (AJOL)

    ... the isolate Delftia acidovorans BP(R2) and it is also coupled to protein with molecular weight 25-26 KDa. As well as, this bacterial contamination was the reason for the false positive results observed during the detection of HCV infections. Journal of Applied Sciences and Environmental Management Vol. 9(1) 2005: 5-10.

  1. Molecular Analysis of Multi-Drug Resistance (MDR) in ...

    African Journals Online (AJOL)

    This review therefore brings to light some of the processes involved in molecular typing of Mycobacterium tuberculosis strains like the use of restriction fragment length polymorphism (RFLP) and spoligotyping, which have become valuable tools in the epidemiology of tuberculosis, identification of genotypes and ...

  2. Cryogenic Collection of Complete Subsurface Samples for Molecular Biological Analysis

    Science.gov (United States)

    2012-05-01

    276.5318.1568 Moser, D. P., J. K. Fredrickson, D. R. Geist, E. V. Arntzen, A. D. Peacock , S.-M. W. Li, T. Spadoni, et al. (2003). Biogeochemical...Influencing Amplification Efficiency and Allele Drop-out in Single Cell PCR: Implications for Preimplantation Genetic Diagnosis. Molecular Human Reproduction

  3. Molecular Analysis of AFP and HSA Interactions with PTEN Protein

    Directory of Open Access Journals (Sweden)

    Mingyue Zhu

    2015-01-01

    Full Text Available Human cytoplasmic alpha-fetoprotein (AFP has been classified as a member of the albuminoid gene family. The protein sequence of AFP has significant homology to that of human serum albumin (HSA, but its biological characteristics are vastly different from HSA. The AFP functions as a regulator in the phosphatidylinositol 3-kinase (PI3K/protein kinase B (AKT pathway, but HSA plays a key role as a transport protein. To probe their molecular mechanisms, we have applied colocalization, coimmunoprecipitation (co-IP, and molecular docking approaches to analyze the differences between AFP and HSA. The data from colocalization and co-IP displayed a strong interaction between AFP and PTEN (phosphatase and tensin homolog, demonstrating that AFP did bind to PTEN, but HSA did not. The molecular docking study further showed that the AFP domains I and III could contact with PTEN. In silicon substitutions of AFP binding site residues at position 490M/K and 105L/R corresponding to residues K490 and R105 in HSA resulted in steric clashes with PTEN residues R150 and K46, respectively. These steric clashes may explain the reason why HSA cannot bind to PTEN. Ultimately, the experimental results and the molecular modeling data from the interactions of AFP and HSA with PTEN will help us to identify targets for designing drugs and vaccines against human hepatocellular carcinoma.

  4. Thermodynamic Models from Fluctuation Solution Theory Analysis of Molecular Simulations

    DEFF Research Database (Denmark)

    Christensen, Steen; Peters, Günther H.j.; Hansen, Flemming Yssing

    2007-01-01

    Fluctuation solution theory (FST) is employed to analyze results of molecular dynamics (MD) simulations of liquid mixtures. The objective is to generate parameters for macroscopic GE-models, here the modified Margules model. We present a strategy for choosing the number of parameters included...

  5. Molecular analysis of candidate probiotic effector molecules of Lactobacillus plantarum

    NARCIS (Netherlands)

    Remus, D.M.

    2012-01-01

    Probiotics are health-promoting microorganisms that exert their beneficial effects in several ways. While it is known that probiotic bacteria interact with cells of the host gastrointestinal tractand modulate cell-signaling responses by which they might promote health, the underlying molecular

  6. Molecular analysis of mutants of the Neurospora adenylosuccinate ...

    Indian Academy of Sciences (India)

    2012-08-07

    Aug 7, 2012 ... and mutants induced with X-ray, UV or chemical mutagens. ... We have sequenced the ad-8 locus from 13 of these mutants and identified the molecular nature ..... mutants in yeast by selection for constitutive behavior in pig-.

  7. Molecular responses and expression analysis of genes in a ...

    African Journals Online (AJOL)

    Haloxylon ammodendron (C.A Mey.) Bunge is a xero-halophytic desert shrub with excellent drought resistance and salt tolerance. To decipher the molecular responses involved in its drought resistance, the cDNA-AFLP (amplified fragment length polymorphism) technique was employed to identify genes expressed ...

  8. Molecular characterization and expression analysis of a hepcidin ...

    African Journals Online (AJOL)

    Jane

    2011-08-03

    Aug 3, 2011 ... the liver, intestine and brain were 2.4, 1.5 and 2-fold increase, respectively, compared with the control animals after 5 days .... (sex change) of RFE attracted more attention (Cheng et al., 2003 ...... Molecular Biology. New York: ...

  9. Physiological response, molecular analysis and water use efficiency ...

    African Journals Online (AJOL)

    With a view to study the effects of irrigation scheduling on the water use efficiency and physiological response and molecular basis of maize hybrids of different maturity groups, a field experiment was conducted at Water Management Research Center (WMRC), Belvatagi, University of Agricultural Sciences, Dharwad, India ...

  10. Comparative molecular analysis of old olive ( Olea europaea L ...

    African Journals Online (AJOL)

    We compared the genetic profiles of six old olive cultivars from an Eastern Mediterranean Region of Turkey to 15 modern Turkish olive cultivars from different geographical origins. The RAPD profiles successfully clarified the molecular relationships among the genotypes tested. Seventeen RAPD primers generated 153 ...

  11. Ciona intestinalis notochord as a new model to investigate the cellular and molecular mechanisms of tubulogenesis.

    Science.gov (United States)

    Denker, Elsa; Jiang, Di

    2012-05-01

    Biological tubes are a prevalent structural design across living organisms. They provide essential functions during the development and adult life of an organism. Increasing progress has been made recently in delineating the cellular and molecular mechanisms underlying tubulogenesis. This review aims to introduce ascidian notochord morphogenesis as an interesting model system to study the cell biology of tube formation, to a wider cell and developmental biology community. We present fundamental morphological and cellular events involved in notochord morphogenesis, compare and contrast them with other more established tubulogenesis model systems, and point out some unique features, including bipolarity of the notochord cells, and using cell shape changes and cell rearrangement to connect lumens. We highlight some initial findings in the molecular mechanisms of notochord morphogenesis. Based on these findings, we present intriguing problems and put forth hypotheses that can be addressed in future studies. Copyright © 2012 Elsevier Ltd. All rights reserved.

  12. Potentiometric investigations of molecular heteroconjugation equilibria of substituted phenol+n-butylamine systems in dimethyl sulfoxide

    Energy Technology Data Exchange (ETDEWEB)

    Czaja, MaIgorzata [Department of General Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk (Poland); Baginska, Katarzyna [Department of General Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk (Poland); Kozak, Anna [Department of General Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk (Poland); Makowski, Mariusz [Department of General Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk (Poland); Chmurzynski, Lech [Department of General Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk (Poland)]. E-mail: lech@chem.univ.gda.pl

    2005-08-15

    Molecular heteroconjugation constants, K{sub BHA}{sup DMSO} and K{sub AHB}{sup DMSO}, expressed as their logarithms, have been determined by potentiometric titration for eleven substituted phenol+n-butylamine systems in a polar protophilic aprotic solvent, dimethyl sulfoxide (DMSO). An increasing tendency towards molecular heteroconjugation in these systems without proton transfer has been found with increasing pK{sub a}{sup DMSO} (HA), i.e., with decreasing phenol acidity. Moreover, a linear correlation has been established between the determined lgK{sub BHA}{sup DMSO} values and pK{sub a}{sup DMSO} (HA). Furthermore, overall stability constants, lgK{sub o}{sup DMSO}, could be correlated linearly with pK{sub a}{sup DMSO} (HA) values.

  13. Ab initio investigation of the switching behavior of the dithiole-benzene nano-molecular wire

    International Nuclear Information System (INIS)

    Darvish Ganji, M.; Rungger, I.

    2008-01-01

    We report a first-principle study of electrical transport and switching behavior in a single molecular conductor consisting of a dithiole-benzene sandwiched between two Au( 100) electrodes. Ab initio total energy calculations reveal dithiole-benzene molecules on a gold surface, contacted by a monoatomic gold scanning tunneling microscope tip to have two classes of low energy conformations with differing symmetries. Lateral motion of the tip or excitation of the molecule cause it 10 change from one conformation class to the other and to switch between a strongly and a weakly conducting state. Thus, surprisingly. despite their apparent simplicity, these Au-dithiole-benzene -Au nano wires are shown to be electrically bi-stable switches, the smallest two-terminal molecular switches to date. The projected density of states and transmission coefficients are analyzed, and it suggests that the variation of the coupling between the molecule and the electrodes with external bias leads to switching behavior

  14. Northern blot analysis to investigate the abundance of microorganisms

    International Nuclear Information System (INIS)

    Krause, D.O.

    2005-01-01

    Modern molecular microbial ecology has its origins in the analysis of informative macromolecules. Zuckerkandl and Pauling proposed that certain macromolecules are relatively free from evolutionary pressure and may be considered a molecular document of the evolutionary history of the organism that carries the molecule. In their paper, they proposed that the sequence difference of a molecule is proportional to the evolutionary distance between the organisms; the greater the sequence differences the greater the evolutionary distance. A significant breakthrough with this approach in microbial systematics resulted from the work of Woese and Fox who used oligonucleotide cataloguing of 16S-rRNA to delineate the phylogenetic relationships between microorganisms. By using this approach, it was possible to demonstrate that all life on earth could be divided into three kingdoms: eukarya, procarya and archaea. The unique findings of this research was that the archaea, made up of many methanogenic and thermophilic microorganisms, were probably the most ancient life forms on earth and were not bacteria at all. One of the first applications of rRNA genes was the recovery of unique 5S-rRNA sequences from the Yellowstone hot spring. Even though the statistical utility of the short 5S sequences was limited, it demonstrated that there was a great deal of uncultured diversity within the ecosystem. This uncultured diversity was demonstrated to be highly significant when clone libraries were constructed from the Yellowstone hot spring. Universal PCR primers were used to amplify 16S-rDNA from the microbial community, and these mixed amplicons were cloned into a vector. Each insert, potentially representing a different species, was sequenced giving a snapshot of microbial diversity in the sample. A unique feature of the rRNAs is that they are hierarchical molecules. This means that there are regions where the molecules is highly conserved, others where the sequence is variable, and even

  15. Experimental investigations of micro-scale flow and heat transfer phenomena by using molecular tagging techniques

    International Nuclear Information System (INIS)

    Hu, Hui; Jin, Zheyan; Lum, Chee; Nocera, Daniel; Koochesfahani, Manoochehr

    2010-01-01

    Recent progress made in the development of novel molecule-based flow diagnostic techniques, including molecular tagging velocimetry (MTV) and lifetime-based molecular tagging thermometry (MTT), to achieve simultaneous measurements of multiple important flow variables for micro-flows and micro-scale heat transfer studies is reported in this study. The focus of the work described here is the particular class of molecular tagging tracers that relies on phosphorescence. Instead of using tiny particles, especially designed phosphorescent molecules, which can be turned into long-lasting glowing marks upon excitation by photons of appropriate wavelength, are used as tracers for both flow velocity and temperature measurements. A pulsed laser is used to 'tag' the tracer molecules in the regions of interest, and the tagged molecules are imaged at two successive times within the photoluminescence lifetime of the tracer molecules. The measured Lagrangian displacement of the tagged molecules provides the estimate of the fluid velocity. The simultaneous temperature measurement is achieved by taking advantage of the temperature dependence of phosphorescence lifetime, which is estimated from the intensity ratio of the tagged molecules in the acquired two phosphorescence images. The implementation and application of the molecular tagging approach for micro-scale thermal flow studies are demonstrated by two examples. The first example is to conduct simultaneous flow velocity and temperature measurements inside a microchannel to quantify the transient behavior of electroosmotic flow (EOF) to elucidate underlying physics associated with the effects of Joule heating on electrokinematically driven flows. The second example is to examine the time evolution of the unsteady heat transfer and phase changing process inside micro-sized, icing water droplets, which is pertinent to the ice formation and accretion processes as water droplets impinge onto cold wind turbine blades

  16. A molecular dynamics investigation of the unusual concentration dependencies of Fick diffusivities in silica mesopores

    NARCIS (Netherlands)

    Krishna, R.; van Baten, J.M.

    2011-01-01

    Molecular Dynamics (MD) simulations were carried out to determine the self-diffusivitiy, Di,self, the Maxwell-Stefan diffusivity, Ði, and the Fick diffusivity, Di, for methane (C1), ethane (C2), propane (C3), n-butane (nC4), n-pentane (nC5), n-hexane (nC6), n-heptane (nC7), and cyclohexane (cC6) in

  17. Raman spectroscopy in investigations of mechanism of binding of human serum albumin to molecular probe fluorescein

    International Nuclear Information System (INIS)

    Vlasova, I M; Saletsky, A M

    2008-01-01

    The mechanism of binding of molecular probe fluorescein to molecules of human serum albumin was studied by the Raman spectroscopy method. The position of binding Center on human serum albumin molecule for fluorescein is determined. The amino acid residues of albumin molecule, participating in binding of fluorescein at different pH values of solution, are established. The conformation rearrangements of globules of human serum albumin, taking place at binding of fluorescein at different pH values of solution, are registered

  18. Molecular investigations of protriptyline as a multi-target directed ligand in Alzheimer's disease.

    Directory of Open Access Journals (Sweden)

    Sneha B Bansode

    Full Text Available Alzheimer's disease (AD is a complex neurodegenerative disorder involving multiple cellular and molecular processes. The discovery of drug molecules capable of targeting multiple factors involved in AD pathogenesis would greatly facilitate in improving therapeutic strategies. The repositioning of existing non-toxic drugs could dramatically reduce the time and costs involved in developmental and clinical trial stages. In this study, preliminary screening of 140 FDA approved nervous system drugs by docking suggested the viability of the tricyclic group of antidepressants against three major AD targets, viz. Acetylcholinesterase (AChE, β-secretase (BACE-1, and amyloid β (Aβ aggregation, with one member, protriptyline, showing highest inhibitory activity. Detailed biophysical assays, together with isothermal calorimetry, fluorescence quenching experiments, kinetic studies and atomic force microscopy established the strong inhibitory activity of protriptyline against all three major targets. The molecular basis of inhibition was supported with comprehensive molecular dynamics simulations. Further, the drug inhibited glycation induced amyloid aggregation, another important causal factor in AD progression. This study has led to the discovery of protriptyline as a potent multi target directed ligand and established its viability as a promising candidate for AD treatment.

  19. Molecular analysis of MECP2 gene in Egyptian patients with Rett ...

    African Journals Online (AJOL)

    Molecular analysis of MECP2 gene in Egyptian patients with Rett syndrome. ... Egyptian Journal of Medical Human Genetics ... This study represents one of the limited MECP2 molecular analyses done on Egyptian patients with RTT, in which direct sequencing of MECP2 coding region in 10 female Egyptian patients ...

  20. The Silica-Water Interface from the Analysis of Molecular Dynamic Simulations

    KAUST Repository

    Lardhi, Sheikha F.

    2013-05-01

    Surface chemistry is an emerging field that can give detailed insight about the elec- tronic properties and the interaction of complex material surfaces with their neigh- bors. This is for both solid-solid and solid-liquid interfaces. Among the latter class, the silica-water interface plays a major role in nature. Silica is among the most abundant materials on earth, as well in advanced technological applications such as catalysis and nanotechnology. This immediately indicates the relevance of a detailed understanding of the silica-water interface. In this study, we investigate the details of this interaction at microscopic level by analyzing trajectories obtained with ab initio molecular dynamic simulations. The system we consider consists of bulk liquid water confined between two β-cristobalite silica surfaces. The molecular dynamics were generated with the CP2K, an ab initio molecular dynamic simulation tool. The simulations are 25 picoseconds long, and the CP2K program was run on 64 cores on a supercomputer cluster. During the simulations the program integrates Newton’s equations of motion for the system and generates the trajectory for analysis. For analysis, we focused on the following properties that characterize the silica water interface. We calculated the density profile of the water layers from the silica surface, and we also calculated the radial distribution function (RDF) of the hydrogen bond at the silanols on the silica surface. The main focus of this thesis is to write the programs for calculating the atom density profile and the RDF from the generated MD trajectories. The atomic probability density profile shows that water is strongly adsorbed on the (001) cristobalite surface, while the RDF indicates differently ad- sorbed water molecules in the first adsorption layer. As final remark, the protocol and the tools developed in this thesis can be applied to the study of basically any crystal-water interface.

  1. Pure and Modified Co-Poly(amide-12-b-ethylene oxide) Membranes for Gas Separation Studied by Molecular Investigations.

    Science.gov (United States)

    De Lorenzo, Luana; Tocci, Elena; Gugliuzza, Annarosa; Drioli, Enrico

    2012-06-28

    This paper deals with a theoretical investigation of gas transport properties in a pure and modified PEBAX block copolymer membrane with N-ethyl-o/p-toluene sulfonamide (KET) as additive molecules. Molecular dynamics simulations using COMPASS force field, Gusev-Suter Transition State Theory (TST) and Monte Carlo methods were used. Bulk models of PEBAX and PEBAX/KET in different copolymer/additive compositions were assembled and analyzed to evaluate gas permeability and morphology to characterize structure-performance relationships.

  2. The Silica-Water Interface from the Analysis of Molecular Dynamic Simulations

    KAUST Repository

    Lardhi, Sheikha F.

    2013-01-01

    detailed understanding of the silica-water interface. In this study, we investigate the details of this interaction at microscopic level by analyzing trajectories obtained with ab initio molecular dynamic simulations. The system we consider consists of bulk

  3. Investigation of the interaction between isomeric derivatives and human serum albumin by fluorescence spectroscopy and molecular modeling

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Ruiyong, E-mail: wangry@zzu.edu.cn; Dou, Huanjing; Yin, Yujing; Xie, Yuanzhe; Sun, Li; Liu, Chunmei; Dong, Jingjing; Huang, Gang; Zhu, Yanyan; Song, Chuanjun, E-mail: chjsong@zzu.edu.cn; Chang, Junbiao, E-mail: changjunbiao@zzu.edu.cn

    2014-10-15

    In this paper, we have synthesized 9H-pyrrolo[1,2-a]indol-9-ones and the isomeric indeno[2,1-b]pyrrol-8-ones. The interactions of human serum albumin with series of isomeric derivatives have been studied by spectrophotometric methods. Results show the intrinsic fluorescence is quenched by the derivatives with a static quenching procedure. The thermodynamics parameters indicate that van der Waals forces and hydrogen bonds play a major role in the interactions. The results of synchronous fluorescence spectra demonstrate that the microenvironments of Trp residue of human serum albumin are disturbed by most derivatives. Thermodynamic results showed that the 9H-pyrrolo[1,2-a]indol-9-ones are stronger quenchers and bind to human serum albumin with the higher affinity than isomeric indeno[2,1-b]pyrrol-8-ones. The influence of molecular structure on the binding aspects has been investigated. - Highlights: • The interactions between isomeric derivatives and HSA have been investigated. • Results reveal that 9H-pyrrolo[1,2-a]indol-9-ones are stronger quenchers for HSA. • Hydrogen bonds and van der Waals forces play major role in the binding process. • The influence of molecular structure on the binding aspects has been investigated. • The binding study was also modeled by molecular docking.

  4. Investigation of the interaction between isomeric derivatives and human serum albumin by fluorescence spectroscopy and molecular modeling

    International Nuclear Information System (INIS)

    Wang, Ruiyong; Dou, Huanjing; Yin, Yujing; Xie, Yuanzhe; Sun, Li; Liu, Chunmei; Dong, Jingjing; Huang, Gang; Zhu, Yanyan; Song, Chuanjun; Chang, Junbiao

    2014-01-01

    In this paper, we have synthesized 9H-pyrrolo[1,2-a]indol-9-ones and the isomeric indeno[2,1-b]pyrrol-8-ones. The interactions of human serum albumin with series of isomeric derivatives have been studied by spectrophotometric methods. Results show the intrinsic fluorescence is quenched by the derivatives with a static quenching procedure. The thermodynamics parameters indicate that van der Waals forces and hydrogen bonds play a major role in the interactions. The results of synchronous fluorescence spectra demonstrate that the microenvironments of Trp residue of human serum albumin are disturbed by most derivatives. Thermodynamic results showed that the 9H-pyrrolo[1,2-a]indol-9-ones are stronger quenchers and bind to human serum albumin with the higher affinity than isomeric indeno[2,1-b]pyrrol-8-ones. The influence of molecular structure on the binding aspects has been investigated. - Highlights: • The interactions between isomeric derivatives and HSA have been investigated. • Results reveal that 9H-pyrrolo[1,2-a]indol-9-ones are stronger quenchers for HSA. • Hydrogen bonds and van der Waals forces play major role in the binding process. • The influence of molecular structure on the binding aspects has been investigated. • The binding study was also modeled by molecular docking

  5. Synthesis, XRD single crystal structure analysis, vibrational spectral analysis, molecular dynamics and molecular docking studies of 2-(3-methoxy-4-hydroxyphenyl) benzothiazole

    Science.gov (United States)

    Sarau Devi, A.; Aswathy, V. V.; Sheena Mary, Y.; Yohannan Panicker, C.; Armaković, Stevan; Armaković, Sanja J.; Ravindran, Reena; Van Alsenoy, C.

    2017-11-01

    The vibrational spectra and corresponding vibrational assignments of 2-(3-methoxy-4-hydroxyphenyl)benzothiazole is reported. Single crystal XRD data of the title compound is reported and the orientation of methoxy group is cis to nitrogen atom of the thiazole ring. The phenyl ring breathing modes of the title compound are assigned at 1042 and 731 cm-1 theoretically. The charge transfer within the molecule is studied using frontier molecular orbital analysis. The chemical reactivity descriptors are calculated theoretically. The NMR spectral data predicted theoretically are in good agreement with the experimental data. The strong negative region spread over the phenyl rings, nitrogen atom and oxygen atom of the hydroxyl group in the MEP plot is due to the immense conjugative and hyper conjugative resonance charge delocalization of π-electrons. Molecule sites prone to electrophilic attacks have been determined by analysis of ALIE surfaces, while Fukui functions provided further insight into the local reactivity properties of title molecule. Autoxidation properties have been investigated by calculation of bond dissociation energies (BDEs) of hydrogen abstraction, while BDEs of the rest of the single acyclic bonds were valuable for the further investigation of degradation properties. Calculation of radial distribution functions was performed in order to determine which atoms of the title molecule have pronounced interactions with water molecules. The title compound forms a stable complex with aryl hydrocarbon receptor and can be a lead compound for developing new anti-tumor drug. Antimicrobial properties of the title compound was screened against one bacterial culture Escherchia coli and four fungal cultures viz., Aspergillus niger, Pencillum chrysogenum, Saccharomyces cerevisiae and Rhyzopus stolonifer.

  6. Investigation of a medieval sword using photon activation analysis

    International Nuclear Information System (INIS)

    Segebade, Chr.

    1993-01-01

    An ancient sword was examined for indications of forgery or, if authentic, any later processing or changes, e.g. replacement of parts of the weapon. Radiochemical as well as non-destructive analyses using high energy photon activation were used as analytical techniques. Metal parts of the hilt were analysed radiochemically and instrumentally whereas the blade was analysed non-destructively. Metallurgical investigations (hardness measurements, microstructure analysis) performed in parallel are also briefly described. No evidence of non-authenticity was found, which agrees well with the results of stylistical and weapon-scientific investigation carried out by an expert of ancient weaponry. (author) 20 refs.; 1 fig.; 2 tabs

  7. Molecular Analysis of Bacterial Microbiota on Brazilian Currency Note Surfaces

    Directory of Open Access Journals (Sweden)

    Tairacan Augusto Pereira da Fonseca

    2015-10-01

    Full Text Available Currency notes have been implicated as a vehicle for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial population residing on banknotes is still unknown in Brazil. In this study, we aimed to investigate the overall bacterial population from 150 different Brazilian Rial (R$ notes in circulation using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Samples were randomly collected from three different street markets or “feiras” in the metropolitan region of São Paulo. Taxonomical composition revealed the abundance of Proteobacteria phyla, followed by Firmicutes and Streptophyta, with a total of 1193 bacterial families and 3310 bacterial genera. Most of these bacterial genera are of human, animal, and environmental origins. Also, our analysis revealed the presence of some potential pathogenic bacterial genera including Salmonella, Staphylococcus, and Klebsiella. The results demonstrate that there is a tremendous diversity of bacterial contamination on currency notes, including organisms known to be opportunistic pathogens. One of the factors that may contribute to the richness of bacterial diversity in currency notes is personal hygiene. Thus, our results underscore the need to increase public awareness of the importance of personal hygiene of money handlers who also handle food.

  8. Molecular Analysis of Bacterial Microbiota on Brazilian Currency Note Surfaces.

    Science.gov (United States)

    Pereira da Fonseca, Tairacan Augusto; Pessôa, Rodrigo; Sanabani, Sabri Saeed

    2015-10-22

    Currency notes have been implicated as a vehicle for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial population residing on banknotes is still unknown in Brazil. In this study, we aimed to investigate the overall bacterial population from 150 different Brazilian Rial (R$) notes in circulation using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Samples were randomly collected from three different street markets or "feiras" in the metropolitan region of São Paulo. Taxonomical composition revealed the abundance of Proteobacteria phyla, followed by Firmicutes and Streptophyta, with a total of 1193 bacterial families and 3310 bacterial genera. Most of these bacterial genera are of human, animal, and environmental origins. Also, our analysis revealed the presence of some potential pathogenic bacterial genera including Salmonella, Staphylococcus, and Klebsiella. The results demonstrate that there is a tremendous diversity of bacterial contamination on currency notes, including organisms known to be opportunistic pathogens. One of the factors that may contribute to the richness of bacterial diversity in currency notes is personal hygiene. Thus, our results underscore the need to increase public awareness of the importance of personal hygiene of money handlers who also handle food.

  9. Chemometric Analysis of High Molecular Mass Glutenin Subunits and Image Data of Bread Crumb Structure from Croatian Wheat Cultivars

    OpenAIRE

    Zorica Jurković; Rezica Sudar; Damir Magdić; Daniela Horvat; Želimir Kurtanjek

    2002-01-01

    The aim of this work is to investigate functional relationships among wheat properties, high molecular mass (weight) (HMW) glutenin subunits and bread quality produced from eleven Croatian wheat cultivars by chemometric analysis. HMW glutenin subunits were fractionated by sodium dodecylsulfate polyacrylamid gel electrophoresis (SDS-PAGE) and subsequently analysed by scanning densitometry in order to quantify HMW glutenin fractions. Wheat properties are characterised by four variables: protein...

  10. Investigating molecular basis of lambda-cyhalothrin resistance in an Anopheles funestus population from Senegal.

    Science.gov (United States)

    Samb, Badara; Konate, Lassana; Irving, Helen; Riveron, Jacob M; Dia, Ibrahima; Faye, Ousmane; Wondji, Charles S

    2016-08-12

    Anopheles funestus is one of the major malaria vectors in tropical Africa, notably in Senegal. The highly anthropophilic and endophilic behaviours of this mosquito make it a good target for vector control operations through the use of insecticide treated nets, long-lasting insecticide nets and indoor residual spraying. However, little is known about patterns of resistance to insecticides and the underlying resistance mechanisms in field populations of this vector in Senegal. Here, we assessed the susceptibility status of An. funestus populations from Gankette Balla, located in northern Senegal and investigated the potential resistance mechanisms. WHO bioassays indicated that An. funestus is resistant to lambda-cyhalothrin 0.05 % (74.64 % mortality), DDT 4 % (83.36 % mortality) and deltamethrin 0.05 % (88.53 % mortality). Suspected resistance was observed to permethrin 0.75 % (91.19 % mortality), bendiocarb 0.1 % (94.13 % mortality) and dieldrin 4 % (96.41 % mortality). However, this population is fully susceptible to malathion 5 % (100 % mortality) and fenitrothion 1 % (100 % mortality). The microarray and qRT-PCR analysis indicated that the lambda-cyhalothrin resistance in Gankette Balla is conferred by metabolic resistance mechanisms under the probable control of cytochrome P450 genes among which CYP6M7 is the most overexpressed. The absence of overexpression of the P450 gene, CYP6P9a, indicates that the resistance mechanism in Senegal is different to that observed in southern Africa. This study represents the first report of pyrethroid and DDT resistance in An. funestus from Senegal and shows that resistance to insecticides is not only confined to An. gambiae as previously thought. Therefore, urgent action should be taken to manage the resistance in this species to ensure the continued effectiveness of malaria control.

  11. Investigating the Interaction of Fe Nanoparticles with Lysozyme by Biophysical and Molecular Docking Studies.

    Directory of Open Access Journals (Sweden)

    Zahra Aghili

    Full Text Available Herein, the interaction of hen egg white lysozyme (HEWL with iron nanoparticle (Fe NP was investigated by spectroscopic and docking studies. The zeta potential analysis revealed that addition of Fe NP (6.45±1.03 mV to HEWL (8.57±0.54 mV can cause to greater charge distribution of nanoparticle-protein system (17.33±1.84 mV. In addition, dynamic light scattering (DLS study revealed that addition of Fe NP (92.95±6.11 nm to HEWL (2.68±0.37 nm increases suspension potential of protein/nanoparticle system (51.17±3.19 nm. Fluorescence quenching studies reveled that both static and dynamic quenching mechanism occur and hydrogen bond and van der Waals interaction give rise to protein-NP system. Synchronous fluorescence spectroscopy of HEWL in the presence of Fe NP showed that the emission maximum wavelength of tryptophan (Trp residues undergoes a red-shift. ANS fluorescence data indicated a dramatic exposure of hydrophobic residues to the solvent. The considerable reduction in melting temperature (T(m of HEWL after addition of Fe NP determines an unfavorable interaction system. Furthermore circular dichoroism (CD experiments demonstrated that, the secondary structure of HEWL has not changed with increasing Fe NP concentrations; however, some conformational changes occur in tertiary structure of HEWL. Moreover, protein-ligand docking study confirmed that the Fe NP forms hydrogen bond contacts with HEWL.

  12. High-molecular products analysis of VOC destruction in atmospheric pressure discharge

    International Nuclear Information System (INIS)

    Grossmannova, Hana; Ciganek, Miroslav; Krcma, Frantisek

    2007-01-01

    We investigate the issue of applicability of the solid phase microextraction (SPME) in the analysis of volatile organic compounds (VOCs) destruction products in the gliding arc discharge. Our research is focused on the measurements with the simple one stage gliding arc reactor, applied voltage was varied in the range of 3.5-4 kV. As a carrier gas, the dry air and its mixtures with nitrogen and oxygen, enriched by toluene, with flow rate of 1000-3500 ml/min was used. Total decomposition of toluene of 97 % was achieved at the oxygen content in carrier gas of 60 %. For measurements with air as a carrier gas, the highest efficiency was 95 %. We also tested the SPME technique suitability for the quantitative analysis of exhausts gases and if this technique can be used efficiently in the field to extract byproducts. Carbowax/divinylbenzene and Carboxen/polydimethylsiloxane/divinylbenzene fibres were chosen for sampling. Tens of various high-molecular substances were observed, especially a large number of oxygenous compounds and further several nitrogenous and C x H y compounds. The concentrations of various generated compounds strongly depend on the oxygen content in gas mixture composition. The results showed that the fiber coated by Carbowax/divinylbenzene can extract more products independently on the used VOC compound. The Carboxen/polydimethylsiloxane/divinylbenzene fiber is useful for the analysis of oxygenous compounds and its use will be recommended especially when the destruction is done in the oxygen rich atmosphere. With the higher ratio of oxygen in the carrier gas a distinctive decline of C x H y compounds amount have been observed. We also tried to describe the significant production of some compounds like benzyl alcohol, benzeneacetaldehyde, even in oxygen content is proximate 0 %. Experimental data demonstrated that it is necessary to use several SPME fibres for full-scale high-molecular products analysis

  13. Dynamics of bone healing after osteotomy with piezosurgery or conventional drilling - histomorphometrical, immunohistochemical, and molecular analysis.

    Science.gov (United States)

    Esteves, Jônatas Caldeira; Marcantonio, Elcio; de Souza Faloni, Ana Paula; Rocha, Fernanda Regina Godoy; Marcantonio, Rosemary Adriana; Wilk, Katarzyna; Intini, Giuseppe

    2013-09-23

    Piezosurgery is an osteotomy system used in medical and dental surgery. Many studies have proven clinical advantages of piezosurgery in terms of quality of cut, maneuverability, ease of use, and safety. However, few investigations have tested its superiority over the traditional osteotomy systems in terms of dynamics of bone healing. Therefore, the aim of this study was to evaluate the dynamics of bone healing after osteotomies with piezosurgery and to compare them with those associated to traditional bone drilling. One hundred and ten rats were divided into two groups with 55 animals each. The animals were anesthetized and the tibiae were surgically exposed to create defects 2 mm in diameter by using piezosurgery (Piezo group) and conventional drilling (Drill group). Animals were sacrificed at 3, 7, 14, 30 and 60 days post-surgery. Bone samples were collected and processed for histological, histomorphometrical, immunohistochemical, and molecular analysis. The histological analysis was performed at all time points (n = 8) whereas the histomorphometrical analysis was performed at 7, 14, 30 and 60 days post-surgery (n = 8). The immunolabeling was performed to detect Vascular Endothelial Growth Factor (VEGF), Caspase-3 (CAS-3), Osteoprotegerin (OPG), Receptor Activator of Nuclear Factor kappa-B Ligand (RANKL), and Osteocalcin (OC) at 3, 7, and 14 days (n = 3). For the molecular analysis, animals were sacrificed at 3, 7 and 14 days, total RNA was collected, and quantification of the expression of 21 genes related to BMP signaling, Wnt signaling, inflammation, osteogenenic and apoptotic pathways was performed by qRT-PCR (n = 5). Histologically and histomorphometrically, bone healing was similar in both groups with the exception of a slightly higher amount of newly formed bone observed at 30 days after piezosurgery (p piezosurgery are comparable to those observed with conventional drilling.

  14. Molecular malaria diagnostics: A systematic review and meta-analysis.

    Science.gov (United States)

    Roth, Johanna M; Korevaar, Daniël A; Leeflang, Mariska M G; Mens, Pètra F

    2016-01-01

    Accurate diagnosis of malaria is essential for identification and subsequent treatment of the disease. Currently, microscopy and rapid diagnostic tests are the most commonly used diagnostics, next to treatment based on clinical signs only. These tests are easy to deploy, but have a relatively high detection limit. With declining prevalence in many areas, there is an increasing need for more sensitive diagnostics. Molecular tools may be a suitable alternative, although costs and technical requirements currently hamper their implementation in resource limited settings. A range of (near) point-of-care diagnostics is therefore under development, including simplifications in sample preparation, amplification and/or read-out of the test. Accuracy data, in combination with technical characteristics, are essential in determining which molecular test, if any, would be the most promising to be deployed. This review presents a comprehensive overview of the currently available molecular malaria diagnostics, ranging from well-known tests to platforms in early stages of evaluation, and systematically evaluates their published accuracy. No important difference in accuracy was found between the most commonly used PCR-based assays (conventional, nested and real-time PCR), with most of them having high sensitivity and specificity, implying that there are no reasons other than practical ones to choose one technique over the other. Loop-mediated isothermal amplification and other (novel) diagnostics appear to be highly accurate as well, with some offering potential to be used in resource-limited settings.

  15. Molecular-beam epitaxial growth and ion-beam analysis systems for functional materials research

    International Nuclear Information System (INIS)

    Takeshita, H.; Aoki, Y.; Yamamoto, S.; Naramoto, H.

    1992-01-01

    Experimental systems for molecular beam epitaxial growth and ion beam analysis have been designed and constructed for the research of inorganic functional materials such as thin films and superlattices. (author)

  16. Application of Molecular Genetics to the Investigation of Inherited Bleeding Disorders

    DEFF Research Database (Denmark)

    Lethagen, Stefan Rune; Dunø, Morten; Nielsen, Lars Bo

    2013-01-01

    Hemophilia is an inherited bleeding disorder primarily caused by deficiency of coagulation factor (F)VIII (hemophilia A) or FIX (hemophilia B). Both conditions are X-linked. More than 2100 different F8 mutations have been described, the most common being a 500 kb inversion involving exon 1 to exo...... quality control systems in place, and participate in established external quality assessment programs....... the causative mutation is unknown. More rare bleeding disorders are generally recessively inherited, and are often caused by mutations that are specific for individual families, and mutations are scattered throughout the genes. Laboratories performing molecular genetic analyses must have validated internal...

  17. Properties of Energy Spectra of Molecular Crystals Investigated by Nonlinear Theory

    Science.gov (United States)

    Pang, Xiao-Feng; Zhang, Huai-Wu

    We calculate the quantum energy spectra of molecular crystals, such as acetanilide, by using discrete nonlinear Schrodinger equation, containing various interactions, appropriate to the systems. The energy spectra consist of many energy bands, in each energy band there are a lot of energy levels including some higher excited states. The result of energy spectrum is basically consistent with experimental values obtained by infrared absorption and Raman scattering in acetanilide and can also explain some experimental results obtained by Careri et al. Finally, we further discuss the influences of variously characteristic parameters on the energy spectra of the systems.

  18. Inelastic neutron scattering investigation of the α-β crossover in glass-formers as a function of molecular architecture

    International Nuclear Information System (INIS)

    Levelut, C.; Faivre, A.; Pelous, J.; Durand, D.

    1999-01-01

    Complete text of publication follows. An experimental investigation of the relaxational processes related to the glass transition in several glass formers with more or less complex molecular architecture is presented. This inelastic neutron scattering study concentrates on the region around 1.1 to 1.5 T g where the two relaxation processes usually identified in most glass formers, the α and the β relaxations, are expected to merge or cross. A recent study comparing the dynamics of Sorbitol and Maltitol (two low molecular and complementary glasses) seems to show that the way on which the α and β processes merge depends on the differences in the chemical architecture of these polyols [1]. In the present work, linear diols, three-arm-star triols and crosslinked polyurethanes, synthesized from the latter are studied. This work is an extension of a previous study of the relaxational processes in cross-linked polyurethanes [2]. For such series of samples of similar chemical composition but with increasing complexity in the architecture, the influence of the molecular complexity on the type of merging between α and β processes is tested. This allows to discuss the α-β cross-over on molecular level. (author)

  19. X-ray diffraction and molecular-dynamics studies: Structural analysis of phases in diglyceride monolayers

    DEFF Research Database (Denmark)

    Peters, Günther H.J.; Larsen, Niels Bent; Bjørnholm, T.

    1998-01-01

    We report a detailed structural analysis of the phases of 1,2-sn-dipalmitoylglycerol Langmuir monolayers at room temperature. Pressure-induced transitions have been investigated by combination of molecular-dynamics simulations and grazing-incidence x-ray diffraction (XRD). The diglyceride film...... undergoes two phase transitions occurring at 38.3 and 39.8 Angstrom(2)/molecule. Simulation indicates that the first transition involves a reorientation of the headgroups while simulation and XRD show that in the second transition the order parameter is the tilt angle of the alkyl chains. A methodology......; At the lowest pressure the tilt angle reaches approximate to 14 degrees in a direction close to a nearest neighbor direction. Both arrangements of the alkyl chains are confirmed by XRD. For higher order and fractional order Bragg peaks, simulations predict higher intensities than observed with XRD. This may...

  20. Molecular analysis and genetic diversity of Aedes albopictus (Diptera, Culicidae) from China.

    Science.gov (United States)

    Ruiling, Zhang; Peien, Leng; Xuejun, Wang; Zhong, Zhang

    2018-05-01

    Aedes albopictus is one of the most invasive species, which can carry Dengue virus, Yellow fever virus and more than twenty arboviruses. Based on mitochondrial gene cytochrome c oxidase I (COI) and samples collected from 17 populations, we investigated the molecular character and genetic diversity of Ae. albopictus from China. Altogether, 25 haplotypes were detected, including 10 shared haplotypes and 15 private haplotypes. H1 was the dominant haplotype, which is widely distributed in 13 populations. Tajima'D value of most populations was significantly negative, demonstrating that populations experienced rapid range expansion recently. Most haplotypes clustered together both in phylogenetic and median-joining network analysis without clear phylogeographic patterns. However, neutrality tests revealed shallow divergences among Hainan and Guangxi with other populations (0.15599 ≤ F ST ≤ 0.75858), which probably due to interrupted gene flow, caused by geographical isolations. In conclusion, Ae. albopictus populations showed low genetic diversity in China.

  1. Application of Deep Learning in Automated Analysis of Molecular Images in Cancer: A Survey

    Science.gov (United States)

    Xue, Yong; Chen, Shihui; Liu, Yong

    2017-01-01

    Molecular imaging enables the visualization and quantitative analysis of the alterations of biological procedures at molecular and/or cellular level, which is of great significance for early detection of cancer. In recent years, deep leaning has been widely used in medical imaging analysis, as it overcomes the limitations of visual assessment and traditional machine learning techniques by extracting hierarchical features with powerful representation capability. Research on cancer molecular images using deep learning techniques is also increasing dynamically. Hence, in this paper, we review the applications of deep learning in molecular imaging in terms of tumor lesion segmentation, tumor classification, and survival prediction. We also outline some future directions in which researchers may develop more powerful deep learning models for better performance in the applications in cancer molecular imaging. PMID:29114182

  2. Doses in radiation accidents investigated by chromosome aberration analysis

    International Nuclear Information System (INIS)

    Lloyd, D.C.; Purrott, R.J.; Prosser, J.S.

    1978-01-01

    Results from cytogenetic investigations into 55 cases of suspected over-exposure to radiation during 1977 are reviewed. This report is the seventh in an annual series (previous results were published in NRPB-R5, R10, R23, R35, R41 and R57) which together contain data on 327 studies. Results from all investigations have been pooled for general analysis. Brief accounts are given in an appendix of the circumstances behind the past year's investigations and, where possible, physical estimates of dose have been included for comparison. Two cases are described in more detail: the first concerned a non-classified worker who put an iridium-192 source in his pocket and took it home; and the second involved the accidental contamination of two people with tritium gas. In a second appendix, the confidence limits on cytogenetic dosimetry for X- and γ-ray over-exposures are given and the derivation of these limits is discussed. (author)

  3. Synthesis, vibrational spectroscopic investigations, molecular docking, antibacterial studies and molecular dynamics study of 5-[(4-nitrophenyl)acetamido]-2-(4-tert-butylphenyl)benzoxazole

    Science.gov (United States)

    Sheena Mary, Y.; Al-Shehri, Mona M.; Jalaja, K.; Al-Omary, Fatmah A. M.; El-Emam, Ali A.; Yohannan Panicker, C.; Armaković, Stevan; Armaković, Sanja J.; Temiz-Arpaci, Ozlem; Van Alsenoy, C.

    2017-04-01

    Antimicrobial active 5-[(4-nitrophenyl)acetamido]-2-(4-tert-butylphenyl)benzoxazole (NATPB) was synthesized and observed IR, Raman bands are compared with the theoretically predicted wave numbers. In the IR spectrum the NH stretching wave number splits into a doublet with a noted difference and is red shifted from the computed value, which indicates the weakening of NH bond resulting in proton transfer to the neighbouring oxygen atom. The HOMO-LUMO plots reveal the charge transfer in the molecular system through the conjugated paths. The electrophilic and nucleophilic reactive sites are identified from the MEP plot. Mapping of average local ionization energy (ALIE) values to the electron density surface served us as a tool for prediction of molecule sites possibly prone to electrophilic attacks. Other important reactive centres of the title molecule were detected by calculations of Fukui functions. Calculations of bond dissociation energies (BDE) for hydrogen abstraction were used in order to assess whether the NATPB molecules is prone to autoxidation mechanism or not, while BDE of the remaining single acyclic bonds were used in order to determine the weakest bond. Interaction properties with water were investigated by molecular dynamics (MD) simulations and calculations of radial distribution functions (RDFs). The compound possessed broad spectrum activity against all of the tested Gram-positive and Gram-negative bacteria and yeasts, their minimum inhibitory concentrations (MICs) ranging between 32 and 128 μg/ml. The compound exhibited significant antibacterial activity (32 μg/ml) against an antibiotic resistant E. faecalis isolate, at same potency with the compared standard drugs vancomycin and gentamycin sulfate. The molecular docking studies show that the compound might exhibit inhibitory activity against CDK inhibitors.

  4. Investigating Alkylsilane Monolayer Tribology at a Single-Asperity Contact with Molecular Dynamics Simulation.

    Science.gov (United States)

    Summers, Andrew Z; Iacovella, Christopher R; Cummings, Peter T; McCabe, Clare

    2017-10-24

    Chemisorbed monolayer films are known to possess favorable characteristics for nanoscale lubrication of micro- and nanoelectromechanical systems (MEMS/NEMS). Prior studies have shown that the friction observed for monolayer-coated surfaces features a strong dependence on the geometry of contact. Specifically, tip-like geometries have been shown to penetrate into monolayer films, inducing defects in the monolayer chains and leading to plowing mechanisms during shear, which result in higher coefficients of friction (COF) than those observed for planar geometries. In this work, we use molecular dynamics simulations to examine the tribology of model silica single-asperity contacts under shear with monolayer-coated substrates featuring various film densities. It is observed that lower monolayer densities lead to reduced COFs, in contrast to results for planar systems where COF is found to be nearly independent of monolayer density. This is attributed to a liquid-like response to shear, whereby fewer defects are imparted in monolayer chains from the asperity, and chains are easily displaced by the tip as a result of the higher free volume. This transition in the mechanism of molecular plowing suggests that liquid-like films should provide favorable lubrication at single-asperity contacts.

  5. Molecular Dynamics Simulation to Investigate the Interaction of Asphaltene and Oxide in Aggregate

    Directory of Open Access Journals (Sweden)

    Rui Li

    2016-01-01

    Full Text Available The asphalt-aggregate interface interaction (AAI plays a significant role in the overall performances of asphalt mixture, which is caused due to the complicated physicochemical processes and is influenced by various factors, including the acid-base property of aggregates. In order to analyze the effects of the chemical constitution of aggregate on the AAI, the average structure C65H74N2S2 is selected to represent the asphaltene in asphalt and magnesium oxide (MgO, calcium oxide (CaO, aluminium sesquioxide (Al2O3, and silicon dioxide (SiO2 are selected to represent the major oxides in aggregate. The molecular models are established for asphaltene and the four oxides, respectively, and the molecular dynamics (MD simulation was conducted for the four kinds of asphaltene-oxide system at different temperatures. The interfacial energy in MD simulation is calculated to evaluate the AAI, and higher value means better interaction. The results show that interfacial energy between asphaltene and oxide reaches the maximum value at 25°C and 80°C and the minimum value at 40°C. In addition, the interfacial energy between asphaltene and MgO was found to be the greatest, followed by CaO, Al2O3, and SiO2, which demonstrates that the AAI between asphalt and alkaline aggregates is better than acidic aggregates.

  6. Experimental Investigation of Molecular Species Formation in Metal Plasmas During Laser Ablation

    Science.gov (United States)

    Radousky, H.; Crowhurst, J.; Rose, T.; Armstrong, M.; Stavrou, E.; Zaug, J.; Weisz, D.; Azer, M.; Finko, M.; Curreli, D.

    2016-10-01

    Atomic and molecular spectra on metal plasmas generated by laser ablation have been measured using single, nominally 6-7 ns pulses at 1064 nm, and with energies less than 50 mJ. The primary goal for these studies is to constrain the physical and chemical mechanisms that control the distribution of radionuclides in fallout after a nuclear detonation. In this work, laser emission spectroscopy was used to obtain in situdata for vapor phase molecular species as they form in a controlled oxygen atmosphere for a variety of metals such as Fe, Al, as well as preliminary results for U. In particular, the ablation plumes created from these metals have been imaged with a resolution of 10 ns, and it is possible to observe the expansion of the plume out to 0.5 us. These data serve as one set of inputs for a semi-empirical model to describe the chemical fractionation of uranium during fallout formation. Prepared by LLNL under Contract DE-AC52-07NA27344. This project was sponsored by the Department of the Defense, Defense Threat Reduction Agency, under Grant Number HDTRA1-16-1-0020.

  7. Prognostic value of Ki-67 index in adult medulloblastoma after accounting for molecular subgroup: a retrospective clinical and molecular analysis.

    Science.gov (United States)

    Zhao, Fu; Zhang, Jing; Li, Peng; Zhou, Qiangyi; Zhang, Shun; Zhao, Chi; Wang, Bo; Yang, Zhijun; Li, Chunde; Liu, Pinan

    2018-04-23

    Medulloblastoma (MB) is a rare primary brain tumor in adults. We previously evaluated that combining both clinical and molecular classification could improve current risk stratification for adult MB. In this study, we aimed to identify the prognostic value of Ki-67 index in adult MB. Ki-67 index of 51 primary adult MBs was reassessed using a computer-based image analysis (Image-Pro Plus). All patients were followed up ranging from 12 months up to 15 years. Gene expression profiling and immunochemistry were used to establish the molecular subgroups in adult MB. Combined risk stratification models were designed based on clinical characteristics, molecular classification and Ki-67 index, and identified by multivariable Cox proportional hazards analysis. In our cohort, the mean Ki-67 value was 30.0 ± 11.3% (range 6.56-63.55%). The average Ki-67 value was significantly higher in LC/AMB than in CMB and DNMB (P = .001). Among three molecular subgroups, Group 4-tumors had the highest average Ki-67 value compared with WNT- and SHH-tumors (P = .004). Patients with Ki-67 index large than 30% displayed poorer overall survival (OS) and progression free survival (PFS) than those with Ki-67 less than 30% (OS: P = .001; PFS: P = .006). Ki-67 index (i.e. > 30%, < 30%) was identified as an independent significant prognostic factor (OS: P = .017; PFS: P = .024) by using multivariate Cox proportional hazards model. In conclusion, Ki-67 index can be considered as a valuable independent prognostic biomarker for adult patients with MB.

  8. Molecular cloning, expression and computational analysis of a water ...

    African Journals Online (AJOL)

    User

    2012-11-06

    Nov 6, 2012 ... analysis of a water stress inducible copper-containing ... Although, in slico analysis of the protein have indicated its probable structure and functions, further ..... based on protein data bank (PDB) template c1ksiA which.

  9. Transcriptome analysis reveals molecular anthelmintic effects of procyanidins in C. elegans.

    Directory of Open Access Journals (Sweden)

    Verena Spiegler

    Full Text Available Worldwide, more than 1 billion people are affected by infestations with soil-transmitted helminths and also in veterinary medicine helminthiases are a severe threat to livestock due to emerging resistances against the common anthelmintics. Proanthocyanidins have been increasingly investigated for their anthelmintic properties, however, except for an interaction with certain proteins of the nematodes, not much is known about their mode of action. To investigate the anthelmintic activity on a molecular level, a transcriptome analysis was performed in Caenorhabditis elegans after treatment with purified and fully characterized oligomeric procyanidins (OPC. The OPCs had previously been obtained from a hydro-ethanolic (1:1 extract from the leaves of Combretum mucronatum, a plant which is traditionally used in West Africa for the treatment of helminthiasis, therefore, also the crude extract was included in the study. Significant changes in differential gene expression were observed mainly for proteins related to the intestine, many of which were located extracellularly or within cellular membranes. Among the up-regulated genes, several hitherto undescribed orthologues of structural proteins in humans were identified, but also genes that are potentially involved in the worms' defense against tannins. For example, T22D1.2, an orthologue of human basic salivary proline-rich protein (PRB 2, and numr-1 (nuclear localized metal responsive were found to be strongly up-regulated. Down-regulated genes were mainly associated with lysosomal activity, glycoside hydrolysis or the worms' innate immune response. No major differences were found between the groups treated with purified OPCs versus the crude extract. Investigations using GFP reporter gene constructs of T22D1.2 and numr-1 corroborated the intestine as the predominant site of the anthelmintic activity. The current findings support previous hypotheses of OPCs interacting with intestinal surface proteins

  10. Molecular Laser Spectroscopy as a Tool for Gas Analysis Applications

    Directory of Open Access Journals (Sweden)

    Javis Anyangwe Nwaboh

    2011-01-01

    Full Text Available We have used the traceable infrared laser spectrometric amount fraction measurement (TILSAM method to perform absolute concentration measurements of molecular species using three laser spectroscopic techniques. We report results performed by tunable diode laser absorption spectroscopy (TDLAS, quantum cascade laser absorption spectroscopy (QCLAS, and cavity ring down spectroscopy (CRDS, all based on the TILSAM methodology. The measured results of the different spectroscopic techniques are in agreement with respective gravimetric values, showing that the TILSAM method is feasible with all different techniques. We emphasize the data quality objectives given by traceability issues and uncertainty analyses.

  11. Molecular Computational Investigation of Electron Transfer Kinetics across Cytochrome-Iron Oxide Interfaces

    International Nuclear Information System (INIS)

    Kerisit, Sebastien N.; Rosso, Kevin M.; Dupuis, Michel; Valiev, Marat

    2007-01-01

    The interface between electron transfer proteins such as cytochromes and solid phase mineral oxides is central to the activity of dissimilatory-metal reducing bacteria. A combination of potential-based molecular dynamics simulations and ab initio electronic structure calculations are used in the framework of Marcus' electron transfer theory to compute elementary electron transfer rates from a well-defined cytochrome model, namely the small tetraheme cytochrome (STC) from Shewanella oneidensis, to surfaces of the iron oxide mineral hematite (a-Fe2O3). Room temperature molecular dynamics simulations show that an isolated STC molecule favors surface attachment via direct contact of hemes I and IV at the poles of the elongated axis, with electron transfer distances as small as 9 Angstroms. The cytochrome remains attached to the mineral surface in the presence of water and shows limited surface diffusion at the interface. Ab initio electronic coupling matrix element (VAB) calculations of configurations excised from the molecular dynamics simulations reveal VAB values ranging from 1 to 20 cm-1, consistent with nonadiabaticity. Using these results, together with experimental data on the redox potential of hematite and hemes in relevant cytochromes and calculations of the reorganization energy from cluster models, we estimate the rate of electron transfer across this model interface to range from 1 to 1000 s-1 for the most exothermic driving force considered in this work, and from 0.01 to 20 s-1 for the most endothermic. This fairly large range of electron transfer rates highlights the sensitivity of the rate upon the electronic coupling matrix element, which is in turn dependent on the fluctuations of the heme configuration at the interface. We characterize this dependence using an idealized bis-imidazole heme to compute from first principles the VAB variation due to porphyrin ring orientation, electron transfer distance, and mineral surface termination. The electronic

  12. The high resolution melting analysis (HRM) as a molecular tool for monitoring parasites of the wildlife.

    Science.gov (United States)

    Héritier, Laurent; Verneau, Olivier; Breuil, Gregory; Meistertzheim, Anne-Leila

    2017-04-01

    In an interconnected world, the international pet trade on wild animals is becoming increasingly important. As a consequence, non-native parasite species are introduced, which affect the health of wildlife and contribute to the loss of biodiversity. Because the investigation of parasite diversity within vulnerable host species implies the molecular identification of large samples of parasite eggs, the sequencing of DNA barcodes is time-consuming and costly. Thereby, the objectives of our study were to apply the high resolution melting (HRM) approach for species determination from pools of parasite eggs. Molecular assays were validated on flatworm parasites (polystomes) infecting the Mediterranean pond turtle Mauremys leprosa and the invasive red-eared slider Trachemys scripta elegans in French natural environments. HRM analysis results indicated that double or multiple parasitic infections could be detected from wild animal populations. They also showed that the cycle of parasite eggs production was not regular over time and may depend on several factors, among which the ecological niche and the target species. Thereby, monitoring parasites from wild endangered animals implies periodic parasitological surveys to avoid false negative diagnostics, based solely on eggs production.

  13. Synthesis and Surface-Specific Analysis of Molecular Constituents Relevant to Biogenic Secondary Organic Aerosol Material

    Science.gov (United States)

    Be, A. G.; Upshur, M. A.; Chase, H. M.; Geiger, F.; Thomson, R. J.

    2017-12-01

    Secondary organic aerosol (SOA) particles formed from the oxidation of biogenic volatile organic compounds (BVOCs) remain a principal, yet elusive, class of airborne particulate matter that impacts the Earth's radiation budget. Given the characteristic molecular complexity comprising biogenic SOA particles, chemical information selective to the gas-aerosol interface may be valuable in the investigation of such systems, as surface considerations likely dictate the phenomena driving particle evolution mechanisms and climate effects. In particular, cloud activation processes may be parameterized using the surface tension depression that coincides with partitioning of surface-active organic species to the gas-droplet interface. However, the extent to which surface chemical processes, such as cloud droplet condensation, are influenced by the chemical structure and reactivity of individual surface-active molecules in SOA particles is largely unknown. We seek to study terpene-derived organic species relevant to the surfaces of biogenic SOA particles via synthesis of putative oxidation products followed by analysis using surface-selective physicochemical measurements. Using dynamic surface tension measurements, considerable differences are observed in the surface tension depression of aqueous pendant droplets that contain synthetically prepared ozonolysis products derived from abundant terpene precursors. Furthermore, sum frequency generation spectroscopy is utilized for comparison of the surface vibrational spectral responses of synthesized reference compounds with those observed for laboratory aerosol toward probing the surface composition of SOA material. Such ongoing findings highlight the underlying importance of molecular structure and reactivity when considering the surface chemistry of biogenic terpene-derived atmospheric aerosols.

  14. Binding of molecular oxygen by an artificial heme analogue: investigation on the formation of an Fe–tetracarbene superoxo complex

    KAUST Repository

    Anneser, Markus R.

    2016-02-26

    The dioxygen reactivity of a cyclic iron(II) tetra–NHC-complex (NHC: N-heterocyclic carbene) is investigated. Divergent oxidation behavior is observed depending on the choice of the solvent (acetonitrile or acetone). In the first case, exposure to molecular oxygen leads to an oxygen free Fe(III) whereas in the latter case an oxide bridged Fe(III) dimer is formed. In acetone, an Fe(III)-superoxide can be trapped, isolated and characterized as intermediate at low temperatures. An Fe(III)–O–Fe(III) dimer is formed from the Fe(III) superoxide in acetone upon warming and the molecular structure has been revealed by single crystal X-ray diffraction. It is shown that the oxidation of the Fe(II) complex in both solvents is a reversible process. For the regeneration of the initial Fe(II) complex both organic and inorganic reducing agents can be used.

  15. Probing the interaction of a therapeutic flavonoid, pinostrobin with human serum albumin: multiple spectroscopic and molecular modeling investigations.

    Directory of Open Access Journals (Sweden)

    Shevin R Feroz

    Full Text Available Interaction of a pharmacologically important flavonoid, pinostrobin (PS with the major transport protein of human blood circulation, human serum albumin (HSA has been examined using a multitude of spectroscopic techniques and molecular docking studies. Analysis of the fluorescence quenching data showed a moderate binding affinity (1.03 × 10(5 M(-1 at 25°C between PS and HSA with a 1∶1 stoichiometry. Thermodynamic analysis of the binding data (ΔS = +44.06 J mol(-1 K(-1 and ΔH = -15.48 kJ mol(-1 and molecular simulation results suggested the involvement of hydrophobic and van der Waals forces, as well as hydrogen bonding in the complex formation. Both secondary and tertiary structural perturbations in HSA were observed upon PS binding, as revealed by intrinsic, synchronous, and three-dimensional fluorescence results. Far-UV circular dichroism data revealed increased thermal stability of the protein upon complexation with PS. Competitive drug displacement results suggested the binding site of PS on HSA as Sudlow's site I, located at subdomain IIA, and was well supported by the molecular modelling data.

  16. Investigation of the interfacial properties of polyurethane/carbon nanotube hybrid composites: A molecular dynamics study

    Science.gov (United States)

    Goclon, Jakub; Panczyk, Tomasz; Winkler, Krzysztof

    2018-03-01

    Considering the varied applications of hybrid polymer/carbon nanotube composites and the constant progress in the synthesis methods of such materials, we report a theoretical study of interfacial layer formation between pristine single-wall carbon nanotubes (SWCNTs) and polyurethane (PU) using molecular dynamic simulations. We vary the SWCNT diameter and the number of PU chains to examine various PU-SWCNT interaction patterns. Our simulations indicate the important role of intra-chain forces in PU. No regular polymeric structures could be identified on the carbon nanotube surface during the simulations. We find that increasing the SWCNT diameter results in stronger polymer binding. However, higher surface loadings of PU lead to stronger interpenetration by the polymeric segments; this effect is more apparent for SWCNTs with small diameters. Our core finding is that the attached PU binds most strongly to the carbon nanotubes with the largest diameters. Polymer dynamics reveal the loose distribution of PU chains in these systems.

  17. Investigation of the intermediate LK molecular orbital radiation in heavy ion-atom collisions

    International Nuclear Information System (INIS)

    Frank, W.; Kaun, K.-H.; Manfrass, P.

    1981-01-01

    The continuum consisting of an intensive low-energy and a high-energy components in heavy-ion atom collision systems with atomic numbers Z 1 , Z 2 > 28 is studied. The aim of the study is to prove that the C1 continuum cannot be caused by ridiative electron capture (REC) being molecular orbital (MO) radiation to the 2ptau level. It is shown that the comparison of the C1 yields obtained in Kr+Nb asymmetric collisions in gas and solid targets is associated with the formation of vacancies in the lower-Z collision partner and can be interpreted as quasimolecular radiation to the 2ptau orbital level. The strong suppression of the C2 component in the gas target experimets indicates that the MO radiation to the 1stau orbit is emitted preferentially in the two-collision process in symmetric and near-symmetric systems with Z 1 , Z 2 [ru

  18. Molecular testing for clinical diagnosis and epidemiological investigations of intestinal parasitic infections.

    Science.gov (United States)

    Verweij, Jaco J; Stensvold, C Rune

    2014-04-01

    Over the past few decades, nucleic acid-based methods have been developed for the diagnosis of intestinal parasitic infections. Advantages of nucleic acid-based methods are numerous; typically, these include increased sensitivity and specificity and simpler standardization of diagnostic procedures. DNA samples can also be stored and used for genetic characterization and molecular typing, providing a valuable tool for surveys and surveillance studies. A variety of technologies have been applied, and some specific and general pitfalls and limitations have been identified. This review provides an overview of the multitude of methods that have been reported for the detection of intestinal parasites and offers some guidance in applying these methods in the clinical laboratory and in epidemiological studies.

  19. Molecular dynamics investigation of carbon nanotube junctions in non-aqueous solutions

    KAUST Repository

    Gkionis, Konstantinos

    2014-07-23

    The properties of liquids in a confined environment are known to differ from those in the bulk. Extending this knowledge to geometries defined by two metallic layers in contact with the ends of a carbon nanotube is important for describing a large class of nanodevices that operate in non-aqueous environments. Here we report a series of classical molecular dynamics simulations for gold-electrode junctions in acetone, cyclohexane and N,N-dimethylformamide solutions and analyze the structure and the dynamics of the solvents in different regions of the nanojunction. The presence of the nanotube has little effect on the ordering of the solvents along its axis, while in the transversal direction deviations are observed. Importantly, the orientational dynamics of the solvents at the electrode-nanotube interface differ dramatically from that found when only the electrodes are present.

  20. Engineered Molecular Layers For Organic Electronic Applications: A Confocal Scanning Raman Spectroscopy (CSRS) Investigation

    International Nuclear Information System (INIS)

    Paez-Sierra, Beynor-Antonio; Kolotovska, Viktoriia; Rangel-Kuoppa, Victor-Tapio

    2011-01-01

    We present CSRS maps of magnetically modified vanadyl phthalocyanine (VOPc) thin films forming conduction channels in organic field-effect transistors (OFETs). The VOPc films with a nominal thickness of about 100 nm were produced by organic molecular beam deposition in high vacuum. During the growth conditions the substrates were exposed to a magnetic field (B) from a bar magnet. The CSRS maps revealed significant changes of the organic fields upon preparation conditions. The highest field effect mobility, electrical current and anisotropy of the CSRS-topography is achieved in layers grown with B parallel to the substrate plane, while intermediate and lowest values are achieved in devices grown with B perpendicular to the substrate and without, respectively.

  1. Investigation of the graphene-electrolyte interface in Li-air batteries: A molecular dynamics study

    Science.gov (United States)

    Pavlov, S. V.; Kislenko, S. A.

    2018-01-01

    In this work the behavior of the main reactants (Li+, O2) of the oxygen reduction reaction (ORR) in acetonitrile solvent near the multi-layer graphene edge has been studied. It was observed by molecular dynamics simulations that the concentration distributions of the Li+ and O2 represent a “chessboard” structure. It was ascertained that the concentrations of the lithium ions and oxygen molecules reach their maximum values near the graphene edges pushed out from the surface, which may act as nucleation centers for the formation of crystalline products of the ORR. The maps of the free energy were estimated for the Li+ and O2. Energy optimal trajectories for the adsorption of oxygen molecules and lithium ions were found. Moreover, the distributions of the electric potential were obtained near the following carbon surfaces: single- and multi-layer graphene edge, graphene plane, which shows the qualitative differences in the double-layer structure.

  2. Structural modeling and molecular simulation analysis of HvAP2/EREBP from barley.

    Science.gov (United States)

    Pandey, Bharati; Sharma, Pradeep; Tyagi, Chetna; Goyal, Sukriti; Grover, Abhinav; Sharma, Indu

    2016-06-01

    AP2/ERF transcription factors play a critical role in plant development and stress adaptation. This study reports the three-dimensional ab initio-based model of AP2/EREBP protein of barley and its interaction with DNA. Full-length coding sequence of HvAP2/EREBP gene isolated from two Indian barley cultivars, RD 2503 and RD 31, was used to model the protein. Of five protein models obtained, the one with lowest C-score was chosen for further analysis. The N- and C-terminal regions of HvAP2 protein were found to be highly disordered. The dynamic properties of AP2/EREBP and its interaction with DNA were investigated by molecular dynamics simulation. Analysis of trajectories from simulation yielded the equilibrated conformation between 2-10ns for protein and 7-15ns for protein-DNA complex. We established relationship between DNA having GCC box and DNA-binding domain of HvAP2/EREBP was established by modeling 11-base-pair-long nucleotide sequence and HvAP2/EREBP protein using ab initio method. Analysis of protein-DNA interaction showed that a β-sheet motif constituting amino acid residues THR105, ARG100, ARG93, and ARG83 seems to play important role in stabilizing the complex as they form strong hydrogen bond interactions with the DNA motif. Taken together, this study provides first-hand comprehensive information detailing structural conformation and interactions of HvAP2/EREBP proteins in barley. The study intensifies the role of computational approaches for preliminary examination of unknown proteins in the absence of experimental information. It also provides molecular insight into protein-DNA binding for understanding and enhancing abiotic stress resistance for improving the water use efficiency in crop plants.

  3. Molecular and morphological approaches for species delimitation and hybridization investigations of two Cichla species

    Directory of Open Access Journals (Sweden)

    Andrea A. F. Mourão

    Full Text Available ABSTRACT The hybridization is a widely-discussed issue in several studies with fish species. For some authors, hybridization may be related with diversification and speciation of several groups, or also with the extinction of populations or species. Difficulties to differentiate species and hybrids may be a problem to correctly apply a management of wild species, because hybrid lineages, especially the advanced ones, may resemble the parental species. The genus Cichla Bloch & Schneider, 1801 constitutes an interesting experimental model, considering that hybridization and taxonomic uncertainties hinder a correct identification. Considering these problems, in this study, we developed genetic methodologies and applied meristic and morphometric approaches in wild samples in order to identify species and for test a possible hybridization between Cichla kelberi Kullander & Ferreira, 2006 and Cichla piquiti Kullander & Ferreira, 2006. For this, C. kelberi, C. piquiti and potential hybrid ( carijó individuals were collected in Paraná and Tietê rivers (SP, Brazil. For meristic and morphometric methods, the individuals were analyzed using the statistical software Pcord 5:31, while for molecular methods, primers for PCR-multiplex were designed and enzyme for PCR-RFLP were selected, under the species-specific nucleotide. All results indicated that the carijó is not an interspecific hybrid, because it presented identical genetic pattern and morphology closed to C. piquiti. Thus, we propose that carijó is a C. piquiti morphotype. In addition, this study promotes a new molecular tool that could be used in future research, monitoring and management programs of the genus Cichla.

  4. Protein rotational dynamics investigated with a dual EPR/optical molecular probe. Spin-labeled eosin.

    Science.gov (United States)

    Cobb, C E; Hustedt, E J; Beechem, J M; Beth, A H

    1993-01-01

    An acyl spin-label derivative of 5-aminoeosin (5-SLE) was chemically synthesized and employed in studies of rotational dynamics of the free probe and of the probe when bound noncovalently to bovine serum albumin using the spectroscopic techniques of fluorescence anisotropy decay and electron paramagnetic resonance (EPR) and their long-lifetime counterparts phosphorescence anisotropy decay and saturation transfer EPR. Previous work (Beth, A. H., Cobb, C. E., and J. M. Beechem, 1992. Synthesis and characterization of a combined fluorescence, phosphorescence, and electron paramagnetic resonance probe. Society of Photo-Optical Instrumentation Engineers. Time-Resolved Laser Spectroscopy III. 504-512) has shown that the spin-label moiety only slightly altered the fluorescence and phosphorescence lifetimes and quantum yields of 5-SLE when compared with 5-SLE whose nitroxide had been reduced with ascorbate and with the diamagnetic homolog 5-acetyleosin. In the present work, we have utilized time-resolved fluorescence anisotropy decay and linear EPR spectroscopies to observe and quantitate the psec motions of 5-SLE in solution and the nsec motions of the 5-SLE-bovine serum albumin complex. Time-resolved phosphorescence anisotropy decay and saturation transfer EPR studies have been carried out to observe and quantitate the microseconds motions of the 5-SLE-albumin complex in glycerol/buffer solutions of varying viscosity. These latter studies have enabled a rigorous comparison of rotational correlation times obtained from these complementary techniques to be made with a single probe. The studies described demonstrate that it is possible to employ a single molecular probe to carry out the full range of fluorescence, phosphorescence, EPR, and saturation transfer EPR studies. It is anticipated that "dual" molecular probes of this general type will significantly enhance capabilities for extracting dynamics and structural information from macromolecules and their functional

  5. Pteros: fast and easy to use open-source C++ library for molecular analysis.

    Science.gov (United States)

    Yesylevskyy, Semen O

    2012-07-15

    An open-source Pteros library for molecular modeling and analysis of molecular dynamics trajectories for C++ programming language is introduced. Pteros provides a number of routine analysis operations ranging from reading and writing trajectory files and geometry transformations to structural alignment and computation of nonbonded interaction energies. The library features asynchronous trajectory reading and parallel execution of several analysis routines, which greatly simplifies development of computationally intensive trajectory analysis algorithms. Pteros programming interface is very simple and intuitive while the source code is well documented and easily extendible. Pteros is available for free under open-source Artistic License from http://sourceforge.net/projects/pteros/. Copyright © 2012 Wiley Periodicals, Inc.

  6. A Theoretical Investigation of the Structure and Reactivity of the Molecular Constituents of Oil Sand and Oil Shale

    Energy Technology Data Exchange (ETDEWEB)

    Parish, Carol A. [Univ. of Richmond, VA (United States)

    2016-11-28

    2 reaction at three different sites on the 2-thienylmethyl radical. The addition is exothermic by 37 ~ 55 kcal mol-1 relative to the entrance channel. These excess energies are available to promote further decomposition or rearrangement of the adducts that lead to nascent products such as H, OH, H2O and CH2O. The reaction surfaces are characterized by relatively low barriers (most are lower than 10 kcal mol-1). Based upon a careful analysis of the overall barrier heights and reaction exothermicities, the formation of O2, OH and H2O is likely to be an important pathway in the radical recombination reactions of 2-thienylmethyl + HO2. This work was published in the Journal of Physical Chemistry A, 2011, 115, 14546-14557. REACTION OF THIOPHENE AND METHYLTHIOPHENE WITH SINGLET AND TRIPLET MOLECULAR OXYGEN Mechanisms for the reaction of thiophene and 2-methylthiophene with molecular oxygen on both the triplet and singlet potential energy surfaces (PESs) were investigated using ab initio methods. Thiophene and 2-methylthiophene where shown to react with O2 via two types of mechanisms; namely, direct hydrogen abstraction and addition/elimination. The barriers for reaction with triplet oxygen are all significantly large (i.e., > 30 kcal mol-1), which indicates that the direct oxidation of thiophene by ground state oxygen might be important only in high temperature processes. Reaction of thiophene with singlet oxygen via a 2+4 cycloaddition leading to endoperoxides is the most favorable channel. Moreover, it was found that alkylation of the thiophene ring (i.e., methyl-substituted thiophene) is capable of lowering the barrier height for the addition pathway. The implication of the current theoretical results may shed new light on the initiation mechanisms for combustion of asphaltenes. This work was published in the Journal of Physical Chemistry A, 2012 116, 4934-4946. JAHN-TELLER STABILIZATION IN POSS CATIONS We have a long

  7. 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

  8. Statistical properties of the dense hydrogen plasma: An ab initio molecular dynamics investigation

    International Nuclear Information System (INIS)

    Kohanoff, J.; Hansen, J.P.

    1995-12-01

    The hydrogen plasma is studied in the very high density (atomic and metallic) regime by extensive ab initio Molecular Dynamics simulations. Protons are treated classically, and electrons in the Born-Oppenheimer framework, within the local density approximation (LDA). Densities and temperatures studied fall within the strong coupling regime of the protons. We address the question of the validity of linear screening, and we find it to yield a reasonably good description up to r s approx. 0.5, but already too crude for r s = 1 (with r s = (3/4πρ) 1/3 the ion sphere radius). Finite-size and Brillouin zone sampling effects in metallic systems are studied and shown to be very delicate also in the fluid (liquid metal) phase. We analyse the low-temperature phase diagram and the melting transition. A remarkably fast decrease of the melting temperature with decreasing density is found, up to a point when it becomes comparable to the Fermi temperature of the protons. The possible vicinity of a triple point bcc-hcp(fcc)- liquid is discussed in the region of r s approx. 1.1 and T approx. 100 - 200K. The fluid phase is studied in detail for several temperatures. Proton-electron correlations show a weak temperature dependence, and proton-proton correlations exhibit a well-defined first coordination shell, thus characterizing fluid H in this regime as an atomic liquid. Diffusion coefficients are compared to the values for the one-component plasma. Vibrational densities of states (VDOS) show a plasmon renormalization due to electron screening, and the presence of a plasmon-coupled single-particle mode up to very high temperatures. Collective modes are studied through dynamical structure factors. In close relationship with the VDOS, the simulations reveal the remarkable persistent of a weakly damped high-frequency ion acoustic mode, even under conditions of strong electron screening. The possibility of using this observation as a diagnostic for the plasma phase transition to the

  9. Investigating Research Streams of Conjoint Analysis: A Bibliometric Study

    Directory of Open Access Journals (Sweden)

    Thorsten Teichert

    2010-05-01

    Full Text Available Conjoint analysis (CA is one of the most important methods for preference elicitation. In this paper we investigate the intellectual structure within the conjoint analytical research community. Analyses based on single papers provide a method-based overview of streams of conjoint research. By using novel bibliometric techniques in this field we complement findings of existing reviews. We use co-citation and factor analysis of the most cited articles in SSCI to identify the most important articles and research streams. Seven research streams are revealed which are visualized by means of multidimensional scaling. Tables and graphics reveal the disciplinary affiliations of contributors to CA, the special structure within the classes as well as links between them.

  10. Wetting and evaporation of salt-water nanodroplets: A molecular dynamics investigation.

    Science.gov (United States)

    Zhang, Jun; Borg, Matthew K; Sefiane, Khellil; Reese, Jason M

    2015-11-01

    We employ molecular dynamics simulations to study the wetting and evaporation of salt-water nanodroplets on platinum surfaces. Our results show that the contact angle of the droplets increases with the salt concentration. To verify this, a second simulation system of a thin salt-water film on a platinum surface is used to calculate the various surface tensions. We find that both the solid-liquid and liquid-vapor surface tensions increase with salt concentration and as a result these cause an increase in the contact angle. However, the evaporation rate of salt-water droplets decreases as the salt concentration increases, due to the hydration of salt ions. When the water molecules have all evaporated from the droplet, two forms of salt crystals are deposited, clump and ringlike, depending on the solid-liquid interaction strength and the evaporation rate. To form salt crystals in a ring, it is crucial that there is a pinned stage in the evaporation process, during which salt ions can move from the center to the rim of the droplets. With a stronger solid-liquid interaction strength, a slower evaporation rate, and a higher salt concentration, a complete salt crystal ring can be deposited on the surface.

  11. Molecular Modeling of Myrosinase from Brassica oleracea: A Structural Investigation of Sinigrin Interaction

    Directory of Open Access Journals (Sweden)

    Sathishkumar Natarajan

    2015-12-01

    Full Text Available Myrosinase, which is present in cruciferous plant species, plays an important role in the hydrolysis of glycosides such as glucosinolates and is involved in plant defense. Brassicaceae myrosinases are diverse although they share common ancestry, and structural knowledge about myrosinases from cabbage (Brassica oleracea was needed. To address this, we constructed a three-dimensional model structure of myrosinase based on Sinapis alba structures using Iterative Threading ASSEmbly Refinement server (I-TASSER webserver, and refined model coordinates were evaluated with ProQ and Verify3D. The resulting model was predicted with β/α fold, ten conserved N-glycosylation sites, and three disulfide bridges. In addition, this model shared features with the known Sinapis alba myrosinase structure. To obtain a better understanding of myrosinase–sinigrin interaction, the refined model was docked using Autodock Vina with crucial key amino acids. The key nucleophile residues GLN207 and GLU427 were found to interact with sinigrin to form a hydrogen bond. Further, 20-ns molecular dynamics simulation was performed to examine myrosinase–sinigrin complex stability, revealing that residue GLU207 maintained its hydrogen bond stability throughout the entire simulation and structural orientation was similar to that of the docked state. This conceptual model should be useful for understanding the structural features of myrosinase and their binding orientation with sinigrin.

  12. Investigations into crazing in glassy amorphous polymers through molecular dynamics simulations

    Science.gov (United States)

    Venkatesan, Sudarkodi; Basu, Sumit

    2015-04-01

    In many glassy amorphous polymers, localisation of deformation during loading leads to crazes. Crazes are crack like features whose faces are bridged either by fibrils or a cellular network of voids and fibrils. While formation of crazes is aided by the presence of surface imperfections and embedded dust particles, in this work, we focus on intrinsic crazes that form spontaneously in the volume of the material. We perform carefully designed molecular dynamics simulations on well equilibrated samples of a model polymer with a view to gaining insights into certain incompletely understood aspects of the crazing process. These include genesis of the early nanovoids leading to craze nucleation, mechanisms of stabilising the cellular or fibrillar structure and the competition between chain scission and chain disentanglement in causing the final breakdown of the craze. Additionally, we identify and enumerate clusters of entanglement points with high functionality as effective topological constraints on macromolecular chains. We show that regions with low density of entanglement clusters serve as sites for nanovoid nucleation under high mean stress. Growth occurs by the repeated triggering of cavitation instabilities above a growing void. The growth of the void is aided by disentanglement in and flow of entanglements away from the cavitating region. Finally, for the chain lengths chosen, scission serves to supply short chains to the growing craze but breakdown occurs by complete disentanglement of the chains. In fact, most of the energy supplied to the material seems to be used in causing disentanglements and very little energy is required to create a stable fibril.

  13. Molecular epigenetics in the management of ovarian cancer: Are we investigating a rational clinical promise?

    Directory of Open Access Journals (Sweden)

    Ha eNguyen

    2014-04-01

    Full Text Available Epigenetics is essentially a phenotypical change in gene expression without any alteration of the DNA sequence; the emergence of epigenetics in cancer research and mainstream oncology is fueling new hope. However, it is not yet known whether this knowledge will translate to improved clinical management of ovarian cancer. In this malignancy, women are still undergoing chemotherapy similar to what was approved in 1978, which to this day represents one of the biggest breakthroughs for treating ovarian cancer. While liquid tumors are benefitting from epigenetically-related therapies, solid tumors like ovarian cancer are not (yet?. Herein we will review the science of molecular epigenetics, especially DNA methylation, histone modifications and microRNA, but also include transcription factors since they, too, are important in ovarian cancer. Preclinical and clinical research on the role of epigenetic modifications is summarized as well. Sadly, ovarian cancer remains an idiopathic disease, for the most part, and there are many areas of patient management which could benefit from improved technology. This review will also highlight the evidence suggesting that epigenetics may have preclinical utility in pharmacology and clinical applications for prognosis and diagnosis. Lastly, drugs currently in clinical trials (i.e. histone deacetylase inhibitors are discussed along with the promise for epigenetics in the exploitation of chemoresistance. Whether epigenetics will ultimately be the answer to better management in ovarian cancer is currently unknown; what we have now is hope.

  14. Size effect on local magnetic moments in ferrimagnetic molecular complexes: an XMCD investigation

    International Nuclear Information System (INIS)

    Champion, G.; Villain, F.; Cartier dit Moulin, C.; Arrio, M.-A.; Sainctavit, P.; Zacchigna, M.; Zangrando, M.; Finazzi, M.; Parmigiani, F.; Mathoniere, C.

    2003-01-01

    Molecular chemistry allows to synthesize new magnetic systems with controlled properties such as size, magnetization or anisotropy. The theoretical study of the magnetic properties of small molecules (from 2 to 10 metallic cations per molecule) predicts that the magnetization at saturation of each ion does not reach the expected value for uncoupled ions when the magnetic interaction is antiferromagnetic. The quantum origin of this effect is due to the linear combination of several spin states building the wave function of the ground state and clusters of finite size and of finite spin value exhibit this property. When single crystals are available, spin densities on each atom can be experimentally given by polarized neutron diffraction (PND) experiments. In the case of bimetallic MnCu powdered samples, we will show that x-ray magnetic circular dichroism (XMCD) spectroscopy can be used to follow the evolution of the spin distribution on the Mn II and Cu II sites when passing from a dinuclear MnCu unit to a one dimensional (MnCu) n compound. (author)

  15. MDM2-MDM4 molecular interaction investigated by atomic force spectroscopy and surface plasmon resonance.

    Science.gov (United States)

    Moscetti, Ilaria; Teveroni, Emanuela; Moretti, Fabiola; Bizzarri, Anna Rita; Cannistraro, Salvatore

    Murine double minute 2 (MDM2) and 4 (MDM4) are known as the main negative regulators of p53, a tumor suppressor. They are able to form heterodimers that are much more effective in the downregulation of p53. Therefore, the MDM2-MDM4 complex could be a target for promising therapeutic restoration of p53 function. To this aim, a deeper understanding of the molecular mechanisms underlining the heterodimerization is needed. The kinetic and thermodynamic characterization of the MDM2-MDM4 complex was performed with two complementary approaches: atomic force spectroscopy and surface plasmon resonance. Both techniques revealed an equilibrium dissociation constant (KD ) in the micromolar range for the MDM2-MDM4 heterodimer, similar to related complexes involved in the p53 network. Furthermore, the MDM2-MDM4 complex is characterized by a relatively high free energy, through a single energy barrier, and by a lifetime in the order of tens of seconds. New insights into the MDM2-MDM4 interaction could be highly important for developing innovative anticancer drugs focused on p53 reactivation.

  16. Pure and Modified Co-Poly(amide-12-b-ethylene oxide Membranes for Gas Separation Studied by Molecular Investigations

    Directory of Open Access Journals (Sweden)

    Luana De Lorenzo

    2012-06-01

    Full Text Available This paper deals with a theoretical investigation of gas transport properties in a pure and modified PEBAX block copolymer membrane with N-ethyl-o/p-toluene sulfonamide (KET as additive molecules. Molecular dynamics simulations using COMPASS force field, Gusev-Suter Transition State Theory (TST and Monte Carlo methods were used. Bulk models of PEBAX and PEBAX/KET in different copolymer/additive compositions were assembled and analyzed to evaluate gas permeability and morphology to characterize structure-performance relationships.

  17. Cluster analysis of accelerated molecular dynamics simulations: A case study of the decahedron to icosahedron transition in Pt nanoparticles

    Science.gov (United States)

    Huang, Rao; Lo, Li-Ta; Wen, Yuhua; Voter, Arthur F.; Perez, Danny

    2017-10-01

    Modern molecular-dynamics-based techniques are extremely powerful to investigate the dynamical evolution of materials. With the increase in sophistication of the simulation techniques and the ubiquity of massively parallel computing platforms, atomistic simulations now generate very large amounts of data, which have to be carefully analyzed in order to reveal key features of the underlying trajectories, including the nature and characteristics of the relevant reaction pathways. We show that clustering algorithms, such as the Perron Cluster Cluster Analysis, can provide reduced representations that greatly facilitate the interpretation of complex trajectories. To illustrate this point, clustering tools are used to identify the key kinetic steps in complex accelerated molecular dynamics trajectories exhibiting shape fluctuations in Pt nanoclusters. This analysis provides an easily interpretable coarse representation of the reaction pathways in terms of a handful of clusters, in contrast to the raw trajectory that contains thousands of unique states and tens of thousands of transitions.

  18. Theoretical investigation of interaction of sorbitol molecules with alcohol dehydrogenase in aqueous solution using molecular dynamics simulation.

    Science.gov (United States)

    Bahrami, Homayoon; Zahedi, Mansour; Moosavi-Movahedi, Ali Akbar; Azizian, Homa; Amanlou, Massoud

    2011-03-01

    The nature of protein-sorbitol-water interaction in solution at the molecular level, has been investigated using molecular dynamics simulations. In order to do this task, two molecular dynamics simulations of the protein ADH in solution at room temperature have been carried out, one in the presence (about 0.9 M) and another in the absence of sorbitol. The results show that the sorbitol molecules cluster and move toward the protein, and form hydrogen bonds with protein. Also, coating by sorbitol reduces the conformational fluctuations of the protein compared to the sorbitol-free system. Thus, it is concluded that at moderate concentration of sorbitol solution, sorbitol molecules interact with ADH via many H-bonds that prevent the protein folding. In fact, at more concentrated sorbitol solution, water and sorbitol molecules accumulate around the protein surface and form a continuous space-filling network to reduce the protein flexibility. Namely, in such solution, sorbitol molecules can stabilize a misfolded state of ADH, and prevent the protein from folding to its native structure.

  19. Numerical methodologies for investigation of moderate-velocity flow using a hybrid computational fluid dynamics - molecular dynamics simulation approach

    International Nuclear Information System (INIS)

    Ko, Soon Heum; Kim, Na Yong; Nikitopoulos, Dimitris E.; Moldovan, Dorel; Jha, Shantenu

    2014-01-01

    Numerical approaches are presented to minimize the statistical errors inherently present due to finite sampling and the presence of thermal fluctuations in the molecular region of a hybrid computational fluid dynamics (CFD) - molecular dynamics (MD) flow solution. Near the fluid-solid interface the hybrid CFD-MD simulation approach provides a more accurate solution, especially in the presence of significant molecular-level phenomena, than the traditional continuum-based simulation techniques. It also involves less computational cost than the pure particle-based MD. Despite these advantages the hybrid CFD-MD methodology has been applied mostly in flow studies at high velocities, mainly because of the higher statistical errors associated with low velocities. As an alternative to the costly increase of the size of the MD region to decrease statistical errors, we investigate a few numerical approaches that reduce sampling noise of the solution at moderate-velocities. These methods are based on sampling of multiple simulation replicas and linear regression of multiple spatial/temporal samples. We discuss the advantages and disadvantages of each technique in the perspective of solution accuracy and computational cost.

  20. Molecular Genetic Analysis of Parasite Survival in P. falciparum Malaria.

    Science.gov (United States)

    1991-03-15

    conducting research utilizing recombinant DNA technology , the investigator(s) adhered to current guidelines promulgated by the National Institute of Health...oligonucleotides unrelated to the conserved elements of Plasmodium falciparum were used (lane marked random oligo). Furthermore, extracts prepared...once with Ix Trager’s buffer. The following steps were carried out on ice. Erythrocytes were lysed in 0.05% saponin (19). The released parasites were

  1. Spectroscopic investigation of the redox properties of CoAPO molecular sieves

    NARCIS (Netherlands)

    Peeters, M.P.J.; Hooff, van J.H.C.; Sheldon, R.A.; Zholobenko, V.L.; Kustov, L.M.; Kazansky, V.B.; Balmoos, von R.; Higgins, J.B.; Treacy, M.M.J

    1993-01-01

    Acid sites in CoAPO-5 and CoAPO-11 and redox properties of these Co-substituted aluminophosphates have been investigated using UV- and IR-spectroscopy. The data obtained show that CoAPO exhibits quite unusual acidic and redox properties. The absence of the bridged OH-group seems to be a common

  2. Integrative Network Analysis Unveils Convergent Molecular Pathways in Parkinson's Disease and Diabetes

    OpenAIRE

    Santiago, Jose A.; Potashkin, Judith A.

    2013-01-01

    Background Shared dysregulated pathways may contribute to Parkinson's disease and type 2 diabetes, chronic diseases that afflict millions of people worldwide. Despite the evidence provided by epidemiological and gene profiling studies, the molecular and functional networks implicated in both diseases, have not been fully explored. In this study, we used an integrated network approach to investigate the extent to which Parkinson's disease and type 2 diabetes are linked at the molecular level. ...

  3. Molecular Dynamics Simulations to Investigate the Binding Mode of the Natural Product Liphagal with Phosphoinositide 3-Kinase α

    Directory of Open Access Journals (Sweden)

    Yanjuan Gao

    2016-06-01

    Full Text Available Phosphatidylinositol 3-kinase α (PI3Kα is an attractive target for anticancer drug design. Liphagal, isolated from the marine sponge Aka coralliphaga, possesses the special “liphagane” meroterpenoid carbon skeleton and has been demonstrated as a PI3Kα inhibitor. Molecular docking and molecular dynamics simulations were performed to explore the dynamic behaviors of PI3Kα binding with liphagal, and free energy calculations and energy decomposition analysis were carried out by use of molecular mechanics/Poisson-Boltzmann (generalized Born surface area (MM/PB(GBSA methods. The results reveal that the heteroatom rich aromatic D-ring of liphagal extends towards the polar region of the binding site, and the D-ring 15-hydroxyl and 16-hydroxyl form three hydrogen bonds with Asp810 and Tyr836. The cyclohexyl A-ring projects up into the upper pocket of the lipophilic region, and the hydrophobic/van der Waals interactions with the residues Met772, Trp780, Ile800, Ile848, Val850, Met922, Phe930, Ile932 could be the key interactions for the affinity of liphagal to PI3Kα. Thus, a new strategy for the rational design of more potent analogs of liphagal against PI3Kα is provided. Our proposed PI3Kα/liphagal binding mode would be beneficial for the discovery of new active analogs of liphagal against PI3Kα.

  4. Neutron activation analysis: a powerful tool in provenance investigations

    International Nuclear Information System (INIS)

    Meloni, Sandro; Oddone, Massimo

    2002-01-01

    It is well known that neutron activation analysis (NAA), both instrumental and destructive, allows the simultaneous determination of a number of elements, mostly trace elements, with high levels of precision and accuracy. These peculiar properties of NAA are very useful when applied to provenance studies, i.e. to the identification of the origin of raw materials with which artifacts had been manufactured in ancient times. Data reduction by statistical procedures, especially multivariate analysis techniques, provides a statistical 'fingerprint' of investigated materials, both raw materials and archaeological artifacts, that, upon comparison, allows the identification of the provenance of prime matters used for artifact manufacturing. Thus information on quarries and flows exploitation in the antiquity, on technological raw materials processing, on trade routes and about the circulation of fakes, can be obtained. In the present paper two case studies are reported. The first one deals with the identification of the provenance of clay used to make ceramic materials, mostly bricks and tiles, recovered from the excavation of a Roman 'villa' in Lomello (Roman name Laumellum) and of Roman settlings in Casteggio (Roman name Clastidium). Both sites are located in the Province of Pavia in areas called Lomellina and Oltrepo respectively. The second one investigates the origin of the white marble used to build medieval arks, Carolingian age, located in the church of San Felice, now property of the University of Pavia. Experimental set-up, analytical results and data reduction procedures are presented and discussed. (author)

  5. Simulated, Emulated, and Physical Investigative Analysis (SEPIA) of networked systems.

    Energy Technology Data Exchange (ETDEWEB)

    Burton, David P.; Van Leeuwen, Brian P.; McDonald, Michael James; Onunkwo, Uzoma A.; Tarman, Thomas David; Urias, Vincent E.

    2009-09-01

    This report describes recent progress made in developing and utilizing hybrid Simulated, Emulated, and Physical Investigative Analysis (SEPIA) environments. Many organizations require advanced tools to analyze their information system's security, reliability, and resilience against cyber attack. Today's security analysis utilize real systems such as computers, network routers and other network equipment, computer emulations (e.g., virtual machines) and simulation models separately to analyze interplay between threats and safeguards. In contrast, this work developed new methods to combine these three approaches to provide integrated hybrid SEPIA environments. Our SEPIA environments enable an analyst to rapidly configure hybrid environments to pass network traffic and perform, from the outside, like real networks. This provides higher fidelity representations of key network nodes while still leveraging the scalability and cost advantages of simulation tools. The result is to rapidly produce large yet relatively low-cost multi-fidelity SEPIA networks of computers and routers that let analysts quickly investigate threats and test protection approaches.

  6. Investigating product development strategy in beverage industry using factor analysis

    Directory of Open Access Journals (Sweden)

    Naser Azad

    2013-03-01

    Full Text Available Selecting a product development strategy that is associated with the company's current service or product innovation, based on customers’ needs and changing environment, plays an important role in increasing demand, increasing market share, increasing sales and profits. Therefore, it is important to extract effective variables associated with product development to improve performance measurement of firms. This paper investigates important factors influencing product development strategies using factor analysis. The proposed model of this paper investigates 36 factors and, using factor analysis, we extract six most influential factors including information sharing, intelligence information, exposure strategy, differentiation, research and development strategy and market survey. The first strategy, partnership, includes five sub-factor including product development partnership, partnership with foreign firms, customers’ perception from competitors’ products, Customer involvement in product development, inter-agency coordination, customer-oriented approach to innovation and transmission of product development change where inter-agency coordination has been considered the most important factor. Internal strengths are the most influential factors impacting the second strategy, intelligence information. The third factor, introducing strategy, introducing strategy, includes four sub criteria and consumer buying behavior is the most influencing factor. Differentiation is the next important factor with five components where knowledge and expertise in product innovation is the most important one. Research and development strategy with four sub-criteria where reducing product development cycle plays the most influential factor and finally, market survey strategy is the last important factor with three factors and finding new market plays the most important role.

  7. Conformational and functional analysis of molecular dynamics trajectories by Self-Organising Maps

    Directory of Open Access Journals (Sweden)

    Stella Fabio

    2011-05-01

    Full Text Available Abstract Background Molecular dynamics (MD simulations are powerful tools to investigate the conformational dynamics of proteins that is often a critical element of their function. Identification of functionally relevant conformations is generally done clustering the large ensemble of structures that are generated. Recently, Self-Organising Maps (SOMs were reported performing more accurately and providing more consistent results than traditional clustering algorithms in various data mining problems. We present a novel strategy to analyse and compare conformational ensembles of protein domains using a two-level approach that combines SOMs and hierarchical clustering. Results The conformational dynamics of the α-spectrin SH3 protein domain and six single mutants were analysed by MD simulations. The Cα's Cartesian coordinates of conformations sampled in the essential space were used as input data vectors for SOM training, then complete linkage clustering was performed on the SOM prototype vectors. A specific protocol to optimize a SOM for structural ensembles was proposed: the optimal SOM was selected by means of a Taguchi experimental design plan applied to different data sets, and the optimal sampling rate of the MD trajectory was selected. The proposed two-level approach was applied to single trajectories of the SH3 domain independently as well as to groups of them at the same time. The results demonstrated the potential of this approach in the analysis of large ensembles of molecular structures: the possibility of producing a topological mapping of the conformational space in a simple 2D visualisation, as well as of effectively highlighting differences in the conformational dynamics directly related to biological functions. Conclusions The use of a two-level approach combining SOMs and hierarchical clustering for conformational analysis of structural ensembles of proteins was proposed. It can easily be extended to other study cases and to

  8. Conformational and functional analysis of molecular dynamics trajectories by Self-Organising Maps

    Science.gov (United States)

    2011-01-01

    Background Molecular dynamics (MD) simulations are powerful tools to investigate the conformational dynamics of proteins that is often a critical element of their function. Identification of functionally relevant conformations is generally done clustering the large ensemble of structures that are generated. Recently, Self-Organising Maps (SOMs) were reported performing more accurately and providing more consistent results than traditional clustering algorithms in various data mining problems. We present a novel strategy to analyse and compare conformational ensembles of protein domains using a two-level approach that combines SOMs and hierarchical clustering. Results The conformational dynamics of the α-spectrin SH3 protein domain and six single mutants were analysed by MD simulations. The Cα's Cartesian coordinates of conformations sampled in the essential space were used as input data vectors for SOM training, then complete linkage clustering was performed on the SOM prototype vectors. A specific protocol to optimize a SOM for structural ensembles was proposed: the optimal SOM was selected by means of a Taguchi experimental design plan applied to different data sets, and the optimal sampling rate of the MD trajectory was selected. The proposed two-level approach was applied to single trajectories of the SH3 domain independently as well as to groups of them at the same time. The results demonstrated the potential of this approach in the analysis of large ensembles of molecular structures: the possibility of producing a topological mapping of the conformational space in a simple 2D visualisation, as well as of effectively highlighting differences in the conformational dynamics directly related to biological functions. Conclusions The use of a two-level approach combining SOMs and hierarchical clustering for conformational analysis of structural ensembles of proteins was proposed. It can easily be extended to other study cases and to conformational ensembles from

  9. Clinical and molecular genetic analysis of best vitelliform macular dystrophy.

    NARCIS (Netherlands)

    Boon, C.J.F.; Theelen, T.; Hoefsloot, L.H.; Schooneveld, M.J. van; Keunen, J.E.E.; Cremers, F.P.M.; Klevering, B.J.; Hoyng, C.B.

    2009-01-01

    PURPOSE: To describe the phenotype of Best vitelliform macular dystrophy (BVMD) and to evaluate genotype-phenotype and histopathologic correlations. METHODS: Retrospective analysis of patients with BVMD who underwent an extensive ophthalmic examination, including best-corrected Snellen visual

  10. CLINICAL AND MOLECULAR GENETIC ANALYSIS OF BEST VITELLIFORM MACULAR DYSTROPHY

    NARCIS (Netherlands)

    Boon, Camiel J. F.; Theelen, Thomas; Hoefsloot, Elisabeth H.; van Schooneveld, Mary J.; Keunen, Jan E. E.; Cremers, Frans P. M.; Klevering, B. Jeroen; Hoyng, Carel B.

    2009-01-01

    Purpose: To describe the phenotype of Best vitelliform macular dystrophy (BVMD) and to evaluate genotype-phenotype and histopathologic correlations. Methods: Retrospective analysis of patients with BVMD who underwent an extensive ophthalmic examination, including best-corrected Snellen visual

  11. Molecular cloning, characterization and functional analysis of a 3 ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-08-04

    Aug 4, 2009 ... other plant HMGRs and contained 2 transmembrane domains and a catalytic domain. The potential significance ... used as animal feed. Therefore ... Table 1. Primers used in the cloning and analysis of JcHMGR gene. Primers.

  12. Investigation of Molecular Structure and Thermal Properties of Thermo-Oxidative Aged SBS in Blends and Their Relations.

    Science.gov (United States)

    Xu, Xiong; Yu, Jianying; Xue, Lihui; Zhang, Canlin; Zha, Yagang; Gu, Yi

    2017-07-07

    Tri-block copolymer styrene-butadiene (SBS) is extensively applied in bituminous highway construction due to its high elasticity and excellent weather resistance. With the extension of time, tri-block structural SBS automatically degrades into bi-block structural SB- with some terminal oxygen-containing groups under the comprehensive effects of light, heat, oxygen, etc. In this paper, the effects of aging temperature, aging time and oxygen concentration on the molecular structure of thermo-oxidative aged SBS were mainly investigated using Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS), and the correlation between oxygen-containing groups and thermal properties (TG-DTG) was further discussed. The FTIR and XPS results show that rapid decomposition of SBS will occur with increments of aging temperature, aging time and oxygen concentration, and a large number of oxygen-containing groups such as -OH, C=O, -COOH, etc. will be formed during thermo-oxidative aging. In short-term aging, changes in aging temperature and oxygen concentration have a significant impact on the structural damage of SBS. However, in long-term aging, it has no further effect on the molecular structure of SBS or on increasing oxygen concentration. The TG and DTG results indicate that the concentration of substances with low molecular weight gradually increases with the improvement of the degree of aging of the SBS, while the initial decomposition rate increases at the beginning of thermal weightlessness and the decomposition rate slows down in comparison with neat SBS. From the relation between the XPS and TG results, it can be seen that the initial thermal stability of SBS rapidly reduces as the relative concentration of the oxygen-containing groups accumulates around 3%, while the maximum decomposition temperature slowly decreases when the relative concentration of the oxygen-containing groups is more than 3%, due to the difficult damage to strong bonds

  13. Detachment of semiflexible polymer chains from a substrate: A molecular dynamics investigation

    Energy Technology Data Exchange (ETDEWEB)

    Paturej, J. [Leibniz-Institut of Poslymer Research Dresden, 01069 Dresden (Germany); Institute of Physics, University of Szczecin, Wielkopolska 15, 70451 Szczecin (Poland); Erbas, A. [Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208 (United States); Milchev, A. [Institute for Physical Chemistry, Bulgarian Academy of Sciences, 1113 Sofia (Bulgaria); Rostiashvili, V. G. [Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128 Mainz (Germany)

    2014-12-07

    Using Molecular Dynamics simulations, we study the force-induced detachment of a coarse-grained model polymer chain from an adhesive substrate. One of the chain ends is thereby pulled at constant speed off the attractive substrate and the resulting saw-tooth profile of the measured mean force 〈f〉 vs height D of the end-segment over the plane is analyzed for a broad variety of parameters. It is shown that the observed characteristic oscillations in the 〈f〉-D profile depend on the bending and not on the torsional stiffness of the detached chains. Allowing for the presence of hydrodynamic interactions (HI) in a setup with explicit solvent and dissipative particle dynamics-thermostat, rather than the case of Langevin thermostat, one finds that HI have little effect on the 〈f〉-D profile. Also the change of substrate affinity with respect to the solvent from solvophilic to solvophobic is found to play negligible role in the desorption process. In contrast, a changing ratio ε{sub s}{sup B}/ε{sub s}{sup A} of the binding energies of A- and B-segments in the detachment of an AB-copolymer from adhesive surface strongly changes the 〈f〉-D profile whereby the B-spikes vanish when ε{sub s}{sup B}/ε{sub s}{sup A}<0.15. Eventually, performing an atomistic simulation of (bio)-polymers, we demonstrate that the simulation results, derived from our coarse-grained model, comply favorably with those from the all-atom simulation.

  14. [Molecular markers of Alzheimer disease early diagnostic: investigation perspectives of peripheral tissues.

    Science.gov (United States)

    Paltsev, M A; Zuev, V A; Kozhevnikova, E O; Linkova, N S; Kvetnaia, T V; Polyakova, V O; Kvetnoy, I M

    2017-01-01

    Alzheimer's disease (AD) is a progressive neurodegenerative disorder of elderly and old age people. For intravital diagnosis of the expression of signaling molecules - AD markers, cerebrospinal fluid (CSF) and peripheral tissues are used: lymphocytes and blood platelets, buccal and olfactory epithelium, skin fibroblasts. There are several changes in the production of hyper phosphorylated form of τ-protein, BACE1 and peptide Аβ42 in CSF in case of AD, but CSF taking may have a number of side effects. Less traumatic taking of sampling tissues for the diagnosis of AD is in use of epithelium biopsy and blood portion. An increase in the expression of the hyper phosphorylated form of τ-protein is shown in blood lymphocytes of AD patients. An increase in the content of high molecular weight forms of phosphorylated t-protein and amyloid precursor protein-APP was also revealed in blood platelets of AD patients. Changes in the amount of 2 miRNA families - miR-132 family and miR-134 family were revealed in blood cells 1-5 years before the manifestation of clinical signs of AD. An increase in the concentration of bound calcium, synthesis of peptides Aβ40 and Aβ42, τ protein was observed in AD skin fibroblasts. In the olfactory and buccal epithelium an increase in the expression of hyper phosphorylated form of τ-protein and Aβ peptide was detected in patients with AD. Verification of AD markers in peripheral tissues for biopsy have the important significant for life diagnostics, prevention and and target AD treatment.

  15. Molecular modelling investigations on the possibility of phenanthrene dimers to be the primary nuclei of soot

    Science.gov (United States)

    Wei, Mingrui; Wu, Sheng; Li, Fan; Zhang, Dongju; Zhang, Tingting; Guo, Guanlun

    2017-11-01

    Pyrene dimerisation was successfully used to model the beginning of soot nucleation in some simulation models. However, the quantum mechanics (QM) calculations proved that the binding energy of a PAH dimer with three six-member rings was similar to that of a pyrene dimer. Meanwhile, the high concentration of phenanthrene at flame conditions indicated high probability of collisions among them. The small difference of the binding energy and high concentration indicated that PAHs structurally smaller than pyrene also could be involved in soot inception. Hence, binary collisions of phenanthrene were simulated to find out whether phenanthrene dimers can serve as soot primary nuclei or not by using non-equilibrium molecular dynamics (MD). Three temperatures, six collision orientations and 155 initial translational velocities (ITVs) were considered. The results indicated that the number of dimers with lifetime over 10 ps which can serve as soot nuclei decreased from 52 at 1000 K to 17 at 1600 K, and further to 6 at 2400 K, which means that low temperature was more favourable for phenanthrene to form soot nuclei. Meanwhile, no soot nuclei were formed at the high velocity region (HVR), compared to 43 and 9 at low and middle velocity regions (LVR and MVR), respectively, when temperature was 1000 K. Also, no soot nuclei were formed at HVR when the temperature was raised to 1600 K and 2400 K. This indicated that HVR was unfavourable for phenanthrene to form soot nuclei. The results computationally further illustrated that small PAHs such as phenanthrene could serve as soot primary nuclei, since they have similar mole fractions in some flames. This may be useful for future soot simulation models.

  16. Shock-wave propagation and reflection in semicrystalline polyethylene: A molecular-level investigation

    Science.gov (United States)

    Elder, Robert M.; O'Connor, Thomas C.; Chantawansri, Tanya L.; Sliozberg, Yelena R.; Sirk, Timothy W.; Yeh, In-Chul; Robbins, Mark O.; Andzelm, Jan W.

    2017-09-01

    Semicrystalline polyethylene (PE) is attractive for a variety of mechanically demanding applications, where shock compression can occur. Although often highly crystalline, PE invariably contains nanoscale amorphous domains that influence shock propagation. Our objective in this work is to study the effects of such domains. To this end, we adopt a novel approach wherein we parametrize a simple continuum-level theory based on the shock impedance from molecular dynamics (MD) simulations. Using this theory, we predict how crystalline/amorphous interfaces attenuate shocks via energy reflection due to the impedance mismatch between the phases. The theory predicts that these interfaces attenuate weak shocks more effectively than strong shocks. We compare the theory to explicit nonequilibrium MD simulations of compressive shocks in semicrystalline PE containing nanometer-scale amorphous regions of varying size, where we analyze the pressure response and reflection of energy. The theory and simulations show good agreement for strong shocks (≥1.0 km /s ), but for weak shocks (shock front. However, the simulations show that when amorphous domains are narrow—with widths comparable to the shock front—reflection is reduced compared to the predictions. We identify several nanoscale mechanisms that reduce the impedance mismatch, and thus reduce reflection, at thin amorphous domains. First, the two-wave elastic-plastic structure of shocks in crystalline PE allows the faster-moving elastic precursor wave to compress small amorphous domains before the plastic wave arrives. Second, confinement between stiff, ordered crystalline domains increases the stiffness and chain ordering in small amorphous regions. Moreover, in terms of stiffness the interfaces are similar in width to the shock front, which may contribute to the underprediction of the theory for weak shocks, where the shock front is widest. We conclude by discussing the significance of these results, namely, how they can

  17. Investigation of cellular and molecular responses to pulsed focused ultrasound in a mouse model.

    Directory of Open Access Journals (Sweden)

    Scott R Burks

    Full Text Available Continuous focused ultrasound (cFUS has been widely used for thermal ablation of tissues, relying on continuous exposures to generate temperatures necessary to induce coagulative necrosis. Pulsed FUS (pFUS employs non-continuous exposures that lower the rate of energy deposition and allow cooling to occur between pulses, thereby minimizing thermal effects and emphasizing effects created by non-thermal mechanisms of FUS (i.e., acoustic radiation forces and acoustic cavitation. pFUS has shown promise for a variety of applications including drug and nanoparticle delivery; however, little is understood about the effects these exposures have on tissue, especially with regard to cellular pro-homing factors (growth factors, cytokines, and cell adhesion molecules. We examined changes in murine hamstring muscle following pFUS or cFUS and demonstrate that pFUS, unlike cFUS, has little effect on the histological integrity of muscle and does not induce cell death. Infiltration of macrophages was observed 3 and 8 days following pFUS or cFUS exposures. pFUS increased expression of several cytokines (e.g., IL-1α, IL-1β, TNFα, INFγ, MIP-1α, MCP-1, and GMCSF creating a local cytokine gradient on days 0 and 1 post-pFUS that returns to baseline levels by day 3 post-pFUS. pFUS exposures induced upregulation of other signaling molecules (e.g., VEGF, FGF, PlGF, HGF, and SDF-1α and cell adhesion molecules (e.g., ICAM-1 and VCAM-1 on muscle vasculature. The observed molecular changes in muscle following pFUS may be utilized to target cellular therapies by increasing homing to areas of pathology.

  18. Ancestry Analysis in the 11-M Madrid Bomb Attack Investigation

    Science.gov (United States)

    Phillips, Christopher; Prieto, Lourdes; Fondevila, Manuel; Salas, Antonio; Gómez-Tato, Antonio; Álvarez-Dios, José; Alonso, Antonio; Blanco-Verea, Alejandro; Brión, María; Montesino, Marta; Carracedo, Ángel; Lareu, María Victoria

    2009-01-01

    The 11-M Madrid commuter train bombings of 2004 constituted the second biggest terrorist attack to occur in Europe after Lockerbie, while the subsequent investigation became the most complex and wide-ranging forensic case in Spain. Standard short tandem repeat (STR) profiling of 600 exhibits left certain key incriminatory samples unmatched to any of the apprehended suspects. A judicial order to perform analyses of unmatched samples to differentiate European and North African ancestry became a critical part of the investigation and was instigated to help refine the search for further suspects. Although mitochondrial DNA (mtDNA) and Y-chromosome markers routinely demonstrate informative geographic differentiation, the populations compared in this analysis were known to show a proportion of shared mtDNA and Y haplotypes as a result of recent gene-flow across the western Mediterranean, while any two loci can be unrepresentative of the ancestry of an individual as a whole. We based our principal analysis on a validated 34plex autosomal ancestry-informative-marker single nucleotide polymorphism (AIM-SNP) assay to make an assignment of ancestry for DNA from seven unmatched case samples including a handprint from a bag containing undetonated explosives together with personal items recovered from various locations in Madrid associated with the suspects. To assess marker informativeness before genotyping, we predicted the probable classification success for the 34plex assay with standard error estimators for a naïve Bayesian classifier using Moroccan and Spanish training sets (each n = 48). Once misclassification error was found to be sufficiently low, genotyping yielded seven near-complete profiles (33 of 34 AIM-SNPs) that in four cases gave probabilities providing a clear assignment of ancestry. One of the suspects predicted to be North African by AIM-SNP analysis of DNA from a toothbrush was identified late in the investigation as Algerian in origin. The results

  19. Sarcocystis neurona and Neospora caninum in Brazilian opossums (Didelphis spp.): Molecular investigation and in vitro isolation of Sarcocystis spp.

    Science.gov (United States)

    Gondim, Leane S Q; Jesus, Rogério F; Ribeiro-Andrade, Müller; Silva, Jean C R; Siqueira, Daniel B; Marvulo, Maria F V; Aléssio, Felipe M; Mauffrey, Jean-François; Julião, Fred S; Savani, Elisa San Martin Mouriz; Soares, Rodrigo M; Gondim, Luís F P

    2017-08-30

    Sarcocystis neurona and Neospora spp. are protozoan parasites that induce neurological diseases in horses and other animal species. Opossums (Didelphis albiventris and Didelphis virginiana) are definitive hosts of S. neurona, which is the major cause of equine protozoal myeloencephalitis (EPM). Neospora caninum causes abortion in cattle and infects a wide range of animal species, while N. hughesi is known to induce neurologic disease in equids. The aims of this study were to investigate S. neurona and N. caninum in tissues from opossums in the northeastern Brazil, and to isolate Brazilian strains of Sarcocystis spp. from wild opossums for comparison with previously isolated strains. Carcasses of 39 opossums from Bahia state were available for molecular identification of Sarcocystis spp. and N. caninum in their tissues, and for sporocyst detection by intestinal scraping. In addition, Sarcocystis-like sporocysts from nine additional opossums, obtained in São Paulo state, were tested. Sarcocystis DNA was found in 16 (41%) of the 39 opossums' carcasses; N. caninum DNA was detected in tissues from three opossums. The sporocysts from the nine additional opossums from São Paulo state were tested by bioassay and induced infection in nine budgerigars, but in none of the gamma-interferon knockout mice. In vitro isolation was successful using tissues from all nine budgerigars. The isolated strains were maintained in CV-1 and Vero cells. Three of nine isolates presented contamination in cell culture and were discarded. Analysis of six isolates based on five loci showed that these parasites were genetically different from each other and also distinct from S. neurona, S. falcatula, S. lindsayi, and S. speeri. In conclusion, opossums in the studied regions were infected with N. caninum and Sarcocystis spp. and represent a potential source of infection to other animals. This is the first report of N. caninum infection in tissues from black-eared opossum (D. aurita or D

  20. Doses in radiation accidents investigated by chromosome aberration analysis

    International Nuclear Information System (INIS)

    Lloyd, D.C.; Purrott, R.J.; Prosser, J.S.; Dolphin, G.W.; Tipper, P.A.; Reeder, E.J.; White, C.M.; Cooper, S.J.; Stephenson, B.D.

    1977-01-01

    Results from cytogenetic investigations into 66 cases of suspected over-exposure to radiation during 1976 are reviewed. This report is the sixth in an annual series which together contain data on 272 studies. Previous results were published in NRPB-R5, R10, R23, R35 and R41. Results from all investigations have been pooled for general analysis. Brief accounts are given in an appendix of the circumstances behind the past year's investigations and, where possible, physical estimates of dose have been included for comparison. A short review is given of the laboratory's recently published dose response data for several energies of neutron radiation. A description is also given of the group's collaboration in an international experiment in which comparisons were made between a variety of dosemeters exposed to a controlled criticality pulse. In a second appendix two experiments are described in which inter- and intra-donor effects on chromosome aberration yields were examined. It was found that differences in dicentric yields were small whereas acentric aberrations were more variable. (author)

  1. Identification of a New Mullet Species Complex Based on an Integrative Molecular and Cytogenetic Investigation of Mugil hospes (Mugilidae: Mugiliformes).

    Science.gov (United States)

    Nirchio, Mauro; Paim, Fabilene G; Milana, Valentina; Rossi, Anna R; Oliveira, Claudio

    2018-01-01

    Mullets are very common fishes included in the family Mugilidae, (Mugiliformes), which are characterized by both a remarkably uniform external morphology and internal anatomy. Recently, within this family, different species complexes were molecularly identified within Mugil , a genus which is characterized by lineages that sometimes show very different karyotypes. Here we report the results of cytogenetic and molecular analyses conducted on Mugil hospes , commonly known as the hospe mullet, from Ecuador. The study aims to verify whether the original described species from the Pacific Ocean corresponds to that identified in the Atlantic Ocean, and to identify species-specific chromosome markers that can add new comparative data about Mugilidae karyotype evolution. The karyotype of M. hospes from Ecuador is composed of 48 acrocentric chromosomes and shows two active nucleolar organizer regions (NORs). In situ hybridization, using different types of repetitive sequences (rDNAs, U1 snDNA, telomeric repeats) as probes, identified species-specific chromosome markers that have been compared with those of other species of the genus Mugil . Cytochrome c oxidase subunit I (COI) sequence analysis shows only 92-93% similarity with sequences previously deposited under this species name in GenBank, all of which were from the Atlantic Ocean. Phylogenetic reconstructions indicate the presence of three well-supported hospe mullet lineages whose molecular divergence is compatible with the presence of distinct species. Indeed, the first lineage includes samples from Ecuador, whereas the other two lineages include the Atlantic samples and correspond to M. brevirostris from Brazil and Mugil sp. R from Belize/Venezuela. Results here provided reiterate the pivotal importance of an integrative molecular and cytogenetic approach in the reconstruction of the relationships within Mugilidae.

  2. Identification of a New Mullet Species Complex Based on an Integrative Molecular and Cytogenetic Investigation of Mugil hospes (Mugilidae: Mugiliformes

    Directory of Open Access Journals (Sweden)

    Mauro Nirchio

    2018-02-01

    Full Text Available Mullets are very common fishes included in the family Mugilidae, (Mugiliformes, which are characterized by both a remarkably uniform external morphology and internal anatomy. Recently, within this family, different species complexes were molecularly identified within Mugil, a genus which is characterized by lineages that sometimes show very different karyotypes. Here we report the results of cytogenetic and molecular analyses conducted on Mugil hospes, commonly known as the hospe mullet, from Ecuador. The study aims to verify whether the original described species from the Pacific Ocean corresponds to that identified in the Atlantic Ocean, and to identify species-specific chromosome markers that can add new comparative data about Mugilidae karyotype evolution. The karyotype of M. hospes from Ecuador is composed of 48 acrocentric chromosomes and shows two active nucleolar organizer regions (NORs. In situ hybridization, using different types of repetitive sequences (rDNAs, U1 snDNA, telomeric repeats as probes, identified species-specific chromosome markers that have been compared with those of other species of the genus Mugil. Cytochrome c oxidase subunit I (COI sequence analysis shows only 92–93% similarity with sequences previously deposited under this species name in GenBank, all of which were from the Atlantic Ocean. Phylogenetic reconstructions indicate the presence of three well-supported hospe mullet lineages whose molecular divergence is compatible with the presence of distinct species. Indeed, the first lineage includes samples from Ecuador, whereas the other two lineages include the Atlantic samples and correspond to M. brevirostris from Brazil and Mugil sp. R from Belize/Venezuela. Results here provided reiterate the pivotal importance of an integrative molecular and cytogenetic approach in the reconstruction of the relationships within Mugilidae.

  3. Molecular analysis of manufactured gas plant soils for naphthalene mineralization

    International Nuclear Information System (INIS)

    Sanseverino, J.; Werner, C.; Fleming, J.; Applegate, B.M.; King, J.M.H.; Sayler, G.S.; Blackburn, J.

    1991-01-01

    New molecular tools are being developed and tested to ascertain the biodegradability of hazardous wastes by soil bacterial population. The potential for manufactured gas plant (MGP) soil bacterial populations to degrade naphthalene, as a component mixture of polynuclear aromatic hydrocarbons, was evaluated by the detection of a naphthalene biodegradative genotype by DNA probe hybridization with DNA extracts and colonies of cultured bacteria of the MGP soils. The activity of the naphthalene-degrading populations was evaluated by mineralization assays, 14 CO 2 production from 14 C-naphthalene. Direct messenger RNA (mRNA) extraction from MGP soil was evaluated as an instantaneous measure of naphthalene catabolic gene expression in MGP soil. The bioavailability of naphthalene for bacterial degradation within the MGP soils was assessed by measuring the bioluminescent response of a naphthalene-lux catabolic reporter strain Pseudomonas fluorescens HK44 (pUTK21). DNA extracted from 5 MGP soils and 1 creosote-contaminated soil and hybridized with a nahA gene probe indicated that the naphthalene degradative genes were present in all samples in the range of 0.06 to 0.95 ng/100 μl DNA extract which was calculated to represent 3.58 x 10 8 to 1.05 x 10 10 nahA positive cells/g soil. Phenanthrene, anthracene, and benzo(a)pyrene were mineralized also by some of the soils. NAH7 homologous messenger RNA transcripts were detectable in one MGP soil and in the creosote-contaminated soil

  4. Molecular analysis of carnitine palmitoyltransferase II deficiency with hepatocardiomuscular expression

    Energy Technology Data Exchange (ETDEWEB)

    Bonnefont, J.P.; Cepanec, C.; Leroux, J.P. [Unite INSERM, Paris (France)] [and others

    1996-05-01

    Carnitine palmitoyltransferase (CPT) II deficiency, an inherited disorder of mitochondrial long-chain fatty-acid (LCFA) oxidation, results in two distinct clinical act phenotypes, namely, an adult (muscular) form and an infantile (hepatocardiomuscular) form. The rationale of this phenotypic heterogeneity is poorly understood. The adult form of the disease is commonly ascribed to the Ser-113-Leu substitution in CPT II. Only few data are available regarding the molecular basis of the infantile form of the disease. We report herein a homozygous A-2399-C transversion predicting a Tyr-628-Ser substitution in a CPT II-deficient infant. In vitro expression of mutant cDNA in COS-1 cells demonstrated the responsibility of this mutation for the disease. Metabolic consequences of the Ser-113-Leu and Tyr-628-Ser substitutions were studied in fibroblasts. The Tyr-628-Ser substitution (infantile form) resulted in a 10% CPT II residual activity, markedly impairing LCFA oxidation, whereas the Ser-113-Leu substitution (adult form) resulted in a 20% CPT II residual activity, without consequence on LCFA oxidation. These data show that CPT II activity has to be reduced below a critical threshold in order for LCFA oxidation in fibroblasts to be impaired. The hypothesis that this critical threshold differs among tissues could provide a basis to explain phenotypic heterogeneity of CPT II deficiency. 32 refs., 5 figs.

  5. Molecular characterization and phylogenetic analysis of Fasciola gigantica from Nigeria.

    Science.gov (United States)

    Ichikawa-Seki, Madoka; Tokashiki, Minami; Opara, Maxwell Nwachukwu; Iroh, Gabriel; Hayashi, Kei; Kumar, Uday Mohanta; Itagaki, Tadashi

    2017-02-01

    Fasciola gigantica is considered the major pathogen causing fasciolosis in Africa; however, molecular characterization of this fluke has not been adequately elucidated. It is important to scientifically elucidate the dispersal history of F. gigantica by analyzing its genetic diversity. Fasciola flukes from Nigeria were analyzed using nuclear and mitochondrial DNA markers. A total of 172 Fasciola flukes collected from cattle were identified as F. gigantica because they displayed the F. gigantica fragment pattern in multiplex PCR for the nuclear marker, phosphoenolpyruvate carboxykinase (pepck). In total, 70 haplotypes were detected from Nigerian F. gigantica on the basis of the concatenated sequence of mitochondrial NADH dehydrogenase subunit 1 (nad1) and cytochrome c oxidase 1 (cox1). The index of neutrality (Fu's Fs) suggests rapid expansion of the Nigerian F. gigantica population. Although four haplogroups, Nigeria 1A, 1B, 2A, and 2B, were detected from Nigerian F. gigantica, a climate-specific genetic structure was not observed among F. gigantica populations from three agro-climatic regions (Sahel, Savannah, and Forest). This is probably because of the frequent transportation of livestock from one part of the country to the other. Nigeria 1A and 1B had close relationships with the Egyptian population of F. gigantica, whereas Nigeria 2A and 2B were comparatively related to the Zambian population. No haplotype was shared among the three countries, and it therefore is difficult to estimate the dispersal route of F. gigantica within the African continent. Copyright © 2016. Published by Elsevier Ireland Ltd.

  6. Molecular analysis of peroxisome proliferation in the hamster.

    Science.gov (United States)

    Choudhury, Agharul I; Sims, Helen M; Horley, Neill J; Roberts, Ruth A; Tomlinson, Simon R; Salter, Andrew M; Bruce, Mary; Shaw, P Nicholas; Kendall, David; Barrett, David A; Bell, David R

    2004-05-15

    Three novel P450 members of the cytochrome P450 4A family were cloned as partial cDNAs from hamster liver, characterised as novel members of the CYP4A subfamily, and designated CYP4A17, 18, and 19. Hamsters were treated with the peroxisome proliferator-activated receptor alpha (PPARalpha) agonists, methylclofenapate (MCP) or Wy-14,643, and shown to develop hepatomegaly and induction of CYP4A17 RNA, and concomitant induction of lauric acid 12- hydroxylase. This treatment also resulted in hypolipidaemia, which was most pronounced in the VLDL fraction, with up to 50% reduction in VLDL-triglycerides; by contrast, blood cholesterol concentration was unaffected by this treatment. These data show that hamster is highly responsive to induction of CYP4A by peroxisome proliferators. To characterise the molecular basis of peroxisome proliferation, the hamster PPARalpha was cloned and shown to encode a 468-amino-acid protein, which is highly similar to rat and mouse PPARalpha proteins. The level of expression of hamster PPARalpha in liver is intermediate between mouse and guinea pig. These results fail to support the hypothesis that the level of PPARalpha in liver is directly responsible for species differences in peroxisome proliferation.

  7. Projection methods for the analysis of molecular-frame photoelectron angular distributions

    International Nuclear Information System (INIS)

    Lucchese, R.R.; Montuoro, R.; Grum-Grzhimailo, A.N.; Liu, X.-J.; Pruemper, G.; Morishita, Y.; Saito, N.; Ueda, K.

    2007-01-01

    The analysis of the molecular-frame photoelectron angular distributions (MFPADs) is discussed within the dipole approximation. The general expressions are reviewed and strategies for extracting the maximum amount of information from different types of experimental measurements are considered. The analysis of the N 1s photoionization of NO is given to illustrate the method

  8. Using Molecular Modeling in Teaching Group Theory Analysis of the Infrared Spectra of Organometallic Compounds

    Science.gov (United States)

    Wang, Lihua

    2012-01-01

    A new method is introduced for teaching group theory analysis of the infrared spectra of organometallic compounds using molecular modeling. The main focus of this method is to enhance student understanding of the symmetry properties of vibrational modes and of the group theory analysis of infrared (IR) spectra by using visual aids provided by…

  9. Experimental investigation of thermal neutron analysis based landmine detection technology

    International Nuclear Information System (INIS)

    Zeng Jun; Chu Chengsheng; Ding Ge; Xiang Qingpei; Hao Fanhua; Luo Xiaobing

    2013-01-01

    Background: Recently, the prompt gamma-rays neutron activation analysis method is wildly used in coal analysis and explosive detection, however there were less application about landmine detection using neutron method especially in the domestic research. Purpose: In order to verify the feasibility of Thermal Neutron Analysis (TNA) method used in landmine detection, and explore the characteristic of this technology. Methods: An experimental system of TNA landmine detection was built based on LaBr 3 (Ce) fast scintillator detector and 252 Cf isotope neutron source. The system is comprised of the thermal neutron transition system, the shield system, and the detector system. Results: On the basis of the TNA, the wide energy area calibration method especially to the high energy area was investigated, and the least detection time for a typical mine was defined. In this study, the 72-type anti-tank mine, the 500 g TNT sample and several interferential objects are tested in loess, red soil, magnetic soil and sand respectively. Conclusions: The experimental results indicate that TNA is a reliable demining method, and it can be used to confirm the existence of Anti-Tank Mines (ATM) and large Anti-Personnel Mines (APM) in complicated condition. (authors)

  10. A hardware investigation of robotic SPECT for functional and molecular imaging onboard radiation therapy systems

    International Nuclear Information System (INIS)

    Yan, Susu; Tough, MengHeng; Bowsher, James; Yin, Fang-Fang; Cheng, Lin

    2014-01-01

    Purpose: To construct a robotic SPECT system and to demonstrate its capability to image a thorax phantom on a radiation therapy flat-top couch, as a step toward onboard functional and molecular imaging in radiation therapy. Methods: A robotic SPECT imaging system was constructed utilizing a gamma camera detector (Digirad 2020tc) and a robot (KUKA KR150 L110 robot). An imaging study was performed with a phantom (PET CT Phantom TM ), which includes five spheres of 10, 13, 17, 22, and 28 mm diameters. The phantom was placed on a flat-top couch. SPECT projections were acquired either with a parallel-hole collimator or a single-pinhole collimator, both without background in the phantom and with background at 1/10th the sphere activity concentration. The imaging trajectories of parallel-hole and pinhole collimated detectors spanned 180° and 228°, respectively. The pinhole detector viewed an off-centered spherical common volume which encompassed the 28 and 22 mm spheres. The common volume for parallel-hole system was centered at the phantom which encompassed all five spheres in the phantom. The maneuverability of the robotic system was tested by navigating the detector to trace the phantom and flat-top table while avoiding collision and maintaining the closest possible proximity to the common volume. The robot base and tool coordinates were used for image reconstruction. Results: The robotic SPECT system was able to maneuver parallel-hole and pinhole collimated SPECT detectors in close proximity to the phantom, minimizing impact of the flat-top couch on detector radius of rotation. Without background, all five spheres were visible in the reconstructed parallel-hole image, while four spheres, all except the smallest one, were visible in the reconstructed pinhole image. With background, three spheres of 17, 22, and 28 mm diameters were readily observed with the parallel-hole imaging, and the targeted spheres (22 and 28 mm diameters) were readily observed in the pinhole

  11. Investigation of 305 patients with myelodysplastic syndromes and 20q deletion for associated cytogenetic and molecular genetic lesions and their prognostic impact.

    Science.gov (United States)

    Bacher, Ulrike; Haferlach, Torsten; Schnittger, Susanne; Zenger, Melanie; Meggendorfer, Manja; Jeromin, Sabine; Roller, Andreas; Grossmann, Vera; Krauth, Maria-Theresa; Alpermann, Tamara; Kern, Wolfgang; Haferlach, Claudia

    2014-03-01

    In patients with myelodysplastic syndromes (MDS), sole 20q deletion [del(20q)] is a recurrent favourable abnormality. We studied additional molecular and cytogenetic lesions and their prognostic impact in 305 MDS patients with del(20q) (229 males/76 females; 29-90 years). All patients were investigated by cytomorphology and chromosome banding analysis (CBA), subsets by fluorescence in situ hybridization, molecular mutation screening, and array comparative genomic hybridization (aCGH). By aCGH (n = 30), the minimal common deleted region (CDR) was flanked by PTPRT (20q13·11) and EYA2 (20q13·12). 210 (68·9%) patients had 'early MDS' without blast increase, 95 (31·1%) 'advanced' MDS with blast increase (5-19%). Additional chromosomal abnormalities (ACAs) were detected in 88/305 (28·9%) patients. Patients with advanced MDS more frequently had ACAs (P = 0·003) and had a higher mean number of ACAs (P = 0·020) and of molecular mutations (P = 0·060). Spliceosome mutations were frequent (U2AF1: n = 31/155; 20·0%; SRSF2: n = 31/159; 19·5%; SF3B1mut: n = 8/159; 5·0%). ASXL1mut (25/153; 16·3%) were associated with advanced MDS (P = 0·001). Presence of ≥3 ACAs (P = 0·003) and ASXL1mut (P = 0·002) were associated with worse 2-year survival. In conclusion, the cytogenetic subgroup of MDS with del(20q) has a good prognosis but may be further subclassified by additional cytogenetic and molecular lesions. U2AF1mut is overrepresented in MDS with del(20q), and ASXL1mut is prognostically adverse. © 2013 John Wiley & Sons Ltd.

  12. Investigation of aluminium ohmic contacts to n-type GaN grown by molecular beam epitaxy

    Science.gov (United States)

    Kribes, Y.; Harrison, I.; Tuck, B.; Kim, K. S.; Cheng, T. S.; Foxon, C. T.

    1997-11-01

    Using epi-layers of different doping concentrations, we have investigated aluminium contacts on n-type gallium nitride grown by plasma source molecular beam epitaxy. To achieve repeatable and reliable results it was found that the semiconductor needed to be etched in aqua-regia before the deposition of the contact metallization. Scanning electron micrographs of the semiconductor surface show a deterioration of the semiconductor surface on etching. The specific contact resistivity of the etched samples were, however, superior. Annealing the contacts at 0268-1242/12/11/030/img9 produced contacts with the lowest specific contact resistance of 0268-1242/12/11/030/img10. The long-term aging of these contacts was also investigated. The contacts and the sheet resistance were both found to deteriorate over a three-month period.

  13. Molecular dynamics investigation of the elastic and fracture properties of the R-graphyne under uniaxial tension

    Energy Technology Data Exchange (ETDEWEB)

    Rouhi, Saeed, E-mail: s_rouhi@iaul.ac.ir

    2017-05-15

    In this paper, the mechanical properties of the R-graphynes are investigated by using molecular dynamics simulations. For this purpose, the uniaxial strain is applied on the nanosheets. The effects of R-graphyne chirality and dimension on their fracture and elastic properties are investigated. It is shown that the fracture properties of the armchair R-graphyne are approximately independent from the nanosheet sizes. However, a clear dependence is observed in the fracture properties of the zigzag R-graphyne on the nanosheet dimensions. Comparing the elastic modulus of the armchair and zigzag R-graphynes, it is shown that for the same sizes, the elastic modulus of armchair R-graphyne is approximately equal to 2.5 times of the elastic modulus of the zigzag ones. Pursuing the fracture process of R-graphynes with different chiralities, it is represented that the fracture propagates in the zigzag nanosheet with a higher velocity than the armchair ones.

  14. Real time spectroscopic ellipsometry investigation of homoepitaxial GaN grown by plasma assisted molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Tong-Ho; Choi, Soojeong; Wu, Pae; Brown, April [Department of Electrical and Computer Engineering, Duke University, 128 Hudson Hall, Durham, NC (United States); Losurdo, Maria; Giangregorio, Maria M.; Bruno, Giovanni [Institute of Inorganic Methodologies and of Plasmas, IMIP-CNR and INSTM UdR Bari, via Orabona, 4, 70126 Bari (Italy); Moto, Akihiro [Innovation Core SEI, Inc., 3235 Kifer Road, Santa Clara, CA 95051 (United States)

    2006-06-15

    The growth of GaN by plasma assisted molecular beam epitaxy on GaN template substrates (GaN on sapphire) is investigated with in-situ multi-channel spectroscopic ellipsometry. Growth is performed under various Ga/N flux ratios at growth temperatures in the range 710-780 C. The thermal roughening of the GaN template caused by decomposition of the surface is investigated through the temporal variation of the GaN pseudodielectric function over the temperature range of 650 C to 850 C. The structural, morphological, and optical properties are also discussed. (copyright 2006 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  15. Molecular epidemiological analysis of Saffold cardiovirus genotype 3 from upper respiratory infection patients in Taiwan.

    Science.gov (United States)

    Lin, Tsuey-Li; Lin, Ting-Han; Chiu, Shu-Chun; Huang, Yuan-Pin; Ho, Cheng-Mao; Lee, Chia-Chi; Wu, Ho-Sheng; Lin, Jih-Hui

    2015-09-01

    Saffold cardiovirus (SAFV) belongs to the Cardiovirus genus of Picornaviridae family, and may be a relevant new human pathogen; Thus far, eleven genotypes have been identified. The SAFV type 3 (SAFV-3) is thought to be the major genotype and is detected relatively frequently in children with acute gastroenteritis and respiratory illness. The epidemiology and pathogenicity of SAFV-3 remain unclear. To investigate the genomic and epidemiologic profiles of SAFV-3 infection in Taiwan. Virus was detected in respiratory samples from children suffering for URI. SAFV-3 isolates were detected by isolation on cell culture and IF assay. The molecular typing was performed by RT-PCR and was sequenced to compare with reference strains available in the NCBI GeneBank. Serum samples were collected from 2005 to 2013 in Taiwan for seroprevalence investigation. A total of 226 specimens collected from children with URIs, 22 (9.73%) were positive for SAFV-3. The majority of SAFV-3 infections were found in children less than 6 years of age (14 of 22, 63.6%). Genetic analysis of VP1 coding region of Taiwanese isolates shown an 83.2-97.7% difference from other available SAFV-3 sequences in NCBI GenBank. Phylogenetic analysis revealed there is three genetic groups of SAFV-3 co-circulated in Taiwan during the study period. In addition, seroprevalence investigation results indicated that SAFV-3 infection occurs early in life and 43.7-77.8% of children aged between 6 months to 9 years old, had neutralizing antibodies against SAFV-3. SAFV-3 may have circulated in Taiwan for some time and it appears to be one of the etiological agents responsible for URIs in children. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Diffraction stress analysis of thin films; investigating elastic grain interaction

    International Nuclear Information System (INIS)

    Kumar, A.

    2005-12-01

    This work is dedicated to the investigation of specimens exhibiting anisotropic microstructures (and thus macroscopic elastic anisotropy) and/or inhomogeneous microstructures, as met near surfaces and in textured materials. The following aspects are covered: (i) Analysis of specimens with direction-dependent (anisotropic) elastic grain-interaction. Elastic grain-interaction determines the distribution of stresses and strains over the (crystallographically) differently oriented grains of a mechanically stressed polycrystal and the mechanical and diffraction (X-ray) elastic constants (relating (diffraction) lattice strains to mechanical stresses). Grain interaction models that allow for anisotropic, direction-dependent grain interaction have been developed very recently. The notion 'direction-dependent' grain-interaction signifies that different grain-interaction constraints prevail along different directions in a specimen. Practical examples of direction-dependent grain interaction are the occurrence of surface anisotropy in thin films and the surface regions of bulk polycrystals and the occurrence of grain-shape (morphological) texture. In this work, for the first time, stress analyses of thin films have been performed on the basis of these newly developed grain-interaction models. It has also been demonstrated that the identification of the (dominant) source of direction-dependent grain interaction is possible. The results for the grain interaction have been discussed in the light of microstructural investigations of the specimens by microscopic techniques. (ii) Analysis of specimens with depth gradients: Diffraction stress analysis can be hindered if gradients of the stress state, the composition or the microstructure occur in the specimen under investigation, as the so-called information depth varies in the course of a traditional stress measurement: Ambiguous results are thus generally obtained. In this work, a strategy for stress measurements at fixed

  17. Molecular cloning and expression analysis of a zeta-class ...

    African Journals Online (AJOL)

    Jane

    2011-07-27

    Jul 27, 2011 ... sugar-signalling pathway (Chi et al., 2010). All the earlier mentioned ... real-time qPCR analysis was the ABI PRISM7500 real-time PCR system. ... Construction of prokaryotic expression vector of Sc-GST gene. pET29a (+) ...

  18. Molecular analysis of genetic diversity in elite II synthetic hexaploid ...

    African Journals Online (AJOL)

    The present study was conducted to assess the genetic diversity of Elite-II synthetic hexaploid (SH) wheat by genome DNA fingerprinting as revealed by random amplified polymorphic DNA (RAPD) analysis. Ten decamer RAPD primers (OPG-1, OPG-2, OPG-3, OPG-4, OPG-5, OPA-3, OPA-4, OPA-5, OPA-8, and OPA-15) ...

  19. Molecular cloning and characteristic analysis of a thioredoxin from ...

    African Journals Online (AJOL)

    Sequence comparison and phylogenetic tree analysis confirmed NmTrx as a distinct member of thioredoxin. Real-time quantitative polymerase chain reaction (PCR) revealed a significantly higher expression of NmTrx transcript in the adult stage compared with the egg and oncomiracidium stages. In the egg and adult ...

  20. Molecular cloning, expression analysis and sequence prediction of ...

    African Journals Online (AJOL)

    CCAAT/enhancer-binding protein beta as an essential transcriptional factor, regulates the differentiation of adipocytes and the deposition of fat. Herein, we cloned the whole open reading frame (ORF) of bovine C/EBPβ gene and analyzed its putative protein structures via DNA cloning and sequence analysis. Then, the ...

  1. Molecular characterization and diversity analysis in chilli pepper ...

    African Journals Online (AJOL)

    India is considered to be the secondary center of diversity of chilli pepper, especially of Capsicum annuum. Simple sequence repeats (SSRs) are the most widely used marker system for plant variety characterization and diversity analysis especially in cultivated species which have low levels of polymorphism. The diversity ...

  2. Gas chromatographic column for the Viking 1975 molecular analysis experiment

    Science.gov (United States)

    Novotny, M.; Hayes, J. M.; Bruner, F.; Simmonds, P. G.

    1975-01-01

    A gas chromatographic column has been developed for use in the remote analysis of the Martian surface. The column, which utilizes a liquid-modified organic adsorbent (Tenax) as the stationary phase, provides efficient transmission and resolution of nanogram quantities of organic materials in the presence of millionfold excesses of water and carbon dioxide.

  3. Molecular marker analysis to differentiate a clonal selection of ...

    African Journals Online (AJOL)

    Lalit Kumar

    2013-04-03

    Apr 3, 2013 ... Microsatellite and amplified fragment length polymorphism (AFLP) markers were used to differentiate. Manjari Naveen, a clonal selection of Centennial Seedless variety of grape. Twenty one (21) microsatellite primers could not detect variation between parent variety and its clone. AFLP analysis.

  4. Molecular mobility in Medicago truncatula seed during early stage of germination: Neutron scattering and NMR investigations

    Energy Technology Data Exchange (ETDEWEB)

    Falourd, Xavier [UR1268 Biopolymères Interactions Assemblages, INRA, F-44316 Nantes (France); Natali, Francesca [CNR-IOM-OGG, c/o Institut Laue-Langevin, 6 rue Jules Horowitz, BP 156, 38042 Grenoble Cedex 9 (France); Institut Laue-Langevin, 6 rue Jules Horowitz, BP 156, 38042 Grenoble Cedex 9 (France); Peters, Judith [Institut Laue-Langevin, 6 rue Jules Horowitz, BP 156, 38042 Grenoble Cedex 9 (France); Université Joseph Fourier UFR PhITEM, BP 53, 38041 Grenoble Cedex 9 (France); Institut de Biologie Structurale, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1 (France); Foucat, Loïc, E-mail: Loic.Foucat@nantes.inra.fr [UR1268 Biopolymères Interactions Assemblages, INRA, F-44316 Nantes (France)

    2014-01-15

    Highlights: • Neutron scattering and NMR approaches were used to characterize seed germination. • A parallel between macromolecular motions and water dynamics was established. • Freezing/thawing cycle revealed a hysteresis connected to the seed hydration level. - Abstract: First hours of Medicago truncatula (MT) seeds germination were investigated using elastic incoherent neutron scattering (EINS) and nuclear magnetic resonance (NMR), to follow respectively how macromolecular motions and water mobility evolve when water permeates into the seed. From EINS results, it was shown that there is an increase in macromolecular mobility with the water uptake. Changes in NMR relaxation parameters reflected microstructural changes associated with the recovery of the metabolic processes. The EINS investigation of the effect of temperature on macromolecular motions showed that there is a relationship between the amount of water in the seeds and the effect of freezing–thawing cycle. The NMR relaxometry results obtained at 253 K allowed establishing possible link between the freezing of water molecules tightly bound to macromolecules and their drastic motion restriction around 250 K, as observed with EINS at the highest water content.

  5. Clinical, biochemical and molecular investigations of three Taiwanese children with Laron syndrome.

    Science.gov (United States)

    Yang, Chen; Chen, Julia Yi-Ru; Lai, Chien-Cherng; Lin, Hsiu-Chen; Yeh, Geng-Chang; Hsu, Hsun-Hui

    2004-02-01

    Three children of two Taiwanese families were diagnosed with Laron syndrome, two sisters and one boy. Both sets of parents were consanguineous. Clinically, all three presented with the typical craniofacies of Laron syndrome, consisting of prominent forehead and hypoplastic nasal bridge, high-pitched voice, short stature, and central obesity. Biochemically, their levels of serum IGF-I were less than 5 microg/ml before and after an IGF-I generation test, and levels of IGFBP-3 were reduced in all three patients. Sequence analysis of the growth hormone receptor gene revealed that all three carried a homozygous missense D152G mutation in exon 6.

  6. Spectroscopic investigations and molecular docking study of 3-(1H-imidazol-1-yl)-1-phenylpropan-1-one, a potential precursor to bioactive agents

    Science.gov (United States)

    Al-Alshaikh, Monirah A.; Mary Y, Sheena; Panicker, C. Yohannan; Attia, Mohamed I.; El-Emam, Ali A.; Alsenoy, C. Van

    2016-04-01

    The optimized molecular structure, vibrational wavenumbers, corresponding vibrational assignments of 3-(1H-imidazol-1-yl)-1-phenylpropan-1-one have been investigated theoretically and experimentally. The calculated geometrical parameters of the title compound are in agreement with the reported XRD data. The HOMO and LUMO analysis is used to determine the charge transfer within the molecule. The stability of the molecule arising from hyper-conjugative interaction and charge delocalization has been analyzed using NBO analysis. Molecular electrostatic potential was performed by the DFT method and from the MEP plot, it is evident that the negative charge covers the carbonyl group and the nitrogen atom N3 of the imidazole ring and the positive region is over the remaining portions of the molecule. The first and second hyperpolarizabilities are calculated and the first hyperpolarizability of the title compound is 16.99 times that of standard NLO material urea and the title compound and its derivatives are good object for further studies in nonlinear optics. The docked ligand title compound forms a stable complex with plasmodium falciparum and gives a binding affinity value of -5.5 kcal/mol and the preliminary results suggest that the compound might exhibit antimalarial activity against plasmodium falciparum.

  7. Investigations on application of multigrid method to MHD equilibrium analysis

    International Nuclear Information System (INIS)

    Ikuno, Soichiro

    2000-01-01

    The potentiality of application for Multi-grid method to MHD equilibrium analysis is investigated. The nonlinear eigenvalue problem often appears when the MHD equilibria are determined by solving the Grad-Shafranov equation numerically. After linearization of the equation, the problem is solved by use of the iterative method. Although the Red-Black SOR method or Gauss-Seidel method is often used for the solution of the linearized equation, it takes much CPU time to solve the problem. The Multi-grid method is compared with the SOR method for the Poisson Problem. The results of computations show that the CPU time required for the Multi-grid method is about 1000 times as small as that for the SOR method. (author)

  8. Investigation and analysis of aircrew ametropia and related factors

    Directory of Open Access Journals (Sweden)

    Li-Juan Zheng

    2014-10-01

    Full Text Available AIM: To investigate the refractive distribution and analysis risk factors for aircrew ametropia.METHODS: The number of 49 cases with ametropia from 1031 aircrew during May 2013 to May 2014 were reviewed. Various types of refraction composition, age, type, position, time of flight with the subjective assessment of aircrew were analyzed and compared. RESULTS: Of 49 cases, 43 cases(88%were myopia, 6 cases(12%were hypermetropia.,Detection rates were higher in age over 50 years aircrew and flight time more than 3000h. Detection rates were lower in self-conscious symptom heavy aircrew, fighter aircrew and good habit of using eyes. CONCLUSION: The myopia incidence in aircrew with age >50 years and long flight time is higher, than that of fighter pilots and good habit of using eyes. We should pay attention to the increasing late-onset myopia of aviators and habit of using eyes, work intensity and time of using eyes about aircrew.

  9. Detection of Low Molecular Weight Adulterants in Beverages by Direct Analysis in Real Time Mass Spectrometry.

    Science.gov (United States)

    Sisco, Edward; Dake, Jeffrey

    2016-04-14

    Direct Analysis in Real Time Mass Spectrometry (DART-MS) has been used to detect the presence of non-narcotic adulterants in beverages. The non-narcotic adulterants that were examined in this work incorporated a number low molecular weight alcohols, acetone, ammonium hydroxide, and sodium hypochlorite. Analysis of the adulterants was completed by pipetting 1 µL deposits onto glass microcapillaries along with an appropriate dopant species followed by introduction into the DART gas stream. It was found that detection of these compounds in the complex matrices of common beverages (soda, energy drinks, etc.) was simplified through the use of a dopant species to allow for adduct formation with the desired compound(s) of interest. Other parameters that were investigated included DART gas stream temperature, in source collision induced dissociation, ion polarity, and DART needle voltage. Sensitivities of the technique were found to range from 0.001 % volume fraction to 0.1 % volume fraction, comparable to traditional analyses completed using headspace gas chromatography mass spectrometry (HS-GC/MS). Once a method was established using aqueous solutions, , fifteen beverages were spiked with each of the nine adulterants, to simulate real world detection, and in nearly all cases the adulterant could be detected either in pure form, or complexed with the added dopant species. This technique provides a rapid way to directly analyze beverages believed to be contaminated with non-narcotic adulterants at sensitivities similar to or exceeding those of traditional confirmatory analyses.

  10. Transcriptome analysis in Concholepas concholepas (Gastropoda, Muricidae): mining and characterization of new genomic and molecular markers.

    Science.gov (United States)

    Cárdenas, Leyla; Sánchez, Roland; Gomez, Daniela; Fuenzalida, Gonzalo; Gallardo-Escárate, Cristián; Tanguy, Arnaud

    2011-09-01

    The marine gastropod Concholepas concholepas, locally known as the "loco", is the main target species of the benthonic Chilean fisheries. Genetic and genomic tools are necessary to study the genome of this species in order to understand the molecular basis of its development, growth, and other key traits to improve the management strategies and to identify local adaptation to prevent loss of biodiversity. Here, we use pyrosequencing technologies to generate the first transcriptomic database from adult specimens of the loco. After trimming, a total of 140,756 Expressed Sequence Tag sequences were achieved. Clustering and assembly analysis identified 19,219 contigs and 105,435 singleton sequences. BlastN analysis showed a significant identity with Expressed Sequence Tags of different gastropod species available in public databases. Similarly, BlastX results showed that only 895 out of the total 124,654 had significant hits and may represent novel genes for marine gastropods. From this database, simple sequence repeat motifs were also identified and a total of 38 primer pairs were designed and tested to assess their potential as informative markers and to investigate their cross-species amplification in different related gastropod species. This dataset represents the first publicly available 454 data for a marine gastropod endemic to the southeastern Pacific coast, providing a valuable transcriptomic resource for future efforts of gene discovery and development of functional markers in other marine gastropods. Copyright © 2011 Elsevier B.V. All rights reserved.

  11. Molecular cytogenetic analysis of human blastocysts andcytotrophoblasts by multi-color FISH and Spectra Imaging analyses

    Energy Technology Data Exchange (ETDEWEB)

    Weier, Jingly F.; Ferlatte, Christy; Baumgartner, Adolf; Jung,Christine J.; Nguyen, Ha-Nam; Chu, Lisa W.; Pedersen, Roger A.; Fisher,Susan J.; Weier, Heinz-Ulrich G.

    2006-02-08

    Numerical chromosome aberrations in gametes typically lead to failed fertilization, spontaneous abortion or a chromosomally abnormal fetus. By means of preimplantation genetic diagnosis (PGD), we now can screen human embryos in vitro for aneuploidy before transferring the embryos to the uterus. PGD allows us to select unaffected embryos for transfer and increases the implantation rate in in vitro fertilization programs. Molecular cytogenetic analyses using multi-color fluorescence in situ hybridization (FISH) of blastomeres have become the major tool for preimplantation genetic screening of aneuploidy. However, current FISH technology can test for only a small number of chromosome abnormalities and hitherto failed to increase the pregnancy rates as expected. We are in the process of developing technologies to score all 24 chromosomes in single cells within a 3 day time limit, which we believe is vital to the clinical setting. Also, human placental cytotrophoblasts (CTBs) at the fetal-maternal interface acquire aneuploidies as they differentiate to an invasive phenotype. About 20-50% of invasive CTB cells from uncomplicated pregnancies were found aneuploidy, suggesting that the acquisition of aneuploidy is an important component of normal placentation, perhaps limiting the proliferative and invasive potential of CTBs. Since most invasive CTBs are interphase cells and possess extreme heterogeneity, we applied multi-color FISH and repeated hybridizations to investigate individual CTBs. In summary, this study demonstrates the strength of Spectral Imaging analysis and repeated hybridizations, which provides a basis for full karyotype analysis of single interphase cells.

  12. Plant and fungal diversity in gut microbiota as revealed by molecular and culture investigations.

    Directory of Open Access Journals (Sweden)

    Nina Gouba

    Full Text Available BACKGROUND: Few studies describing eukaryotic communities in the human gut microbiota have been published. The objective of this study was to investigate comprehensively the repertoire of plant and fungal species in the gut microbiota of an obese patient. METHODOLOGY/PRINCIPAL FINDINGS: A stool specimen was collected from a 27-year-old Caucasian woman with a body mass index of 48.9 who was living in Marseille, France. Plant and fungal species were identified using a PCR-based method incorporating 25 primer pairs specific for each eukaryotic phylum and universal eukaryotic primers targeting 18S rRNA, internal transcribed spacer (ITS and a chloroplast gene. The PCR products amplified using these primers were cloned and sequenced. Three different culture media were used to isolate fungi, and these cultured fungi were further identified by ITS sequencing. A total of 37 eukaryotic species were identified, including a Diatoms (Blastocystis sp. species, 18 plant species from the Streptophyta phylum and 18 fungal species from the Ascomycota, Basidiomycota and Chytridiocomycota phyla. Cultures yielded 16 fungal species, while PCR-sequencing identified 7 fungal species. Of these 7 species of fungi, 5 were also identified by culture. Twenty-one eukaryotic species were discovered for the first time in human gut microbiota, including 8 fungi (Aspergillus flavipes, Beauveria bassiana, Isaria farinosa, Penicillium brevicompactum, Penicillium dipodomyicola, Penicillium camemberti, Climacocystis sp. and Malassezia restricta. Many fungal species apparently originated from food, as did 11 plant species. However, four plant species (Atractylodes japonica, Fibraurea tinctoria, Angelica anomala, Mitella nuda are used as medicinal plants. CONCLUSIONS/SIGNIFICANCE: Investigating the eukaryotic components of gut microbiota may help us to understand their role in human health.

  13. Investigation, Analysis, and Testing of Self-contained Oxygen Generators

    Science.gov (United States)

    Keddy, Christopher P.; Haas, Jon P.; Starritt, Larry

    2008-01-01

    Self Contained Oxygen Generators (SCOGs) have widespread use in providing emergency breathing oxygen in a variety of environments including mines, submarines, spacecraft, and aircraft. These devices have definite advantages over storing of gaseous or liquid oxygen. The oxygen is not generated until a chemical briquette containing a chlorate or perchlorate oxidizer and a solid metallic fuel such as iron is ignited starting a thermal decomposition process allowing gaseous oxygen to be produced. These devices are typically very safe to store, easy to operate, and have primarily only a thermal hazard to the operator that can be controlled by barriers or furnaces. Tens of thousands of these devices are operated worldwide every year without major incident. This report examines the rare case of a SCOG whose behavior was both abnormal and lethal. This particular type of SCOG reviewed is nearly identical to a flight qualified version of SCOG slated for use on manned space vehicles. This Investigative Report is a compilation of a NASA effort in conjunction with other interested parties including military and aerospace to understand the causes of the particular SCOG accident and what preventative measures can be taken to ensure this incident is not repeated. This report details the incident and examines the root causes of the observed SCOG behavior from forensic evidence. A summary of chemical and numerical analysis is provided as a background to physical testing of identical SCOG devices. The results and findings of both small scale and full scale testing are documented on a test-by-test basis along with observations and summaries. Finally, conclusions are presented on the findings of this investigation, analysis, and testing along with suggestions on preventative measures for any entity interested in the safe use of these devices.

  14. Molecular cloning and functional analysis of the gene encoding ...

    African Journals Online (AJOL)

    Here we report for the first time the cloning of a full-length cDNA encoding GGPPS (Jc-GGPPS) from Jatropha curcas L. The full-length cDNA was 1414 base pair (bp), with an 1110-bp open reading frame (ORF) encoding a 370- amino-acids polypeptide. Bioinformatic analysis revealed that Jc-GGPPS is a member of the ...

  15. Molecular cloning and expression analysis of an Mnsuperoxide ...

    African Journals Online (AJOL)

    Superoxide dismutases (SODs) play an important role in stress-tolerance in plants. In this study, for the first time, a full-length cDNA sequence of MnSOD gene, termed as Sc-MnSOD (GenBank accession number: GQ246460), was obtained in sugarcane. Sequence analysis revealed that Sc-MnSOD gene was 919 bp long, ...

  16. Molecular Analysis of Microbial Diversity in Advanced Caries

    OpenAIRE

    Chhour, Kim-Ly; Nadkarni, Mangala A.; Byun, Roy; Martin, F. Elizabeth; Jacques, Nicholas A.; Hunter, Neil

    2005-01-01

    Real-time PCR analysis of the total bacterial load in advanced carious lesions has shown that the total load exceeds the number of cultivable bacteria. This suggests that an unresolved complexity exists in bacteria associated with advanced caries. In this report, the profile of the microflora of carious dentine was explored by using DNA extracted from 10 lesions selected on the basis of comparable total microbial load and on the relative abundance of Prevotella spp. Using universal primers fo...

  17. Trypsin Binding with Copper Ions Scavenges Superoxide: Molecular Dynamics-Based Mechanism Investigation

    Directory of Open Access Journals (Sweden)

    Xin Li

    2018-01-01

    Full Text Available Trypsin is a serine protease, which has been proved to be a novel superoxide scavenger. The burst of superoxide induced by polychlorinated biphenyls can be impeded by trypsin in both wild type and sod knockout mutants of Escherichia coli. The experimental results demonstrated that the activities of superoxide scavenging of trypsin were significantly accelerated by Cu ions. Also, with the addition of Cu ions, a new β-sheet (β7 transited from a random coil in the Cu(II-trypsin (TP system, which was favorable for the formation of more contacts with other sheets of trypsin. Residue–residue network analysis and the porcupine plots proved that the Cu ion in trypsin strengthened some native interactions among residues, which ultimately resulted in much greater stability of the Cu(II-TP system. Moreover, compact and stable trypsin structures with Cu ions might be responsible for significantly provoking the activity of superoxide scavenging.

  18. The Sample Analysis at Mars Investigation and Instrument Suite

    Science.gov (United States)

    Mahaffy, Paul; Webster, Christopher R.; Conrad, Pamela G.; Arvey, Robert; Bleacher, Lora; Brinckerhoff, William B.; Eigenbrode, Jennifer L.; Chalmers, Robert A.; Dworkin, Jason P.; Errigo, Therese; hide

    2012-01-01

    The Sample Analysis at Mars (SAM) investigation of the Mars Science Laboratory (MSL) addresses the chemical and isotopic composition of the atmosphere and volatiles extracted from solid samples. The SAM investigation is designed to contribute substantially to the mission goal of quantitatively assessing the habitability of Mars as an essential step in the search for past or present life on Mars. SAM is a 40 kg instrument suite located in the interior of MSL's Curiosity rover. The SAM instruments are a quadrupole mass spectrometer, a tunable laser spectrometer, and a 6-column gas chromatograph all coupled through solid and gas processing systems to provide complementary information on the same samples. The SAM suite is able to measure a suite of light isotopes and to analyze volatiles directly from the atmosphere or thermally released from solid samples. In addition to measurements of simple inorganic compounds and noble gases SAM will conduct a sensitive search for organic compounds with either thermal or chemical extraction from sieved samples delivered by the sample processing system on the Curiosity rover's robotic arm,

  19. An interactive data management and analysis system for clinical investigators.

    Science.gov (United States)

    Groner, G F; Hopwood, M D; Palley, N A; Sibley, W L; Baker, W R; Christopher, T G; Thompson, H K

    1978-09-01

    An interactive minicomputer-based system has been developed that enables the clinical research investigator to personally explore and analyze his research data and, as a consequence of these explorations, to acquire more information. This system, which does not require extensive training or computer programming, enables the investigator to describe his data interactively in his own terms, enter data values while having them checked for validity, store time-oriented patient data in a carefully controlled on-line data base, retrieve data by patient, variable, and time, create subsets of patients with common characteristics, perform statistical analyses, and produce tables and graphs. It also permits data to be transferred to and from other computers. The system is well accepted and is being used by a variety of medical specialists at the three clinical research centers where it is operational. Reported benefits include less elapsed and nonproductive time, more thorough analysis of more data, greater and earlier insight into the meaning of research data, and increased publishable results.

  20. Nitinol Embolic Protection Filters: Design Investigation by Finite Element Analysis

    Science.gov (United States)

    Conti, Michele; de Beule, Matthieu; Mortier, Peter; van Loo, Denis; Verdonck, Pascal; Vermassen, Frank; Segers, Patrick; Auricchio, Ferdinando; Verhegghe, Benedict

    2009-08-01

    The widespread acceptance of carotid artery stenting (CAS) to treat carotid artery stenosis and its effectiveness compared with surgical counterpart, carotid endarterectomy (CEA), is still a matter of debate. Transient or permanent neurological deficits may develop in patients undergoing CAS due to distal embolization or hemodynamic changes. Design, development, and usage of embolic protection devices (EPDs), such as embolic protection filters, appear to have a significant impact on the success of CAS. Unfortunately, some drawbacks, such as filtering failure, inability to cross tortuous high-grade stenoses, malpositioning and vessel injury, still remain and require design improvement. Currently, many different designs of such devices are available on the rapidly growing dedicated market. In spite of such a growing commercial interest, there is a significant need for design tools as well as for careful engineering investigations and design analyses of such nitinol devices. The present study aims to investigate the embolic protection filter design by finite element analysis. We first developed a parametrical computer-aided design model of an embolic filter based on micro-CT scans of the Angioguard™ XP (Cordis Endovascular, FL) EPD by means of the open source pyFormex software. Subsequently, we used the finite element method to simulate the deployment of the nitinol filter as it exits the delivery sheath. Comparison of the simulations with micro-CT images of the real device exiting the catheter showed excellent correspondence with our simulations. Finally, we evaluated circumferential basket-vessel wall apposition of a 4 mm size filter in a straight vessel of different sizes and shape. We conclude that the proposed methodology offers a useful tool to evaluate and to compare current or new designs of EPDs. Further simulations will investigate vessel wall apposition in a realistic tortuous anatomy.

  1. QSAR analysis of salicylamide isosteres with the use of quantum chemical molecular descriptors.

    Science.gov (United States)

    Dolezal, R; Van Damme, S; Bultinck, P; Waisser, K

    2009-02-01

    Quantitative relationships between the molecular structure and the biological activity of 49 isosteric salicylamide derivatives as potential antituberculotics with a new mechanism of action against three Mycobacterial strains were investigated. The molecular structures were represented by quantum chemical B3LYP/6-31G( *) based molecular descriptors. A resulting set of 220 molecular descriptors, including especially electronic properties, was statistically analyzed using multiple linear regression, resulting in acceptable and robust QSAR models. The best QSAR model was found for Mycobacterium tuberculosis (r(2)=0.92; q(2)=0.89), and somewhat less good QSAR models were found for Mycobacterium avium (r(2)=0.84; q(2)=0.78) and Mycobacterium kansasii (r(2)=0.80; q(2)=0.56). All QSAR models were cross-validated using the leave-10-out procedure.

  2. Analysis of small molecular phase in coal involved in pyrolysis and solvent extraction by PGC

    Energy Technology Data Exchange (ETDEWEB)

    Jie Feng; Wen-Ying Li; Ke-Chang Xie [Taiyuan University of Technology, Taiyuan (China). Key Laboratory of Coal Science and Technology

    2004-06-01

    The small molecular phase, which strongly affects coal's reactivity, is the main part of the structure unit in coal. At present, its composition and structure features have not been clearly understood. In this paper, a flash pyrolysis technique with on-line GC (PGC) was used to investigate the properties of the small molecular phase from six kinds of rank coal in China. Experiments were divided into two parts: one is PGC of parent coal; another is PGC of coal extracts from NMP + CS{sub 2} (75:1) solvent extraction at 373 K. Results show that the small molecular phase mainly consists of C12-C16 compounds that could be integrally released when the heating rate was greater than 10 K/ms and the final pyrolysis temperature was 1373 K; other compounds may be the products of decomposition and polymerization from this small molecular phase during pyrolysis. 13 refs., 7 figs., 1 tab.

  3. Investigation of Apple Vibration Characteristics Using Finite Element Modal Analysis

    Directory of Open Access Journals (Sweden)

    R Mirzaei

    2013-02-01

    Full Text Available The most important quality indicator of fruits is the flesh firmness which is well correlated to their young’s modulus. In this research variation of vibration characteristics (shape modes, natural frequency of apple due to change of material characteristics (density, young's models, Poisson ratio and apple volume was investigated using Finite Element simulation. An image processing technique was used to obtain an unsymmetrical and non-spherical geometric model of apple. The exact three-dimensional shape of the fruit was created by determining the coordinates of apple surface and forming uneven rotational curvatures. Modal analysis with no boundary constraints has been applied. The first 20 Eigen frequencies and the corresponding mode shape were determined. Six rigid body modes possess zero resonant frequency which is related to the degree of freedom of a rigid body in space indicated the validity of finite element model. The modal analysis results showed that resonant frequency increased by increasing young's modulus of the fruit, while it decreased by increasing apple density. First mode torsion has a mean resonant frequency of 584 Hz. Variations of natural frequency due to change in young's modulus, density, and Poisson ratio were 80%, 11% and 4%, respectively. Coefficient of variation of resonant frequency in response to changing young's modulus was 2-3 times of that of density which shows the greatest effect of young modulus changes on natural frequency of fruits. Consequently with determination of fruits' natural frequency, their young modulus and firmness can be estimated.

  4. Contribution of molecular analysis to the typification of the non-functioning pituitary adenomas

    Science.gov (United States)

    Sanchez-Ortiga, Ruth; Aranda, Francisco Ignacio

    2017-01-01

    Aim The WHO Classification of Tumours of Endocrine Organs considers the inmunohistochemical characterization of pituitary adenomas (PA) as mandatory for patient diagnosis. Recent advances in the knowledge of the molecular patterns of these tumours could complement this classification with gene expression profiling. Methods Within the context of the Spanish Molecular Registry of Pituitary Adenomas (REMAH), a multicentre clinical-basic research project, we analysed the molecular phenotype of 142 PAs with complete IHC and clinical information. Gene expression levels of all pituitary hormones, type 1 corticotrophin-releasing hormone receptor, dopamine receptors and arginine vasopressin receptor 1b were measured by quantitative real-time polymerase chain reaction. In addition, we used three housekeeping genes for normalization and a pool of nine healthy pituitary glands from autopsies as calibration reference standard. Results Based on the clinically functioning PA (FPA: somatotroph, corticotroph, thyrotroph and lactotroph adenomas), we established the interquartile range of relative expression for all genes studied in each PA subtype. That allowed molecularly the different PA subtypes, including the clinically non-functioning PA (NFPA). Afterwards, we estimated the concordance of the molecular and immunohistochemical classification with clinical diagnosis in FPA and between them in NFPA. The kappa values were higher in molecular than in immunohistochemical classification in FPA and showed a bad concordance in all NFPA subtypes. Conclusions According to these results, the molecular characterization of the PA complements the IHC analysis, allowing a better typification of the NFPA. PMID:28692683

  5. Contribution of molecular analysis to the typification of the non-functioning pituitary adenomas.

    Directory of Open Access Journals (Sweden)

    Laura Sanchez-Tejada

    Full Text Available The WHO Classification of Tumours of Endocrine Organs considers the inmunohistochemical characterization of pituitary adenomas (PA as mandatory for patient diagnosis. Recent advances in the knowledge of the molecular patterns of these tumours could complement this classification with gene expression profiling.Within the context of the Spanish Molecular Registry of Pituitary Adenomas (REMAH, a multicentre clinical-basic research project, we analysed the molecular phenotype of 142 PAs with complete IHC and clinical information. Gene expression levels of all pituitary hormones, type 1 corticotrophin-releasing hormone receptor, dopamine receptors and arginine vasopressin receptor 1b were measured by quantitative real-time polymerase chain reaction. In addition, we used three housekeeping genes for normalization and a pool of nine healthy pituitary glands from autopsies as calibration reference standard.Based on the clinically functioning PA (FPA: somatotroph, corticotroph, thyrotroph and lactotroph adenomas, we established the interquartile range of relative expression for all genes studied in each PA subtype. That allowed molecularly the different PA subtypes, including the clinically non-functioning PA (NFPA. Afterwards, we estimated the concordance of the molecular and immunohistochemical classification with clinical diagnosis in FPA and between them in NFPA. The kappa values were higher in molecular than in immunohistochemical classification in FPA and showed a bad concordance in all NFPA subtypes.According to these results, the molecular characterization of the PA complements the IHC analysis, allowing a better typification of the NFPA.

  6. Studies on molecular structure, vibrational spectra and molecular docking analysis of 3-Methyl-1,4-dioxo-1,4-dihydronaphthalen-2-yl 4-aminobenzoate

    Science.gov (United States)

    Suresh, D. M.; Amalanathan, M.; Hubert Joe, I.; Bena Jothy, V.; Diao, Yun-Peng

    2014-09-01

    The molecular structure, vibrational analysis and molecular docking analysis of the 3-Methyl-1,4-dioxo-1,4-dihydronaphthalen-2-yl 4-aminobenzoate (MDDNAB) molecule have been carried out using FT-IR and FT-Raman spectroscopic techniques and DFT method. The equilibrium geometry, harmonic vibrational wave numbers, various bonding features have been computed using density functional method. The calculated molecular geometry has been compared with experimental data. The detailed interpretation of the vibrational spectra has been carried out by using VEDA program. The hyper-conjugative interactions and charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The simulated FT-IR and FT-Raman spectra satisfactorily coincide with the experimental spectra. The PES and charge analysis have been made. The molecular docking was done to identify the binding energy and the Hydrogen bonding with the cancer protein molecule.

  7. Origins of the amphiploid species Brassica napus L. investigated by chloroplast and nuclear molecular markers

    Directory of Open Access Journals (Sweden)

    Allender Charlotte J

    2010-03-01

    Full Text Available Abstract Background The amphiploid species Brassica napus (oilseed rape, Canola is a globally important oil crop yielding food, biofuels and industrial compounds such as lubricants and surfactants. Identification of the likely ancestors of each of the two genomes (designated A and C found in B. napus would facilitate incorporation of novel alleles from the wider Brassica genepool in oilseed rape crop genetic improvement programmes. Knowledge of the closest extant relatives of the genotypes involved in the initial formation of B. napus would also allow further investigation of the genetic factors required for the formation of a stable amphiploid and permit the more efficient creation of fully fertile re-synthesised B. napus. We have used a combination of chloroplast and nuclear genetic markers to investigate the closest extant relatives of the original maternal progenitors of B. napus. This was based on a comprehensive sampling of the relevant genepools, including 83 accessions of A genome B. rapa L. (both wild and cultivated types, 94 accessions of B. napus and 181 accessions of C genome wild and cultivated B. oleracea L. and related species. Results Three chloroplast haplotypes occurred in B. napus. The most prevalent haplotype (found in 79% of accessions was not present within the C genome accessions but was found at low frequencies in B. rapa. Chloroplast haplotypes characteristic of B. napus were found in a small number of wild and weedy B. rapa populations, and also in two accessions of cultivated B. rapa 'brocoletto'. Whilst introgression of the B. napus chloroplast type in the wild and weedy B. rapa populations has been proposed by other studies, the presence of this haplotype within the two brocoletto accessions is unexplained. Conclusions The distribution of chloroplast haplotypes eliminate any of the C genome species as being the maternal ancestor of the majority of the B. napus accessions. The presence of multiple chloroplast

  8. MOLECULARLY IMPRINTED SOLID PHASE EXTRACTION FOR TRACE ANALYSIS OF DIAZINON IN DRINKING WATER

    Directory of Open Access Journals (Sweden)

    M. Rahiminejad ، S. J. Shahtaheri ، M. R. Ganjali ، A. Rahimi Forushani ، F. Golbabaei

    2009-04-01

    Full Text Available Amongst organophosphate pesticides, the one most widely used and common environmental contaminant is diazinon; thus methods for its trace analysis in environmental samples must be developed. Use of diazinon imprinted polymers such as sorbents in solid phase extraction, is a prominent and novel application area of molecular imprinted polymers. For diazinon extraction, high performance liquid chromatography analysis was demonstrated in this study. During optimization of the molecular imprinted solid phase extraction procedure for efficient solid phase extraction of diazinon, Plackett-Burman design was conducted. Eight experimental factors with critical influence on molecular imprinted solid phase extraction performance were selected, and 12 different experimental runs based on Plackett-Burman design were carried out. The applicability of diazinon imprinted polymers as the sorbent in solid phase extraction, presented obtained good recoveries of diazinon from LC-grade water. An increase in pH caused an increase in the recovery on molecular imprinted solid phase extraction. From these results, the optimal molecular imprinted solid phase extraction procedure was as follows: solid phase extraction packing with 100 mg diazinon imprinted polymers; conditioning with 5 mL of methanol and 6 mL of LC-grade water; sample loading containing diazinon (pH=10; washing with 1 mL of LC-grade water, 1 mL LC- grade water containing 30% acetonitrile and 0.5 mL of acetonitrile, respectively; eluting with 1 mL of methanol containing 2% acetic acid. The percentage recoveries obtained by the optimized molecular imprinted solid phase extraction were more than 90% with drinking water spiked at different trace levels of diazinon. Generally speaking, the molecular imprinted solid phase extraction procedure and subsequent high performance liquid chromatography analysis can be a relatively fast and proper approach for qualitative and quantitative analysis of diazinon in

  9. Investigation of the chemical mechanisms involved in the electropulsation of membranes at the molecular level.

    Science.gov (United States)

    Breton, Marie; Mir, Lluis M

    2018-02-01

    The chemical consequences of electropulsation on giant unilamellar vesicles (GUVs), in particular the possible oxidation of unsaturated phospholipids, have been investigated by mass spectrometry, flow cytometry and absorbance methods. Pulse application induced oxidation of the GUV phospholipids and the oxidation level depended on the duration of the pulse. Light and O 2 increased the level of pulse-induced lipid peroxidation whereas the presence of antioxidants either in the membrane or in the solution completely suppressed peroxidation. Importantly, pulse application did not create additional reactive oxygen species (ROS) in GUV-free solution. Lipid peroxidation seems to result from a facilitation of the lipid peroxidation by the ROS already present in the solution before pulsing, not from a direct pulse-induced peroxidation. The pulse would facilitate the entrance of ROS in the core of the membrane, allowing the contact between ROS and lipid chains and provoking the oxidation. Our findings demonstrate that the application of electric pulses on cells could induce the oxidation of the membrane phospholipids since cell membranes contain unsaturated lipids. The chemical consequences of electropulsation will therefore have to be taken into account in future biomedical applications of electropulsation since oxidized phospholipids play a key role in many signaling pathways and diseases. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Experimental Investigation of the Influence of Molecular Weight on Mixing and Penetration in Supersonic Dissimilar Gaseous Injection into a Supersonic Cross-Flow

    National Research Council Canada - National Science Library

    Giese, Troy

    1997-01-01

    In pursuit of a more efficient and effective fuel-air mixing for a SCRAMjet combustor, this study investigated relative near field effects of molecular weight on mixing and penetration of different...

  11. Geriatric information analysis of the molecular properties of mexidole

    Directory of Open Access Journals (Sweden)

    O. A. Gromova

    2017-01-01

    Full Text Available Objective: by using the pharmacoinformation profiling, to comprehensively assess all possible effects of the molecules of mexidol, choline alfoscerate, piracetam, glycine, and semax in accordance with the anatomical therapeutic and chemical (ATC classification system.Material and methods. Chemoreactomic, pharmacoinformation, and geriatric information analyses of the properties of the molecules are based on chemoreactomic methodology. The chemoreactomic analysis uses the information from the PubChem, HMDB, and String databases; the pharmacoinformation analysis applies the information from the international ATC classification and a combined sample of data from the Therapeutic Target Database (TTD, SuperTarget, Manually Annotated Targets and Drugs Online Resource (MATADOR, and Potential Drug Target Database (PDTD; geriatric information analysis employs the data on the geroprotective effect of individual substances from the PubChem database and the data available in the literature data on geroprotection from the PubMed database, which have been collected through the artificial intelligence system.Results and discussion. Mexidol is characterized by the maximum set of positive effects (the drug is used to treat CNS and cardiovascular diseases and metabolic disorders and has anti-inflammatory and anti-infective properties, etc.. Mexidol and glycine are predicted to cause the lowest frequency of adverse reactions, such as itching, constipation, paresthesia, vomiting, etc. Geriatric information assessments of changes in the life span of model organisms have shown that mexidol contributes to the higher life expectancy of C. elegans (by 22.7±10%, Drosophila (by 14.4±15%, and mice (by 14.6±3%; the control drugs do by no more than 6.1%.Conclusion. The results of the study indicate that mexidol has a high potential to be used as a geroprotector.

  12. Molecular-based recursive partitioning analysis model for glioblastoma in the temozolomide era a correlative analysis based on nrg oncology RTOG 0525

    NARCIS (Netherlands)

    Bell, Erica Hlavin; Pugh, Stephanie L.; McElroy, Joseph P.; Gilbert, Mark R.; Mehta, Minesh; Klimowicz, Alexander C.; Magliocco, Anthony; Bredel, Markus; Robe, Pierre; Grosu, Anca L.; Stupp, Roger; Curran, Walter; Becker, Aline P.; Salavaggione, Andrea L.; Barnholtz-Sloan, Jill S.; Aldape, Kenneth; Blumenthal, Deborah T.; Brown, Paul D.; Glass, Jon; Souhami, Luis; Lee, R. Jeffrey; Brachman, David; Flickinger, John; Won, Minhee; Chakravarti, Arnab

    2017-01-01

    IMPORTANCE: There is a need for a more refined, molecularly based classification model for glioblastoma (GBM) in the temozolomide era. OBJECTIVE: To refine the existing clinically based recursive partitioning analysis (RPA) model by incorporating molecular variables. DESIGN, SETTING, AND

  13. Structure and Dynamics of Urea/Water Mixtures Investigated by Vibrational Spectroscopy and Molecular Dynamics Simulation

    Science.gov (United States)

    Carr, J. K.; Buchanan, L. E.; Schmidt, J. R.; Zanni, M. T.; Skinner, J. L.

    2013-01-01

    Urea/water is an archetypical “biological” mixture, and is especially well known for its relevance to protein thermodynamics, as urea acts as a protein denaturant at high concentration. This behavior has given rise to an extended debate concerning urea’s influence on water structure. Based on a variety of methods and of definitions of water structure, urea has been variously described as a structure-breaker, a structure-maker, or as remarkably neutral towards water. Because of its sensitivity to microscopic structure and dynamics, vibrational spectroscopy can help resolve these debates. We report experimental and theoretical spectroscopic results for the OD stretch of HOD/H2O/urea mixtures (linear IR, 2DIR, and pump-probe anisotropy decay) and for the CO stretch of urea-D4/D2O mixtures (linear IR only). Theoretical results are obtained using existing approaches for water, and a modification of a frequency map developed for acetamide. All absorption spectra are remarkably insensitive to urea concentration, consistent with the idea that urea only very weakly perturbs water structure. Both this work and experiments by Rezus and Bakker, however, show that water’s rotational dynamics are slowed down by urea. Analysis of the simulations casts doubt on the suggestion that urea immobilizes particular doubly hydrogen bonded water molecules. PMID:23841646

  14. 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.

  15. Systems theoretic analysis of the central dogma of molecular biology: some recent results.

    Science.gov (United States)

    Gao, Rui; Yu, Juanyi; Zhang, Mingjun; Tarn, Tzyh-Jong; Li, Jr-Shin

    2010-03-01

    This paper extends our early study on a mathematical formulation of the central dogma of molecular biology, and focuses discussions on recent insights obtained by employing advanced systems theoretic analysis. The goal of this paper is to mathematically represent and interpret the genetic information flow at the molecular level, and explore the fundamental principle of molecular biology at the system level. Specifically, group theory was employed to interpret concepts and properties of gene mutation, and predict backbone torsion angle along the peptide chain. Finite state machine theory was extensively applied to interpret key concepts and analyze the processes related to DNA hybridization. Using the proposed model, we have transferred the character-based model in molecular biology to a sophisticated mathematical model for calculation and interpretation.

  16. Bioinformatics analysis on molecular mechanism of rheum officinale in treatment of jaundice

    Science.gov (United States)

    Shan, Si; Tu, Jun; Nie, Peng; Yan, Xiaojun

    2017-01-01

    Objective: To study the molecular mechanism of Rheum officinale in the treatment of Jaundice by building molecular networks and comparing canonical pathways. Methods: Target proteins of Rheum officinale and related genes of Jaundice were searched from Pubchem and Gene databases online respectively. Molecular networks and canonical pathways comparison analyses were performed by Ingenuity Pathway Analysis (IPA). Results: The molecular networks of Rheum officinale and Jaundice were complex and multifunctional. The 40 target proteins of Rheum officinale and 33 Homo sapiens genes of Jaundice were found in databases. There were 19 common pathways both related networks. Rheum officinale could regulate endothelial differentiation, Interleukin-1B (IL-1B) and Tumor Necrosis Factor (TNF) in these pathways. Conclusions: Rheum officinale treat Jaundice by regulating many effective nodes of Apoptotic pathway and cellular immunity related pathways.

  17. Molecularly imprinted solid-phase extraction in the analysis of agrochemicals.

    Science.gov (United States)

    Yi, Ling-Xiao; Fang, Rou; Chen, Guan-Hua

    2013-08-01

    The molecular imprinting technique is a highly predeterminative recognition technology. Molecularly imprinted polymers (MIPs) can be applied to the cleanup and preconcentration of analytes as the selective adsorbent of solid-phase extraction (SPE). In recent years, a new type of SPE has formed, molecularly imprinted polymer solid-phase extraction (MISPE), and has been widely applied to the extraction of agrochemicals. In this review, the mechanism of the molecular imprinting technique and the methodology of MIP preparations are explained. The extraction modes of MISPE, including offline and online, are discussed, and the applications of MISPE in the analysis of agrochemicals such as herbicides, fungicides and insecticides are summarized. It is concluded that MISPE is a powerful tool to selectively isolate agrochemicals from real samples with higher extraction and cleanup efficiency than commercial SPE and that it has great potential for broad applications.

  18. In situ diffraction profile analysis during tensile deformation motivated by molecular dynamics

    International Nuclear Information System (INIS)

    Van Swygenhoven, H.; Budrovic, Z.; Derlet, P.M.; Froseth, A.G.; Van Petegem, S.

    2005-01-01

    Molecular dynamics simulations can provide insight into the slip mechanism at the atomic scale and suggest that in nanocrystalline metals dislocations are nucleated and absorbed by the grain boundaries. However, this technique is limited by very short simulation times. Using suggestions from molecular dynamics, we have developed a new in situ X-ray diffraction technique wherein the profile analysis of several Bragg diffraction peaks during tensile deformation is possible. Combining experiment and careful structural analysis the results confirm the suggestions from atomistic simulations

  19. Transcriptomic analysis of molecular responses in Malus domestica 'M26' roots affected by apple replant disease.

    Science.gov (United States)

    Weiß, Stefan; Bartsch, Melanie; Winkelmann, Traud

    2017-06-01

    Gene expression studies in roots of apple replant disease affected plants suggested defense reactions towards biotic stress to occur which did not lead to adequate responses to the biotic stressors. Apple replant disease (ARD) leads to growth inhibition and fruit yield reduction in replanted populations and results in economic losses for tree nurseries and fruit producers. The etiology is not well understood on a molecular level and causal agents show a great diversity indicating that no definitive cause, which applies to the majority of cases, has been found out yet. Hence, it is pivotal to gain a better understanding of the molecular and physiological reactions of the plant when affected by ARD and later to overcome the disease, for example by developing tolerant rootstocks. For the first time, gene expression was investigated in roots of ARD affected plants employing massive analysis of cDNA ends (MACE) and RT-qPCR. In reaction to ARD, genes in secondary metabolite production as well as plant defense, regulatory and signaling genes were upregulated whereas for several genes involved in primary metabolism lower expression was detected. For internal verification of MACE data, candidate genes were tested via RT-qPCR and a strong positive correlation between both datasets was observed. Comparison of apple 'M26' roots cultivated in ARD soil or γ-irradiated ARD soil suggests that typical defense reactions towards biotic stress take place in ARD affected plants but they did not allow responding to the biotic stressors attack adequately, leading to the observed growth depressions in ARD variants.

  20. Molecular analysis of infectious bursal disease virus from bursal tissues collected on FTA filter paper.

    Science.gov (United States)

    Moscoso, Hugo; Alvarado, Ivan; Hofacre, Charles L

    2006-09-01

    We investigated the feasibility of using FTA filter cards for the storage of bursas of Fabricius containing infectious bursal disease virus (IBDV) and for IBDV detection by reverse transcriptase (RT)-polymerase chain reaction (PCR), and characterization by restriction fragment length polymorphism (RFLP) or nucleotide sequencing. The FTA card is a cotton-based cellulose membrane containing lyophilized chemicals that lyses many types of bacteria and viruses. IBDV was inactivated upon contact with the FTA as shown by the inability of the virus to be propagated in embryonating chicken eggs. Viral RNA in minced bursas or stamped bursas could be amplified by RT-PCR (VP2 gene fragment, 248 base pairs) after storage on FTA for at least 15 days at room temperature or 8 mo at -20 C. Analytical sensitivity of the test was between 0.5-5 ng of RNA template or 5 x 10(1) mean tissue culture infective dose (TCID50)/FTA spot. Detection rate of IBDV in domestic clinical samples collected on FTA or collected by the non-FTA standard procedure was 36.7% and 41.7%, respectively, which represents 88% agreement. Detection of IBDV from FTA cards inoculated with bursal tissues in the laboratory or in the field was 36.7% and 37.1%, respectively. Detection of IBDV from FTA samples when the cards were inoculated with bursal tissues and sent through customs into the United States was 32.9%. Analysis of the amplified products showed that molecular characterization of IBDV by RFLP or nucleotide sequencing is feasible in bursas stored on FTA at 25 C for 1-3 mo or at -20 C for at least 8 mo. The use of FTA for the collection of bursal tissues and simultaneous inactivation of IBDV allows the movement of specimens within the United States and also from outside the United States in compliance with federal regulations and in a manner adequate for molecular characterization.

  1. Molecular characterization and analysis of the porcine NURR1 gene

    Directory of Open Access Journals (Sweden)

    Knud Larsen

    2016-12-01

    Here we report the isolation and characterization of porcine NURR1 cDNA. The NURR1 cDNA was RT-PCR cloned using NURR1-specific oligonucleotide primers derived from in silico sequences. The porcine NURR1 cDNA encodes a polypeptide of 598 amino acids, displaying a very high similarity with bovine, human and mouse (99% NURR1 protein. Expression analysis revealed a differential NURR1 mRNA expression in various organs and tissues. NURR1 transcripts could be detected as early as at 60 days of embryo development in different brain tissues. A significant increase in NURR1 transcript in the cerebellum and a decrease in NURR1 transcript in the basal ganglia was observed during embryo development. The porcine NURR1 gene was mapped to chromosome 15. Two missense mutations were found in exon 3, the first coding exon of NURR1. Methylation analysis of the porcine NURR1 gene body revealed a high methylation degree in brain tissue, whereas methylation of the promoter was very low. A decrease in DNA methylation in a discrete region of the NURR1 promoter was observed in pig frontal cortex during pig embryo development. This observation correlated with an increase in NURR1 transcripts. Therefore, methylation might be a determinant of NURR1 expression at certain time points in embryo development.

  2. Molecular neutron activation analysis of selenium metabolites in urine

    International Nuclear Information System (INIS)

    Blotcky, A.J.; Hansen, G.T.; Ebrahim, A.; Rack, E.P.

    1988-01-01

    Because of the biological importance of selenium in living biological systems, various analytical procedures have been developed for analysis of microquantities of elemental selenium, in urine, serum, and tissue. For urine selenium, these include atomic absorption spectrometry, solution absorption spectrometry, solution fluorescence spectrometry, volumetry, and neutron activation analysis. Of equal or greater importance is the determination of selenium metabolites present in urine for the purpose of describing the biological pathways for the metabolism of selenium in living organisms. While it is known from previous studies that trimethylselenonium ion (TMSe) is a major metabolite in urine, probably the result of reduction and methylation reaction, there are no definitive results in the literature indicating the nature or quantity of other selenium metabolic products in urine. Early techniques to measure TMSe levels in urine involved the use of the radiotracer 75 Se. Because of the long biological half-life of selenium and issues of radiation exposure, its use in humans has been limited. In this paper, the authors report the experimental procedure for the determination of total selenoamino acid concentration in urine and present total selenium values, and, where applicable, TMSe, SeO 2- 3 , and total selenoamino acid concentrations in the urine of normal and diseased subjects

  3. Genomic analysis and selected molecular pathways in rare cancers

    International Nuclear Information System (INIS)

    Liu, Stephen V; Lenkiewicz, Elizabeth; Evers, Lisa; Holley, Tara; Kiefer, Jeffrey; Demeure, Michael J; Ramanathan, Ramesh K; Von Hoff, Daniel D; Barrett, Michael T; Ruiz, Christian; Glatz, Katharina; Bubendorf, Lukas; Eng, Cathy

    2012-01-01

    It is widely accepted that many cancers arise as a result of an acquired genomic instability and the subsequent evolution of tumor cells with variable patterns of selected and background aberrations. The presence and behaviors of distinct neoplastic cell populations within a patient's tumor may underlie multiple clinical phenotypes in cancers. A goal of many current cancer genome studies is the identification of recurring selected driver events that can be advanced for the development of personalized therapies. Unfortunately, in the majority of rare tumors, this type of analysis can be particularly challenging. Large series of specimens for analysis are simply not available, allowing recurring patterns to remain hidden. In this paper, we highlight the use of DNA content-based flow sorting to identify and isolate DNA-diploid and DNA-aneuploid populations from tumor biopsies as a strategy to comprehensively study the genomic composition and behaviors of individual cancers in a series of rare solid tumors: intrahepatic cholangiocarcinoma, anal carcinoma, adrenal leiomyosarcoma, and pancreatic neuroendocrine tumors. We propose that the identification of highly selected genomic events in distinct tumor populations within each tumor can identify candidate driver events that can facilitate the development of novel, personalized treatment strategies for patients with cancer. (paper)

  4. Molecular analysis of microbial diversity in advanced caries.

    Science.gov (United States)

    Chhour, Kim-Ly; Nadkarni, Mangala A; Byun, Roy; Martin, F Elizabeth; Jacques, Nicholas A; Hunter, Neil

    2005-02-01

    Real-time PCR analysis of the total bacterial load in advanced carious lesions has shown that the total load exceeds the number of cultivable bacteria. This suggests that an unresolved complexity exists in bacteria associated with advanced caries. In this report, the profile of the microflora of carious dentine was explored by using DNA extracted from 10 lesions selected on the basis of comparable total microbial load and on the relative abundance of Prevotella spp. Using universal primers for the 16S rRNA gene, PCR amplicons were cloned, and approximately 100 transformants were processed for each lesion. Phylogenetic analysis of 942 edited sequences demonstrated the presence of 75 species or phylotypes in the 10 carious lesions. Up to 31 taxa were represented in each sample. A diverse array of lactobacilli were found to comprise 50% of the species, with prevotellae also abundant, comprising 15% of the species. Other taxa present in a number of lesions or occurring with high abundance included Selenomonas spp., Dialister spp., Fusobacterium nucleatum, Eubacterium spp., members of the Lachnospiraceae family, Olsenella spp., Bifidobacterium spp., Propionibacterium sp., and Pseudoramibacter alactolyticus. The mechanisms by which such diverse patterns of bacteria extend carious lesions, including the aspect of infection of the vital dental pulp, remain unclear.

  5. Chemical and structural investigation of lipid nanoparticles: drug-lipid interaction and molecular distribution

    Energy Technology Data Exchange (ETDEWEB)

    Anantachaisilp, Suranan; Smith, Siwaporn Meejoo [Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University, Rama VI Road, Bangkok 10400 (Thailand); Treetong, Alongkot; Ruktanonchai, Uracha Rungsardthong [National Nanotechnology Center, National Science and Technology Development Agency, 111 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120 (Thailand); Pratontep, Sirapat [College of KMITL Nanotechnology, King Mongkut' s Institute of Technology Ladkrabang, Bangkok (Thailand); Puttipipatkhachorn, Satit, E-mail: uracha@nanotec.or.th [Department of Manufacturing Pharmacy, Faculty of Pharmacy, Mahidol University, Bangkok 10400 (Thailand)

    2010-03-26

    Lipid nanoparticles are a promising alternative to existing carriers in chemical or drug delivery systems. A key challenge is to determine how chemicals are incorporated and distributed inside nanoparticles, which assists in controlling chemical retention and release characteristics. This study reports the chemical and structural investigation of {gamma}-oryzanol loading inside a model lipid nanoparticle drug delivery system composed of cetyl palmitate as solid lipid and Miglyol 812 as liquid lipid. The lipid nanoparticles were prepared by high pressure homogenization at varying liquid lipid content, in comparison with the {gamma}-oryzanol free systems. The size of the lipid nanoparticles, as measured by the photon correlation spectroscopy, was found to decrease with increased liquid lipid content from 200 to 160 nm. High-resolution proton nuclear magnetic resonance ({sup 1}H-NMR) measurements of the medium chain triglyceride of the liquid lipid has confirmed successful incorporation of the liquid lipid in the lipid nanoparticles. Differential scanning calorimetric and powder x-ray diffraction measurements provide complementary results to the {sup 1}H-NMR, whereby the crystallinity of the lipid nanoparticles diminishes with an increase in the liquid lipid content. For the distribution of {gamma}-oryzanol inside the lipid nanoparticles, the {sup 1}H-NMR revealed that the chemical shifts of the liquid lipid in {gamma}-oryzanol loaded systems were found at rather higher field than those in {gamma}-oryzanol free systems, suggesting incorporation of {gamma}-oryzanol in the liquid lipid. In addition, the phase-separated structure was observed by atomic force microscopy for lipid nanoparticles with 0% liquid lipid, but not for lipid nanoparticles with 5 and 10% liquid lipid. Raman spectroscopic and mapping measurements further revealed preferential incorporation of {gamma}-oryzanol in the liquid part rather than the solid part of in the lipid nanoparticles. Simple models

  6. Chemical and structural investigation of lipid nanoparticles: drug-lipid interaction and molecular distribution

    Science.gov (United States)

    Anantachaisilp, Suranan; Meejoo Smith, Siwaporn; Treetong, Alongkot; Pratontep, Sirapat; Puttipipatkhachorn, Satit; Rungsardthong Ruktanonchai, Uracha

    2010-03-01

    Lipid nanoparticles are a promising alternative to existing carriers in chemical or drug delivery systems. A key challenge is to determine how chemicals are incorporated and distributed inside nanoparticles, which assists in controlling chemical retention and release characteristics. This study reports the chemical and structural investigation of γ-oryzanol loading inside a model lipid nanoparticle drug delivery system composed of cetyl palmitate as solid lipid and Miglyol 812® as liquid lipid. The lipid nanoparticles were prepared by high pressure homogenization at varying liquid lipid content, in comparison with the γ-oryzanol free systems. The size of the lipid nanoparticles, as measured by the photon correlation spectroscopy, was found to decrease with increased liquid lipid content from 200 to 160 nm. High-resolution proton nuclear magnetic resonance (1H-NMR) measurements of the medium chain triglyceride of the liquid lipid has confirmed successful incorporation of the liquid lipid in the lipid nanoparticles. Differential scanning calorimetric and powder x-ray diffraction measurements provide complementary results to the 1H-NMR, whereby the crystallinity of the lipid nanoparticles diminishes with an increase in the liquid lipid content. For the distribution of γ-oryzanol inside the lipid nanoparticles, the 1H-NMR revealed that the chemical shifts of the liquid lipid in γ-oryzanol loaded systems were found at rather higher field than those in γ-oryzanol free systems, suggesting incorporation of γ-oryzanol in the liquid lipid. In addition, the phase-separated structure was observed by atomic force microscopy for lipid nanoparticles with 0% liquid lipid, but not for lipid nanoparticles with 5 and 10% liquid lipid. Raman spectroscopic and mapping measurements further revealed preferential incorporation of γ-oryzanol in the liquid part rather than the solid part of in the lipid nanoparticles. Simple models representing the distribution of γ-oryzanol and

  7. Chemical and structural investigation of lipid nanoparticles: drug-lipid interaction and molecular distribution

    International Nuclear Information System (INIS)

    Anantachaisilp, Suranan; Smith, Siwaporn Meejoo; Treetong, Alongkot; Ruktanonchai, Uracha Rungsardthong; Pratontep, Sirapat; Puttipipatkhachorn, Satit

    2010-01-01

    Lipid nanoparticles are a promising alternative to existing carriers in chemical or drug delivery systems. A key challenge is to determine how chemicals are incorporated and distributed inside nanoparticles, which assists in controlling chemical retention and release characteristics. This study reports the chemical and structural investigation of γ-oryzanol loading inside a model lipid nanoparticle drug delivery system composed of cetyl palmitate as solid lipid and Miglyol 812 as liquid lipid. The lipid nanoparticles were prepared by high pressure homogenization at varying liquid lipid content, in comparison with the γ-oryzanol free systems. The size of the lipid nanoparticles, as measured by the photon correlation spectroscopy, was found to decrease with increased liquid lipid content from 200 to 160 nm. High-resolution proton nuclear magnetic resonance ( 1 H-NMR) measurements of the medium chain triglyceride of the liquid lipid has confirmed successful incorporation of the liquid lipid in the lipid nanoparticles. Differential scanning calorimetric and powder x-ray diffraction measurements provide complementary results to the 1 H-NMR, whereby the crystallinity of the lipid nanoparticles diminishes with an increase in the liquid lipid content. For the distribution of γ-oryzanol inside the lipid nanoparticles, the 1 H-NMR revealed that the chemical shifts of the liquid lipid in γ-oryzanol loaded systems were found at rather higher field than those in γ-oryzanol free systems, suggesting incorporation of γ-oryzanol in the liquid lipid. In addition, the phase-separated structure was observed by atomic force microscopy for lipid nanoparticles with 0% liquid lipid, but not for lipid nanoparticles with 5 and 10% liquid lipid. Raman spectroscopic and mapping measurements further revealed preferential incorporation of γ-oryzanol in the liquid part rather than the solid part of in the lipid nanoparticles. Simple models representing the distribution of γ-oryzanol and

  8. Investigations into the molecular mechanism of chromatid breakage in the G2-phase of mammalian cells

    International Nuclear Information System (INIS)

    Bryant, P.E.; Armstrong, G.N.; Gray, L.; Frankenberg, D.; Mozdarani, H.

    2003-01-01

    Chromatid breakage following irradiation of cells in the G2-phase of the cell cycle results from the induction of DNA double-strand breaks (dsb). The conversion of dsb into chromatid breaks (cb) has a genetic basis, seemingly different from that of dsb rejoining. The variation in extent of this conversion is exemplified by the stiking variation in frequency of cb in irradiated cycling T-lymphocytes between different normal individuals. Elevated cb frequency in lymphocytes of around 40% of breast cancer patients and their first-degree relatives suggests the presence of mutations in low penetrance cancer predisposing genes that also affect conversion of dsb to cb. Investigation of the mechanism of chromatid radiosensitivity using genetically engineered rodent cell lines containing unique dsb break sites indicate that a single isolated dsb is sufficient to cause a cb. The single-event nature of chromatid breakage is confirmed by the fact that cb are induced as a linear function of radiation dose. Moreover, we have recently shown that ultrasoft carbon-K X-rays also induce chromatid breakage. In this case the energy of the secondary electrons produced by carbon-K X-rays is too low to span more than one DNA double helix, thus further supporting our conclusion that a single dsb is responsible for the formation of a cb. Chromatid breakage is thought to involve a rearrangement between DNA strands at the crossover points of chromatin loop(s) triggered by the presence of a dsb within the loop structure. The occasional observation of 'looped-out' sections of chromatin at cb sites supports this hypothesis. The occurrence of 'colour-switches' between FPG stained chromatids at a proportion of break sites (e.g. about 16% in CHO cells) shows that a significant proportion of cb definitely result from chromatin rearrangements. Measurements of altered colour-switch ratio (csr) in mutant rodent and human cells (irs1 and AT cells respectively) also indicate a genetic basis for the

  9. Molecular Dynamics Investigation of the Effects of Concentration on Hydrogen Bonding in Aqueous Solutions of Methanol, Ethylene Glycol and Glycerol

    International Nuclear Information System (INIS)

    Zhang, Ning; Li, Weizhong; Chen, Cong; Zuo, Jianguo; Weng, Lindong

    2013-01-01

    Hydrogen bonding interaction between alcohols and water molecules is an important characteristic in the aqueous solutions of alcohols. In this paper, a series of molecular dynamics simulations have been performed to investigate the aqueous solutions of low molecular weight alcohols (methanol, ethylene glycol and glycerol) at the concentrations covering a broad range from 1 to 90 mol %. The work focuses on studying the effect of the alcohols molecules on the hydrogen bonding of water molecules in binary mixtures. By analyzing the hydrogen bonding ability of the hydroxyl (-OH) groups for the three alcohols, it is found that the hydroxyl group of methanol prefers to form more hydrogen bonds than that of ethylene glycol and glycerol due to the intra-and intermolecular effects. It is also shown that concentration has significant effect on the ability of alcohol molecule to hydrogen bond water molecules. Understanding the hydrogen bonding characteristics of the aqueous solutions is helpful to reveal the cryoprotective mechanisms of methanol, ethylene glycol and glycerol in aqueous solutions

  10. Molecular investigation on the binding of Cd(II) by the binary mixtures of montmorillonite with two bacterial species

    Energy Technology Data Exchange (ETDEWEB)

    Du, Huihui; Qu, ChenChen; Liu, Jing; Chen, Wenli; Cai, Peng; Shi, Zhihua; Yu, Xiao-Ying; Huang, Qiaoyun

    2017-10-01

    Bacteria and phyllosilicate commonly coexist in the natural environment, producing various bacteria–clay complexes that are capable of immobilizing heavy metals, such as cadmium, via adsorption. However, the molecular binding mechanisms of heavy metals on these complex aggregates still remain poorly understood. This study investigated Cd adsorption on Gram-positive B. subtilis, Gram-negative P. putida and their binary mixtures with montmorillonite (Mont) using the Cd K-edge x-ray absorption spectroscopy (XAS) and isothermal titration calorimetry (ITC). We observed a lower adsorptive capacity for P. putida than B. subtilis, whereas P. putida–Mont and B. subtilis–Mont mixtures showed nearly identical Cd adsorption behaviors. EXAFS fits and ITC measurements demonstrated more phosphoryl binding of Cd in P. putida. The decreased coordination of C atoms around Cd and the reduced adsorption enthalpies and entropies for the binary mixtures compared to that for individual bacteria suggested that the bidentate Cd-carboxyl complexes in pure bacteria systems were probably transformed into monodentate complexes that acted as ionic bridging structure between bacteria and motmorillonite. This study clarified the binding mechanism of Cd at the bacteria–phyllosilicate interfaces from a molecular and thermodynamic view, which has an environmental significance for predicting the chemical behavior of trace elements in complex mineral–organic systems.

  11. Spatial distribution of intra-molecular water and polymeric components in polyelectrolyte dendrimers revealed by small angle scattering investigations

    Science.gov (United States)

    Wu, Bin; Li, Xin; Do, Changwoo; Kim, Tae-Hwan; Shew, Chwen-Yang; Liu, Yun; Yang, Jun; Hong, Kunlun; Porcar, Lionel; Chen, Chun-Yu; Liu, Emily L.; Smith, Gregory S.; Herwig, Kenneth W.; Chen, Wei-Ren

    2011-10-01

    An experimental scheme using contrast variation small angle neutron scattering technique is developed to investigate the structural characteristics of amine-terminated poly(amidoamine) dendrimers solutions. Using this methodology, we present the dependence of both the intra-dendrimer water and the polymer distribution on molecular protonation, which can be precisely adjusted by tuning the pH of the solution. Assuming spherical symmetry of the spatial arrangement of the constituent components of dendrimer, and that the atomic ratio of hydrogen-to-deuterium for the solvent residing within the cavities of dendrimer is identical to that for the solvent outside the dendrimer, the intra-dendrimer water distribution along the radial direction is determined. Our result clearly reveals an outward relocation of the peripheral groups, as well as enhanced intra-dendrimer hydration, upon increasing the molecular protonation and, therefore, allows the determination of segmental backfolding in a quantitative manner. The connection between these charge-induced structural changes and our recently observed progressively active segmental dynamics is also discussed.

  12. Investigation of the Interaction between Patulin and Human Serum Albumin by a Spectroscopic Method, Atomic Force Microscopy, and Molecular Modeling

    Directory of Open Access Journals (Sweden)

    Li Yuqin

    2014-01-01

    Full Text Available The interaction of patulin with human serum albumin (HSA was studied in vitro under normal physiological conditions. The study was performed using fluorescence, ultraviolet-visible spectroscopy (UV-Vis, circular dichroism (CD, atomic force microscopy (AFM, and molecular modeling techniques. The quenching mechanism was investigated using the association constants, the number of binding sites, and basic thermodynamic parameters. A dynamic quenching mechanism occurred between HSA and patulin, and the binding constants (K were 2.60 × 104, 4.59 × 104, and 7.01 × 104 M−1 at 288, 300, and 310 K, respectively. Based on fluorescence resonance energy transfer, the distance between the HSA and patulin was determined to be 2.847 nm. The ΔG0, ΔH0, and ΔS0 values across various temperatures indicated that hydrophobic interaction was the predominant binding force. The UV-Vis and CD results confirmed that the secondary structure of HSA was altered in the presence of patulin. The AFM results revealed that the individual HSA molecule dimensions were larger after interaction with patulin. In addition, molecular modeling showed that the patulin-HSA complex was stabilized by hydrophobic and hydrogen bond forces. The study results suggested that a weak intermolecular interaction occurred between patulin and HSA. Overall, the results are potentially useful for elucidating the toxigenicity of patulin when it is combined with the biomolecular function effect, transmembrane transport, toxicological, testing and other experiments.

  13. Massively Parallel, Molecular Analysis Platform Developed Using a CMOS Integrated Circuit With Biological Nanopores

    Science.gov (United States)

    Roever, Stefan

    2012-01-01

    A massively parallel, low cost molecular analysis platform will dramatically change the nature of protein, molecular and genomics research, DNA sequencing, and ultimately, molecular diagnostics. An integrated circuit (IC) with 264 sensors was fabricated using standard CMOS semiconductor processing technology. Each of these sensors is individually controlled with precision analog circuitry and is capable of single molecule measurements. Under electronic and software control, the IC was used to demonstrate the feasibility of creating and detecting lipid bilayers and biological nanopores using wild type α-hemolysin. The ability to dynamically create bilayers over each of the sensors will greatly accelerate pore development and pore mutation analysis. In addition, the noise performance of the IC was measured to be 30fA(rms). With this noise performance, single base detection of DNA was demonstrated using α-hemolysin. The data shows that a single molecule, electrical detection platform using biological nanopores can be operationalized and can ultimately scale to millions of sensors. Such a massively parallel platform will revolutionize molecular analysis and will completely change the field of molecular diagnostics in the future.

  14. Adrenocortical carcinoma: the dawn of a new era of genomic and molecular biology analysis.

    Science.gov (United States)

    Armignacco, R; Cantini, G; Canu, L; Poli, G; Ercolino, T; Mannelli, M; Luconi, M

    2018-05-01

    Over the last decade, the development of novel and high penetrance genomic approaches to analyze biological samples has provided very new insights in the comprehension of the molecular biology and genetics of tumors. The use of these techniques, consisting of exome sequencing, transcriptome, miRNome, chromosome alteration, genome, and epigenome analysis, has also been successfully applied to adrenocortical carcinoma (ACC). In fact, the analysis of large cohorts of patients allowed the stratification of ACC with different patterns of molecular alterations, associated with different outcomes, thus providing a novel molecular classification of the malignancy to be associated with the classical pathological analysis. Improving our knowledge about ACC molecular features will result not only in a better diagnostic and prognostic accuracy, but also in the identification of more specific therapeutic targets for the development of more effective pharmacological anti-cancer approaches. In particular, the specific molecular alteration profiles identified in ACC may represent targetable events by the use of already developed or newly designed drugs enabling a better and more efficacious management of the ACC patient in the context of new frontiers of personalized precision medicine.

  15. Identification and in silico analysis of the Citrus HSP70 molecular chaperone gene family

    Directory of Open Access Journals (Sweden)

    Luciano G. Fietto

    2007-01-01

    Full Text Available The completion of the genome sequencing of the Arabidopsis thaliana model system provided a powerful molecular tool for comparative analysis of gene families present in the genome of economically relevant plant species. In this investigation, we used the sequences of the Arabidopsis Hsp70 gene family to identify and annotate the Citrus Hsp70 genes represented in the CitEST database. Based on sequence comparison analysis, we identified 18 clusters that were further divided into 5 subgroups encoding four mitochondrial mtHsp70s, three plastid csHsp70s, one ER luminal Hsp70 BiP, two HSP110/SSE-related proteins and eight cytosolic Hsp/Hsc70s. We also analyzed the expression profile by digital Northern of each Hsp70 transcript in different organs and in response to stress conditions. The EST database revealed a distinct population distribution of Hsp70 ESTs among isoforms and across the organs surveyed. The Hsp70-5 isoform was highly expressed in seeds, whereas BiP, mitochondrial and plastid HSp70 mRNAs displayed a similar expression profile in the organs analyzed, and were predominantly represented in flowers. Distinct Hsp70 mRNAs were also differentially expressed during Xylella infection and Citrus tristeza viral infection as well as during water deficit. This in silico study sets the groundwork for future investigations to fully characterize functionally the Citrus Hsp70 family and underscores the relevance of Hsp70s in response to abiotic and biotic stresses in Citrus.

  16. Molecular characterization and interactome analysis of Trypanosoma cruzi tryparedoxin II.

    Science.gov (United States)

    Arias, Diego G; Piñeyro, María Dolores; Iglesias, Alberto A; Guerrero, Sergio A; Robello, Carlos

    2015-04-29

    antioxidant mechanisms constitute an active field of investigation, since they could provide the basis for a rational drug development. Peroxide detoxification in this parasite is achieved by ascorbate peroxidase and different thiol-dependent peroxidases. Among them, both mitochondrial and cytosolic tryparedoxin peroxidases, typical two-cysteine peroxiredoxins, were found to be important for hydrogen peroxide and peroxynitrite detoxification and their expression levels correlated with parasite infectivity and virulence. In trypanosomes tryparedoxins and not thioredoxins act as peroxiredoxin reductases, suggesting that these enzymes substitute thioredoxins in these parasites. T. cruzi possesses two tryparedoxin genes, TcTXNI and TcTXN II. Since thioredoxins are proteins with several targets actively participating of complex redox networks, we have previously investigated if this is the case also for TcTXNI, for which we described relevant partners (J Proteomics. 2011;74(9):1683-92). In this manuscript we investigated the interactions of TcTXNII. We have designed an active site mutant tryparedoxin II lacking the resolving cysteine and, through the expression of this mutant protein and its incubation with T. cruzi proteins, hetero disulfide complexes were isolated by affinity chromatography purification and identified by electrophoresis separation and MS identification. This allowed us to identify sixteen TcTXNII interacting proteins which are involved in different and relevant cellular processes. Moreover, we demonstrate that TcTXNII is a transmembrane protein anchored to the surface of the mitochondria and endoplasmic reticulum. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. Pteros 2.0: Evolution of the fast parallel molecular analysis library for C++ and python.

    Science.gov (United States)

    Yesylevskyy, Semen O

    2015-07-15

    Pteros is the high-performance open-source library for molecular modeling and analysis of molecular dynamics trajectories. Starting from version 2.0 Pteros is available for C++ and Python programming languages with very similar interfaces. This makes it suitable for writing complex reusable programs in C++ and simple interactive scripts in Python alike. New version improves the facilities for asynchronous trajectory reading and parallel execution of analysis tasks by introducing analysis plugins which could be written in either C++ or Python in completely uniform way. The high level of abstraction provided by analysis plugins greatly simplifies prototyping and implementation of complex analysis algorithms. Pteros is available for free under Artistic License from http://sourceforge.net/projects/pteros/. © 2015 Wiley Periodicals, Inc.

  18. In Situ Investigation of the Adsorption of Styrene Phosphonic Acid on Cassiterite (110 Surface by Molecular Modeling

    Directory of Open Access Journals (Sweden)

    Guichen Gong

    2017-09-01

    Full Text Available Abstract: The flotation, adsorption and bonding mechanisms of styrene phosphonic acid (SPA to cassiterite were studied using microflotation tests, zeta potential measurements, solution chemistry analysis and density functional theory (DFT calculations in this paper. Flotation results demonstrated SPA was an excellent collector for cassiterite which could recover over 85% cassiterite particles with the pH range 4.3–6.06 and 40 mg/L SPA. Zeta potential measurements and solution chemistry analysis revealed the adsorption of SPA was mainly contributed by the chemisorption of the monoanions on cassiterite surfaces. Frontier molecular orbital theory analysis and adsorption energy calculation results proved the monoanion of SPA was able to replace the OH− on cassiterite surfaces. The adsorption structure optimization results confirmed the binuclear complex was the most favorable adsorption configuration of SPA on cassiterite (110 surface. Mulliken population calculations and density of states analysis indicated during the bonding process the Sn3 atom lost electrons to O3 atom, and the bonding interaction between O3 and Sn3 atoms was mainly from the contribution of the 2p orbital of O3 atom and the 5s and 5p orbitals of Sn3 atom.

  19. Biomedical analysis of formalin-fixed, paraffin-embedded tissue samples: The Holy Grail for molecular diagnostics.

    Science.gov (United States)

    Donczo, Boglarka; Guttman, Andras

    2018-06-05

    More than a century ago in 1893, a revolutionary idea about fixing biological tissue specimens was introduced by Ferdinand Blum, a German physician. Since then, a plethora of fixation methods have been investigated and used. Formalin fixation with paraffin embedment became the most widely used types of fixation and preservation method, due to its proper architectural conservation of tissue structures and cellular shape. The huge collection of formalin-fixed, paraffin-embedded (FFPE) sample archives worldwide holds a large amount of unearthed information about diseases that could be the Holy Grail in contemporary biomarker research utilizing analytical omics based molecular diagnostics. The aim of this review is to critically evaluate the omics options for FFPE tissue sample analysis in the molecular diagnostics field. Copyright © 2018. Published by Elsevier B.V.

  20. Molecular characterization and phylogenetic analysis of Fasciola hepatica from Peru.

    Science.gov (United States)

    Ichikawa-Seki, Madoka; Ortiz, Pedro; Cabrera, Maria; Hobán, Cristian; Itagaki, Tadashi

    2016-06-01

    The causative agent of fasciolosis in South America is thought to be Fasciola hepatica. In this study, Fasciola flukes from Peru were analyzed to investigate their genetic structure and phylogenetic relationships with those from other countries. Fasciola flukes were collected from the three definitive host species: cattle, sheep, and pigs. They were identified as F. hepatica because mature sperms were observed in their seminal vesicles, and also they displayed Fh type, which has an identical fragment pattern to F. hepatica in the nuclear internal transcribed spacer 1. Eight haplotypes were obtained from the mitochondrial NADH dehydrogenase subunit 1 (nad1) sequences of Peruvian F. hepatica; however, no special difference in genetic structure was observed between the three host species. Its extremely low genetic diversity suggests that the Peruvian population was introduced from other regions. Nad1 haplotypes identical to those of Peruvian F. hepatica were detected in China, Uruguay, Italy, Iran, and Australia. Our results indicate that F. hepatica rapidly expanded its range due to human migration. Future studies are required to elucidate dispersal route of F. hepatica from Europe, its probable origin, to other areas, including Peru. Copyright © 2015. Published by Elsevier Ireland Ltd.

  1. Credibility assessment in child sexual abuse investigations: A descriptive analysis.

    Science.gov (United States)

    Melkman, Eran P; Hershkowitz, Irit; Zur, Ronit

    2017-05-01

    A major challenge in cases of child sexual abuse (CSA) is determining the credibility of children's reports. Consequently cases may be misclassified as false or deemed 'no judgment possible'. Based on a large national sample of reports of CSA made in Israel in 2014, the study examines child and event characteristics contributing to the probability that reports of abuse would be judged credible. National data files of all children aged 3-14, who were referred for investigation following suspected victimization of sexual abuse, and had disclosed sexual abuse, were analyzed. Cases were classified as either 'credible' or 'no judgment possible'. The probability of reaching a 'credible' judgment was examined in relation to characteristics of the child (age, gender, cognitive delay, marital status of the parents,) and of the abusive event (abuse severity, frequency, perpetrator-victim relationship, perpetrator's use of grooming, and perpetrator's use of coercion), controlling for investigator's identity at the cluster level of the analysis. Of 1563 cases analyzed, 57.9% were assessed as credible. The most powerful predictors of a credible judgment were older age and absence of a cognitive delay. Reports of children to married parents, who experienced a single abusive event that involved perpetrator's use of grooming, were also more likely to be judged as credible. Rates of credible judgments found are lower than expected suggesting under-identification of truthful reports of CSA. In particular, those cases of severe and multiple abuse involving younger and cognitively delayed children are the ones with the lowest chances of being assessed as credible. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. LiDAR Vegetation Investigation and Signature Analysis System (LVISA)

    Science.gov (United States)

    Höfle, Bernhard; Koenig, Kristina; Griesbaum, Luisa; Kiefer, Andreas; Hämmerle, Martin; Eitel, Jan; Koma, Zsófia

    2015-04-01

    lacks behind. We propose a novel concept, the LiDAR Vegetation Investigation and Signature Analysis System (LVISA), which shall enhance sharing of i) reference datasets of single vegetation objects with rich reference data (e.g., plant species, basic plant morphometric information) and ii) approaches for information extraction (e.g., single tree detection, tree species classification based on waveform LiDAR features). We will build an extensive LiDAR data repository for supporting the development and benchmarking of LiDAR-based object information extraction. The LiDAR Vegetation Investigation and Signature Analysis System (LVISA) uses international web service standards (Open Geospatial Consortium, OGC) for geospatial data access and also analysis (e.g., OGC Web Processing Services). This will allow the research community identifying plant object specific vegetation features from LiDAR data, while accounting for differences in LiDAR systems (e.g., beam divergence), settings (e.g., point spacing), and calibration techniques. It is the goal of LVISA to develop generic 3D information extraction approaches, which can be seamlessly transferred to other datasets, timestamps and also extraction tasks. The current prototype of LVISA can be visited and tested online via http://uni-heidelberg.de/lvisa. Video tutorials provide a quick overview and entry into the functionality of LVISA. We will present the current advances of LVISA and we will highlight future research and extension of LVISA, such as integrating low-cost LiDAR data and datasets acquired by highly temporal scanning of vegetation (e.g., continuous measurements). Everybody is invited to join the LVISA development and share datasets and analysis approaches in an interoperable way via the web-based LVISA geoportal.

  3. Molecular gas analysis by Raman scattering in intracavity laser configuration

    International Nuclear Information System (INIS)

    Benner, R.E.; Andrade, J.D.; Van Wagenen, R.A.; Westenskow, D.R.

    1987-01-01

    A system is described for the near simultaneous analysis and quantitation of selected multiple polyatomic gases in a gas sample by Raman light scattering comprising in combination: (a) laser means capable of producing a polarized laser beam of a selected wavelength containing a laser cavity the laser cavity containing a plasma tube and wherein one end of the laser cavity contains a high reflectivity output coupler mirror; (b) a gas sampling cell located within the laser cavity between the plasma tube and the output coupler mirror, the cell having opposing parallel end windows interconnected by a continuous sidewall. The end windows and sidewall define a longitudinal gas chamber oriented such that, when the laser beam is activated, the laser beam is coincident with and traverses the axis of the longitudinal gas chamber, the end windows being positioned to be substantially normal to the axis of the longitudinal gas cell chamber. The cell also has opposing, aligned side windows in the sidewall parallel to and on either side of the axis of the longitudinal gas chamber. The gas cell further contains inlet and outlet means communicating with the chamber to pass a sample gas through the cell

  4. Molecular analysis of sourdough reveals Lactobacillus mindensis sp. nov.

    Science.gov (United States)

    Ehrmann, Matthias A; Müller, Martin R A; Vogel, Rudi F

    2003-01-01

    Genotypic fingerprinting to analyse the bacterial flora of an industrial sourdough revealed a coherent group of strains which could not be associated with a valid species. Comparative 16S rDNA sequence analysis showed that these strains formed a homogeneous cluster distinct from their closest relatives, Lactobacillus farciminis, Lactobacillus alimentarius and Lactobacillus kimchii. To characterize them further, physiological (sugar fermentation, formation of DL-lactate, hydrolysis of arginine, growth temperature, CO2 production) and chemotaxonomic properties have been determined. The DNA G +C content was 37.5 0.2 mol%. The peptidoglycan was of the lysine-D-iso-asparagine (L-Lys-D-Asp) type. The strains were homofermentative, Gram-positive, catalase-negative, non-spore-forming, non-motile rods. They were found as a major stable component of a rye flour sourdough fermentation. Physiological, biochemical as well as genotypic data suggested them to be a new species of the genus Lactobacillus. This was confirmed by DNA-DNA hybridization of genomic DNA, and the name Lactobacillus mindensis is proposed. The type strain of this species is DSM 14500T (=LMG 21508T).

  5. Productivity Analysis of Public and Private Airports: A Causal Investigation

    Science.gov (United States)

    Vasigh, Bijan; Gorjidooz, Javad

    2007-01-01

    Around the world, airports are being viewed as enterprises, rather than public services, which are expected to be managed efficiently and provide passengers with courteous customer services. Governments are, increasingly, turning to the private sectors for their efficiency in managing the operation, financing, and development, as well as providing security for airports. Operational and financial performance evaluation has become increasingly important to airport operators due to recent trends in airport privatization. Assessing performance allows the airport operators to plan for human resources and capital investment as efficiently as possible. Productivity measurements may be used as comparisons and guidelines in strategic planning, in the internal analysis of operational efficiency and effectiveness, and in assessing the competitive position of an airport in transportation industry. The primary purpose of this paper is to investigate the operational and financial efficiencies of 22 major airports in the United States and Europe. These airports are divided into three groups based on private ownership (7 British Airport Authority airports), public ownership (8 major United States airports), and a mix of private and public ownership (7 major European Union airports. The detail ownership structures of these airports are presented in Appendix A. Total factor productivity (TFP) model was utilized to measure airport performance in terms of financial and operational efficiencies and to develop a benchmarking tool to identify the areas of strength and weakness. A regression model was then employed to measure the relationship between TFP and ownership structure. Finally a Granger causality test was performed to determine whether ownership structure is a Granger cause of TFP. The results of the analysis presented in this paper demonstrate that there is not a significant relationship between airport TFP and ownership structure. Airport productivity and efficiency is

  6. Investigation of tribological properties of graphene oxide reinforced ultrahigh molecular weight polyethylene under artificial seawater lubricating condition

    Science.gov (United States)

    Pang, Wenchao; Ni, Zifeng; Wu, JiaLiang; Zhao, Yongwu

    2018-03-01

    A range of ultrahigh molecular weight polyethylene (UHMWPE)/graphene oxide (GO) nanocomposites were fabricated using liquid-phase ultrasonication mixing followed by hot-pressing. The wettability, water absorption and corrosion resistance of composites were studied to prove the composites were suitable for application in liquid environment. The tribological properties of composites under dry, deionized water and seawater lubricating condition were investigated. The results showed that the incorporation of GO decreased the wear rate of UHMWPE under different lubricating conditions and with the increase of GO addition, the wear rate of UHMWPE/GO composites decreased. UHMWPE/GO composites exhibited better tribological behaviors under seawater lubricating condition than other conditions, because good corrosion resistance and excellent wear resistance of UHMWPE/GO composites, and the lubricating effect of seawater is also indispensable.

  7. Comparative investigation of third- and fifth-harmonic generation in atomic and molecular gases driven by midinfrared ultrafast laser pulses

    Energy Technology Data Exchange (ETDEWEB)

    Ni Jielei; Yao Jinping; Zeng Bin; Chu Wei; Li Guihua; Zhang Haisu; Jing Chenrui [State Key Laboratory of High Field Laser Physics, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, P.O. Box 800-211, Shanghai 201800 (China); Graduate School of the Chinese Academy of Sciences, Beijing 100039 (China); Chin, S. L. [Department of Physics, Engineering Physics and Optics, and Center for Optics, Photonics and Laser (COPL), Laval University, Laval, Quebec, G1K 7P4 (Canada); Cheng, Y.; Xu, Z. [State Key Laboratory of High Field Laser Physics, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, P.O. Box 800-211, Shanghai 201800 (China)

    2011-12-15

    We report on the comparative experimental investigation on third- and fifth-harmonic generation (THG and FHG) in atomic and molecular gases driven by midinfrared ultrafast laser pulses at a wavelength of {approx}1500 nm. We observe that the conversion efficiencies of both the THG and FHG processes saturate at similar peak intensities close to {approx}1.5 x 10{sup 14} W/cm{sup 2} for argon, nitrogen, and air, whose ionization potentials are close to each other. Near the saturation intensity, the ratio of yields of the FHG and THG reaches {approx}10{sup -1} for all the gases. Our results show that high-order Kerr effect seems to exist; however, contribution from the fourth-order Kerr refractive index coefficient alone is insufficient to balance the Kerr self-focusing without the assistance of plasma generation.

  8. Combined molecular docking and multi-spectroscopic investigation on the interaction between Eosin B and human serum albumin

    Energy Technology Data Exchange (ETDEWEB)

    Yang Qing; Zhou Ximin [National Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000 (China); Department of Chemistry, Lanzhou University, Lanzhou 730000 (China); Chen Xingguo, E-mail: chenxg@lzu.edu.c [National Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000 (China); Department of Chemistry, Lanzhou University, Lanzhou 730000 (China)

    2011-04-15

    The binding of Eosin B to human serum albumin (HSA) was studied using molecular docking, fluorescence, UV-vis, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy. The mechanism of interaction between Eosin B and HSA in terms of the binding parameters, the thermodynamic functions and the effect of Eosin B on the conformation of HSA were investigated. Protein-ligand docking study indicated that Eosin B bound to residues located in the subdomain IIA of HSA and Eosin B-HSA complex was stabilized by hydrophobic force and hydrogen bonding. In addition, fluorescence data revealed that Eosin B strongly quenched the intrinsic fluorescence of HSA through a static quenching procedure. Furthermore, alteration of the secondary structure of HSA in the presence of the dye was conformed by UV-vis, FT-IR and CD spectroscopy.

  9. Combined molecular docking and multi-spectroscopic investigation on the interaction between Eosin B and human serum albumin

    International Nuclear Information System (INIS)

    Yang Qing; Zhou Ximin; Chen Xingguo

    2011-01-01

    The binding of Eosin B to human serum albumin (HSA) was studied using molecular docking, fluorescence, UV-vis, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy. The mechanism of interaction between Eosin B and HSA in terms of the binding parameters, the thermodynamic functions and the effect of Eosin B on the conformation of HSA were investigated. Protein-ligand docking study indicated that Eosin B bound to residues located in the subdomain IIA of HSA and Eosin B-HSA complex was stabilized by hydrophobic force and hydrogen bonding. In addition, fluorescence data revealed that Eosin B strongly quenched the intrinsic fluorescence of HSA through a static quenching procedure. Furthermore, alteration of the secondary structure of HSA in the presence of the dye was conformed by UV-vis, FT-IR and CD spectroscopy.

  10. Theoretical investigation on current-voltage characteristics in all-carbon molecular device with different contact geometries

    International Nuclear Information System (INIS)

    Ye Fuqiu; Fan Zhiqiang; He Jun; Peng Jun; Tang Liming

    2012-01-01

    Applying nonequilibrium Green's functions in combination with the first-principles density-functional theory, we investigate electronic transport properties of an all-carbon molecular device consisting of one phenalenyl molecule and two zigzag graphene nanoribbons. The results show that the electronic transport properties are strongly dependent on the contact geometry and device's currents can drop obviously when the connect sites change from second-nearest sites from the central atom of the molecule (S site) to third-nearest sites from the central atom of the molecule (T site). More importantly, the negative differential resistance behavior is only observed on the negative bias region when the molecule connects the graphene nanoribbons through two T sites.

  11. A Real-Time PCR with Melting Curve Analysis for Molecular Typing of Vibrio parahaemolyticus.

    Science.gov (United States)

    He, Peiyan; Wang, Henghui; Luo, Jianyong; Yan, Yong; Chen, Zhongwen

    2018-05-23

    Foodborne disease caused by Vibrio parahaemolyticus is a serious public health problem in many countries. Molecular typing has a great scientific significance and application value for epidemiological research of V. parahaemolyticus. In this study, a real-time PCR with melting curve analysis was established for molecular typing of V. parahaemolyticus. Eighteen large variably presented gene clusters (LVPCs) of V. parahaemolyticus which have different distributions in the genome of different strains were selected as targets. Primer pairs of 18 LVPCs were distributed into three tubes. To validate this newly developed assay, we tested 53 Vibrio parahaemolyticus strains, which were classified in 13 different types. Furthermore, cluster analysis using NTSYS PC 2.02 software could divide 53 V. parahaemolyticus strains into six clusters at a relative similarity coefficient of 0.85. This method is fast, simple, and conveniently for molecular typing of V. parahaemolyticus.

  12. Molecular characterization of Giardia psittaci by multilocus sequence analysis.

    Science.gov (United States)

    Abe, Niichiro; Makino, Ikuko; Kojima, Atsushi

    2012-12-01

    Multilocus sequence analyses targeting small subunit ribosomal DNA (SSU rDNA), elongation factor 1 alpha (ef1α), glutamate dehydrogenase (gdh), and beta giardin (β-giardin) were performed on Giardia psittaci isolates from three Budgerigars (Melopsittacus undulates) and four Barred parakeets (Bolborhynchus lineola) kept in individual households or imported from overseas. Nucleotide differences and phylogenetic analyses at four loci indicate the distinction of G. psittaci from the other known Giardia species: Giardia muris, Giardia microti, Giardia ardeae, and Giardia duodenalis assemblages. Furthermore, G. psittaci was related more closely to G. duodenalis than to the other known Giardia species, except for G. microti. Conflicting signals regarded as "double peaks" were found at the same nucleotide positions of the ef1α in all isolates. However, the sequences of the other three loci, including gdh and β-giardin, which are known to be highly variable, from all isolates were also mutually identical at every locus. They showed no double peaks. These results suggest that double peaks found in the ef1α sequences are caused not by mixed infection with genetically different G. psittaci isolates but by allelic sequence heterogeneity (ASH), which is observed in diplomonad lineages including G. duodenalis. No sequence difference was found in any G. psittaci isolates at the gdh and β-giardin, suggesting that G. psittaci is indeed not more diverse genetically than other Giardia species. This report is the first to provide evidence related to the genetic characteristics of G. psittaci obtained using multilocus sequence analysis. Copyright © 2012 Elsevier B.V. All rights reserved.

  13. Compound-Specific Isotope Analysis of Diesel Fuels in a Forensic Investigation

    Science.gov (United States)

    Muhammad, Syahidah; Frew, Russell; Hayman, Alan

    2015-02-01

    Compound-specific isotope analysis (CSIA) offers great potential as a tool to provide chemical evidence in a forensic investigation. Many attempts to trace environmental oil spills were successful where isotopic values were particularly distinct. However, difficulties arise when a large data set is analyzed and the isotopic differences between samples are subtle. In the present study, discrimination of diesel oils involved in a diesel theft case was carried out to infer the relatedness of the samples to potential source samples. This discriminatory analysis used a suite of hydrocarbon diagnostic indices, alkanes, to generate carbon and hydrogen isotopic data of the compositions of the compounds which were then processed using multivariate statistical analyses to infer the relatedness of the data set. The results from this analysis were put into context by comparing the data with the δ13C and δ2H of alkanes in commercial diesel samples obtained from various locations in the South Island of New Zealand. Based on the isotopic character of the alkanes, it is suggested that diesel fuels involved in the diesel theft case were distinguishable. This manuscript shows that CSIA when used in tandem with multivariate statistical analysis provide a defensible means to differentiate and source-apportion qualitatively similar oils at the molecular level. This approach was able to overcome confounding challenges posed by the near single-point source of origin i.e. the very subtle differences in isotopic values between the samples.

  14. Compound-Specific Isotope Analysis of Diesel Fuels in a Forensic Investigation

    Directory of Open Access Journals (Sweden)

    Syahidah Akmal Muhammad

    2015-02-01

    Full Text Available Compound-specific isotope analysis (CSIA offers great potential as a tool to provide chemical evidence in a forensic investigation. Many attempts to trace environmental oil spills were successful where isotopic values were particularly distinct. However, difficulties arise when a large data set is analyzed and the isotopic differences between samples are subtle. In the present study, discrimination of diesel oils involved in a diesel theft case was carried out to infer the relatedness of the samples to potential source samples. This discriminatory analysis used a suite of hydrocarbon diagnostic indices, alkanes, to generate carbon and hydrogen isotopic data of the compositions of the compounds which were then processed using multivariate statistical analyses to infer the relatedness of the data set. The results from this analysis were put into context by comparing the data with the δ13C and δ2H of alkanes in commercial diesel samples obtained from various locations in the South Island of New Zealand. Based on the isotopic character of the alkanes, it is suggested that diesel fuels involved in the diesel theft case were distinguishable. This manuscript shows that CSIA when used in tandem with multivariate statistical analysis provide a defensible means to differentiate and source-apportion qualitatively similar oils at the molecular level. This approach was able to overcome confounding challenges posed by the near single-point source of origin i.e. the very subtle differences in isotopic values between the samples.

  15. Compound-specific isotope analysis of diesel fuels in a forensic investigation.

    Science.gov (United States)

    Muhammad, Syahidah A; Frew, Russell D; Hayman, Alan R

    2015-01-01

    Compound-specific isotope analysis (CSIA) offers great potential as a tool to provide chemical evidence in a forensic investigation. Many attempts to trace environmental oil spills were successful where isotopic values were particularly distinct. However, difficulties arise when a large data set is analyzed and the isotopic differences between samples are subtle. In the present study, discrimination of diesel oils involved in a diesel theft case was carried out to infer the relatedness of the samples to potential source samples. This discriminatory analysis used a suite of hydrocarbon diagnostic indices, alkanes, to generate carbon and hydrogen isotopic data of the compositions of the compounds which were then processed using multivariate statistical analyses to infer the relatedness of the data set. The results from this analysis were put into context by comparing the data with the δ(13)C and δ(2)H of alkanes in commercial diesel samples obtained from various locations in the South Island of New Zealand. Based on the isotopic character of the alkanes, it is suggested that diesel fuels involved in the diesel theft case were distinguishable. This manuscript shows that CSIA when used in tandem with multivariate statistical analysis provide a defensible means to differentiate and source-apportion qualitatively similar oils at the molecular level. This approach was able to overcome confounding challenges posed by the near single-point source of origin, i.e., the very subtle differences in isotopic values between the samples.

  16. Molecular cloning and expression analysis of the sucrose transporter gene family from Theobroma cacao L.

    Science.gov (United States)

    Li, Fupeng; Wu, Baoduo; Qin, Xiaowei; Yan, Lin; Hao, Chaoyun; Tan, Lehe; Lai, Jianxiong

    2014-08-10

    In this study, we performed cloning and expression analysis of six putative sucrose transporter genes, designated TcSUT1, TcSUT2, TcSUT3, TcSUT4, TcSUT5 and TcSUT6, from the cacao genotype 'TAS-R8'. The combination of cDNA and genomic DNA sequences revealed that the cacao SUT genes contained exon numbers ranging from 1 to 14. The average molecular mass of all six deduced proteins was approximately 56 kDa (range 52 to 66 kDa). All six proteins were predicted to exhibit typical features of sucrose transporters with 12 trans-membrane spanning domains. Phylogenetic analysis revealed that TcSUT2 and TcSUT4 belonged to Group 2 SUT and Group 4 SUT, respectively, and the other TcSUT proteins were belonging to Group 1 SUT. Real-time PCR was conducted to investigate the expression pattern of each member of the SUT family in cacao. Our experiment showed that TcSUT1 was expressed dominantly in pods and that, TcSUT3 and TcSUT4 were highly expressed in both pods and in bark with phloem. Within pods, TcSUT1 and TcSUT4 were expressed more in the seed coat and seed from the pod enlargement stage to the ripening stage. TcSUT5 expression sharply increased to its highest expression level in the seed coat during the ripening stage. Expression pattern analysis indicated that TcSUT genes may be associated with photoassimilate transport into developing seeds and may, therefore, have an impact on seed production. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. Flurbiprofen–antioxidant mutual prodrugs as safer nonsteroidal anti-inflammatory drugs: synthesis, pharmacological investigation, and computational molecular modeling

    Directory of Open Access Journals (Sweden)

    Ashraf Z

    2016-07-01

    prodrugs at all times of assessment. The results of ulcerogenic activity showed that all prodrugs produced less GI irritation than flurbiprofen. Molecular docking and simulation studies were carried out with cyclooxygenase (COX-1 and COX-2 proteins, and it was observed that our prodrugs have more potential to selectively bind to COX-2 than to COX-1. It is concluded that the synthesized prodrugs have promising pharmacological activities with reduced GI adverse effects than the parent drug. Keywords: flurbiprofen prodrugs, natural antioxidants, molecular docking, molecular dynamic simulation, pharmacological investigation, NSAIDs

  18. Automated Analysis and Classification of Histological Tissue Features by Multi-Dimensional Microscopic Molecular Profiling.

    Directory of Open Access Journals (Sweden)

    Daniel P Riordan

    Full Text Available Characterization of the molecular attributes and spatial arrangements of cells and features within complex human tissues provides a critical basis for understanding processes involved in development and disease. Moreover, the ability to automate steps in the analysis and interpretation of histological images that currently require manual inspection by pathologists could revolutionize medical diagnostics. Toward this end, we developed a new imaging approach called multidimensional microscopic molecular profiling (MMMP that can measure several independent molecular properties in situ at subcellular resolution for the same tissue specimen. MMMP involves repeated cycles of antibody or histochemical staining, imaging, and signal removal, which ultimately can generate information analogous to a multidimensional flow cytometry analysis on intact tissue sections. We performed a MMMP analysis on a tissue microarray containing a diverse set of 102 human tissues using a panel of 15 informative antibody and 5 histochemical stains plus DAPI. Large-scale unsupervised analysis of MMMP data, and visualization of the resulting classifications, identified molecular profiles that were associated with functional tissue features. We then directly annotated H&E images from this MMMP series such that canonical histological features of interest (e.g. blood vessels, epithelium, red blood cells were individually labeled. By integrating image annotation data, we identified molecular signatures that were associated with specific histological annotations and we developed statistical models for automatically classifying these features. The classification accuracy for automated histology labeling was objectively evaluated using a cross-validation strategy, and significant accuracy (with a median per-pixel rate of 77% per feature from 15 annotated samples for de novo feature prediction was obtained. These results suggest that high-dimensional profiling may advance the

  19. Molecular and biochemical analysis of symbiotic plant receptor kinase complexes

    Energy Technology Data Exchange (ETDEWEB)

    Cook, Douglas R; Riely, Brendan K

    2010-09-01

    -localize (i.e., the flotillin FLOT4) with symbiotic receptor-like proteins. As controls for TAP tag analysis we have generated protein isoforms that carry fluorescent domains (translational fusions to GFP) and these have been used to establish the subcellular location and dynamics of two symbiotic receptors, LYK3 and DMI2. Both proteins localize to membrane microdomains, or putative lipid rafts, and display dynamic behavior following elicitation with the Nod factor ligand. Finally, mass spectrometry of interacting proteins is yielding lists of candidate proteins that we are poised to test using semi-high throughput RNAi technology and Tnt1 knockout collections in Medicago truncatula.

  20. Genetic influences on attention deficit hyperactivity disorder symptoms from age 2 to 3: A quantitative and molecular genetic investigation

    Directory of Open Access Journals (Sweden)

    Saudino Kimberly J

    2010-12-01

    Full Text Available Abstract Background A twin study design was used to assess the degree to which additive genetic variance influences ADHD symptom scores across two ages during infancy. A further objective in the study was to observe whether genetic association with a number of candidate markers reflects results from the quantitative genetic analysis. Method We have studied 312 twin pairs at two time-points, age 2 and age 3. A composite measure of ADHD symptoms from two parent-rating scales: The Child Behavior Checklist/1.5 - 5 years (CBCL hyperactivity scale and the Revised Rutter Parent Scale for Preschool Children (RRPSPC was used for both quantitative and molecular genetic analyses. Results At ages 2 and 3 ADHD symptoms are highly heritable (h2 = 0.79 and 0.78, respectively with a high level of genetic stability across these ages. However, we also observe a significant level of genetic change from age 2 to age 3. There are modest influences of non-shared environment at each age independently (e2 = 0.22 and 0.21, respectively, with these influences being largely age-specific. In addition, we find modest association signals in DAT1 and NET1 at both ages, along with suggestive specific effects of 5-HTT and DRD4 at age 3. Conclusions ADHD symptoms are heritable at ages 2 and 3. Additive genetic variance is largely shared across these ages, although there are significant new effects emerging at age 3. Results from our genetic association analysis reflect these levels of stability and change and, more generally, suggest a requirement for consideration of age-specific genotypic effects in future molecular studies.