WorldWideScience

Sample records for surface marker analysis

  1. A comparison of surface marker analysis and FAB classification in acute myeloid leukemia

    NARCIS (Netherlands)

    van der Reijden, H. J.; van Rhenen, D. J.; Lansdorp, P. M.; van't Veer, M. B.; Langenhuijsen, M. M.; Engelfriet, C. P.; von dem Borne, A. E.

    1983-01-01

    Surface marker analysis with rosette tests and a large panel of xenoantisera and monoclonal antibodies was done on the malignant cells of 55 patients with acute myeloid leukemia (AML). The diagnosis was made on morphological and cytochemical grounds, and the leukemias were classified according to

  2. Quantitative studies of rhubarb using quantitative analysis of multicomponents by single marker and response surface methodology.

    Science.gov (United States)

    Sun, Jiachen; Wu, Yueting; Dong, Shengjie; Li, Xia; Gao, Wenyuan

    2017-10-01

    In this work, we developed a novel approach to evaluate the contents of bioactive components in rhubarb. The present method was based on the quantitative analysis of multicomponents by a single-marker and response surface methodology approaches. The quantitative analysis of multicomponents by a single-marker method based on high-performance liquid chromatography coupled with photodiode array detection was developed and applied to determine the contents of 12 bioactive components in rhubarb. No significant differences were found in the results from the quantitative analysis of multicomponents by a single-marker and the external standard method. In order to maximize the extraction of 12 bioactive compounds in rhubarb, the ultrasonic-assisted extraction conditions were obtained by the response surface methodology coupled with Box-Behnken design. According to the obtained results, we showed that the optimal conditions would be as follows: proportion of ethanol/water 74.39%, solvent-to-solid ratio 24.07:1 v/w, extraction time 51.13 min, and extraction temperature 63.61°C. The analytical scheme established in this research should be a reliable, convenient, and appropriate method for quantitative determination of bioactive compounds in rhubarb. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. A Software for the Analysis of Scripted Dialogs Based on Surface Markers

    Directory of Open Access Journals (Sweden)

    Sylvain Delisle

    2003-04-01

    Full Text Available Most information systems that deal with natural language texts do not tolerate much deviation from their idealized and simplified model of language. Spoken dialog is notoriously ungrammatical however. Because the MAREDI project focuses in particular on the automatic analysis of scripted dialogs, we needed to develop a robust capacity to analyze transcribed spoken language. This paper presents the main elements of our approach, which is based on exploiting surface markers as the best route to the semantics of the conversation modelled. We highlight the foundations of our particular conversational model and give an overview of the MAREDI system. The latter consists of three key modules, which are 1 a connectionist network to recognise speech acts, 2 a robust syntactic parser, and 3 a semantic analyzer. These three modules are fully implemented in Prolog and C++ and have been packaged into an integrated software.

  4. Comparative analysis of the expression of surface markers on fibroblasts and fibroblast-like cells isolated from different human tissues.

    Science.gov (United States)

    Lupatov, A Yu; Vdovin, A S; Vakhrushev, I V; Poltavtseva, R A; Yarygin, K N

    2015-02-01

    Expression of 20 surface markers was analyzed in cultures of mesenchymal stromal cells of the umbilical cord, fibroblasts from adult and fetal human skin, and fibroblast-like cells of fetal liver was analyzed by fl ow cytometry. The studied cultures did not express hemopoietic cells markers, but were positive for CD73, CD90, and CD105 markers recommended by the International Society of Cell Therapy for the identification of the multipotent mesenchymal stromal cells. Fetal liver fibroblast-like cells were positive for CD54; this marker was absent in skin fibroblast cultures, but was expressed by umbilical cord mesenchymal stromal cells. Further study of these cells revealed a minor subpopulation of cells co-expressing CD24 and CD90 or CD24 and CD54. We hypothesized that these cells probably participate in epithelial mesenchymal transition.

  5. Efficient Isolation and Quantitative Proteomic Analysis of Cancer Cell Plasma Membrane Proteins for Identification of Metastasis-Associated Cell Surface Markers

    DEFF Research Database (Denmark)

    Lund, Rikke; Leth-Larsen, Rikke; Jensen, Ole N

    2009-01-01

    Cell surface membrane proteins are involved in central processes such as cell signaling, cell-cell interactions, ion and solute transport, and they seem to play a pivotal role in several steps of the metastatic process of cancer cells. The low abundance and hydrophobic nature of cell surface...... membrane proteins complicate their purification and identification by MS. We used two isogenic cell lines with opposite metastatic capabilities in nude mice to optimize cell surface membrane protein purification and to identify potential novel markers of metastatic cancer. The cell surface membrane...... peptides of which 622 (300 at SL80) were membrane proteins. The quantitative proteomic analysis identified 16 cell surface proteins as potential markers of the ability of breast cancer cells to form distant metastases....

  6. Surface markers. [Quarterly report, January 1--June 30, 1995

    Energy Technology Data Exchange (ETDEWEB)

    Andrews, W.B.

    1995-08-01

    This research examined information on natural phenomena and human activities to ultimately recommend specific sites for surface markers to warn future generations of the potential hazards of disposed waste. Literature pertaining to previous marker designs was reviewed and summarized. This literature primarily addressed the recommendations of a consultant team for developing a marker system to warn future generations about radioactive waste (WIPP, New Mexico). Literature on archeological markers (e.g., Nazca lines in Peru, pyramids) and their durability was also covered. Application to Yucca Mountain is discussed; sites for possible placement of surface markers are considered.

  7. HLA-F is a surface marker on activated lymphocytes.

    Science.gov (United States)

    Lee, Ni; Ishitani, Akiko; Geraghty, Daniel E

    2010-08-01

    Of the three nonclassical class I antigens expressed in humans, HLA-F has been least characterized with regard to expression or function. In this study, we examined HLA-F expression focusing on lymphoid cells, where our previous work with homologous cell lines had demonstrated surface HLA-F expression. HLA-F protein expression was observed by Western blot analysis in all resting lymphocytes, including B cells, T cells, NK cells, and monocytes, all of which lacked surface expression in the resting state. Upon activation, using a variety of methods to activate different lymphocyte subpopulations, all cell types that expressed HLA-F intracellularly showed an induction of surface HLA-F protein. An examination of peripheral blood from individuals genetically deficient for TAP and tapasin expression demonstrated the same activation expression profiles for HLA-F,but with altered kinetics post-activation. Further analysis of CD41+CD25+1 Treg showed that HLA-F was not upregulated on the major fraction of these cells when they were activated,whereas CD41+CD25- T cells showed strong expression of surface HLA-F when activated under identical conditions. These findings are discussed with regard to possible functions for HLA-F and its potential clinical use as a marker of an activated immune response.

  8. Intersection tests for single marker QTL analysis can be more powerful than two marker QTL analysis

    Directory of Open Access Journals (Sweden)

    Doerge RW

    2003-06-01

    Full Text Available Abstract Background It has been reported in the quantitative trait locus (QTL literature that when testing for QTL location and effect, the statistical power supporting methodologies based on two markers and their estimated genetic map is higher than for the genetic map independent methodologies known as single marker analyses. Close examination of these reports reveals that the two marker approaches are more powerful than single marker analyses only in certain cases. Simulation studies are a commonly used tool to determine the behavior of test statistics under known conditions. We conducted a simulation study to assess the general behavior of an intersection test and a two marker test under a variety of conditions. The study was designed to reveal whether two marker tests are always more powerful than intersection tests, or whether there are cases when an intersection test may outperform the two marker approach. We present a reanalysis of a data set from a QTL study of ovariole number in Drosophila melanogaster. Results Our simulation study results show that there are situations where the single marker intersection test equals or outperforms the two marker test. The intersection test and the two marker test identify overlapping regions in the reanalysis of the Drosophila melanogaster data. The region identified is consistent with a regression based interval mapping analysis. Conclusion We find that the intersection test is appropriate for analysis of QTL data. This approach has the advantage of simplicity and for certain situations supplies equivalent or more powerful results than a comparable two marker test.

  9. Ultraviolet light depletes surface markers of Langerhans cells

    International Nuclear Information System (INIS)

    Aberer, W.; Schuler, G.; Stingl, G.; Hoenigsmann, H.; Wolff, K.

    1981-01-01

    This report defines the influence of ultraviolet light (UV) on Langerhans cells (LC). Human volunteers and hairless mice (Swiss ha/ha) were exposed to various single and/or cumulative doses of either UV-A, UV-B, or UV-A plus small amounts of UV-B (UV-A (+B)). 24 hr after the last irradiation, morphology of the entire epidermis was evaluated by both light and electron microscopy while LC, in addition, were tested for expression of specific histochemical (ATPase) and functional immunological markers (Ia antigens). In both men and mice, cumulative doses of either 80-120 J/cm2 UV-A (+B) or 1-2 X 100 J/cm2 UV-A resulted in a dramatic reduction of cells exhibiting ATPase and Ia-reactivity. In the UV-B spectrum, single doses of 60-80 mJ/cm2 produced a virtually complete elimination of LC membrane markers. By contrast, pemphigus antigens of keratinocytes were unaffected by these energy doses. Electron microscopy revealed cellular damage of some LC after UV-doses which produce a virtually complete abolition of LC membrane markers. At certain dose ranges (15-30 mJ/cm2 UV-B and 1 x 40 to 2 x 100 J/cm2 UV-A) LC were the only epidermal cells to display morphological damage at the ultrastructural level whereas higher doses affected all epidermal cells. The finding that LC surface markers and to a lesser extent the cells themselves are particularly susceptible to UV irradiation has important implications in view of previous findings that LC are potent stimulators of antigen-specific and allogeneic T cell activation. UV-induced alteration of LC plasma membrane integrity may represent a tool to manipulate adverse immune reactions involving the epidermis

  10. Use of wand markers on the pelvis in three dimensional gait analysis

    DEFF Research Database (Denmark)

    Smith, Martin; Curtis, Derek; Bencke, Jesper

    2013-01-01

    During clinical gait analysis, surface markers are placed over the anterior superior iliac spines (ASIS) of the pelvis. However, this can be problematic in overweight or obese subjects, where excessive adipose tissue can obscure the markers and prevent accurate tracking. A novel solution to this ......During clinical gait analysis, surface markers are placed over the anterior superior iliac spines (ASIS) of the pelvis. However, this can be problematic in overweight or obese subjects, where excessive adipose tissue can obscure the markers and prevent accurate tracking. A novel solution...... to this problem has previously been proposed and tested on a limited sample of healthy, adult subjects. This involves use of wand markers on the pelvis, to virtually recreate the ASIS markers. The method was tested here on 20 typical subjects presenting for clinical gait analysis (adults and children, including...

  11. LOGISTIC REGRESSION ANALYSIS WITH STANDARDIZED MARKERS.

    Science.gov (United States)

    Huang, Ying; Pepe, Margaret S; Feng, Ziding

    2013-09-01

    Two different approaches to analysis of data from diagnostic biomarker studies are commonly employed. Logistic regression is used to fit models for probability of disease given marker values while ROC curves and risk distributions are used to evaluate classification performance. In this paper we present a method that simultaneously accomplishes both tasks. The key step is to standardize markers relative to the non-diseased population before including them in the logistic regression model. Among the advantages of this method are: (i) ensuring that results from regression and performance assessments are consistent with each other; (ii) allowing covariate adjustment and covariate effects on ROC curves to be handled in a familiar way, and (iii) providing a mechanism to incorporate important assumptions about structure in the ROC curve into the fitted risk model. We develop the method in detail for the problem of combining biomarker datasets derived from multiple studies, populations or biomarker measurement platforms, when ROC curves are similar across data sources. The methods are applicable to both cohort and case-control sampling designs. The dataset motivating this application concerns Prostate Cancer Antigen 3 (PCA3) for diagnosis of prostate cancer in patients with or without previous negative biopsy where the ROC curves for PCA3 are found to be the same in the two populations. Estimated constrained maximum likelihood and empirical likelihood estimators are derived. The estimators are compared in simulation studies and the methods are illustrated with the PCA3 dataset.

  12. From analysis to surface

    DEFF Research Database (Denmark)

    Bemman, Brian; Meredith, David

    In recent years, a significant body of research has focused on developing algorithms for computing analyses of mu- sical works automatically from encodings of these works' surfaces [3,4,7,10,11]. The quality of the output of such analysis algorithms is typically evaluated by comparing it with a “......In recent years, a significant body of research has focused on developing algorithms for computing analyses of mu- sical works automatically from encodings of these works' surfaces [3,4,7,10,11]. The quality of the output of such analysis algorithms is typically evaluated by comparing...... an effective (i.e., comput- able), correct and complete description of some aspect of the structure of the music. Generating the surface struc- ture of a piece from an analysis in this manner serves as a proof of the analysis' correctness, effectiveness and com- pleteness. We present a reductive analysis...

  13. Cell surface differences of Naegleria fowleri and Naegleria lovaniensis exposed with surface markers.

    Science.gov (United States)

    González-Robles, Arturo; Castañón, Guadalupe; Cristóbal-Ramos, Ana Ruth; Hernández-Ramírez, Verónica Ivonne; Omaña-Molina, Maritza; Martínez-Palomo, Adolfo

    2007-12-01

    Differences in the distribution of diverse cell surface coat markers were found between Naegleria fowleri and Naegleria lovaniensis. The presence of carbohydrate-containing components in the cell coat of the two species was detected by selective staining with ruthenium red and alcian blue. Using both markers, N. fowleri presented a thicker deposit than N. lovaniensis. The existence of exposed mannose or glucose residues was revealed by discriminatory agglutination with the plant lectin Concanavalin A. These sugar residues were also visualized at the cell surface of these parasites either by transmission electron microscopy or by fluorescein-tagged Concanavalin A. Using this lectin cap formation was induced only in N. fowleri. The anionic sites on the cell surface detected by means of cationized ferritin were more apparent in N. fowleri. Biotinylation assays confirmed that even though the two amoebae species have some analogous plasma membrane proteins, there is a clear difference in their composition.

  14. Quantitative Hydrocarbon Surface Analysis

    Science.gov (United States)

    Douglas, Vonnie M.

    2000-01-01

    The elimination of ozone depleting substances, such as carbon tetrachloride, has resulted in the use of new analytical techniques for cleanliness verification and contamination sampling. The last remaining application at Rocketdyne which required a replacement technique was the quantitative analysis of hydrocarbons by infrared spectrometry. This application, which previously utilized carbon tetrachloride, was successfully modified using the SOC-400, a compact portable FTIR manufactured by Surface Optics Corporation. This instrument can quantitatively measure and identify hydrocarbons from solvent flush of hardware as well as directly analyze the surface of metallic components without the use of ozone depleting chemicals. Several sampling accessories are utilized to perform analysis for various applications.

  15. Established cell surface markers efficiently isolate highly overlapping populations of skeletal muscle satellite cells by fluorescence-activated cell sorting.

    Science.gov (United States)

    Maesner, Claire C; Almada, Albert E; Wagers, Amy J

    2016-01-01

    Fluorescent-activated cell sorting (FACS) has enabled the direct isolation of highly enriched skeletal muscle stem cell, or satellite cell, populations from postnatal tissue. Several distinct surface marker panels containing different positively selecting surface antigens have been used to distinguish muscle satellite cells from other non-myogenic cell types. Because functional and transcriptional heterogeneity is known to exist within the satellite cell population, a direct comparison of results obtained in different laboratories has been complicated by a lack of clarity as to whether commonly utilized surface marker combinations select for distinct or overlapping subsets of the satellite cell pool. This study therefore sought to evaluate phenotypic and functional overlap among popular satellite cell sorting paradigms. Utilizing a transgenic Pax7 -zsGreen reporter mouse, we compared the overlap between the fluorescent signal of canonical paired homeobox protein 7 ( Pax7 ) expressing satellite cells to cells identified by combinations of surface markers previously published for satellite cells isolation. We designed two panels for mouse skeletal muscle analysis, each composed of markers that exclude hematopoietic and stromal cells (CD45, CD11b, Ter119, CD31, and Sca1), combined with previously published antibody clones recognizing surface markers present on satellite cells (β1-integrin/CXCR4, α7-integrin/CD34, and Vcam1). Cell populations were comparatively analyzed by flow cytometry and FACS sorted for functional assessment of myogenic activity. Consistent with prior reports, each of the commonly used surface marker schemes evaluated here identified a highly enriched satellite cell population, with 89-90 % positivity for Pax7 expression based on zsGreen fluorescence. Distinct surface marker panels were also equivalent in their ability to identify the majority of the satellite cell pool, with 90-93 % of all Pax7-zsGreen positive cells marked by each of the

  16. 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) ...

  17. Markers

    Science.gov (United States)

    Healthy Schools Network, Inc., 2011

    2011-01-01

    Dry erase whiteboards come with toxic dry erase markers and toxic cleaning products. Dry erase markers labeled "nontoxic" are not free of toxic chemicals and can cause health problems. Children are especially vulnerable to environmental health hazards; moreover, schools commonly have problems with indoor air pollution, as they are more densely…

  18. Hepatitis B Viral Markers in Surface Antigen Negative Blood Donors ...

    African Journals Online (AJOL)

    Of the 20 who were anti-HBc positive, seven had tattoo/traditional marks on their body and one had previous history of blood transfusion. Conclusion: This study has shown that some potential blood units containing HBV are being transfused to patients unknowingly by screening for HBsAg only. Screening for other markers ...

  19. Analogy of ISSR and RAPD markers for comparative analysis of ...

    African Journals Online (AJOL)

    Analogy of ISSR and RAPD markers for comparative analysis of genetic diversity among different Jatropha curcas genotypes. S Gupta, M Srivastava, GP Mishra, PK Naik, RS Chauhan, SK Tiwari, M Kumar, R Singh ...

  20. Automated vehicle guidance using discrete reference markers. [road surface steering techniques

    Science.gov (United States)

    Johnston, A. R.; Assefi, T.; Lai, J. Y.

    1979-01-01

    Techniques for providing steering control for an automated vehicle using discrete reference markers fixed to the road surface are investigated analytically. Either optical or magnetic approaches can be used for the sensor, which generates a measurement of the lateral offset of the vehicle path at each marker to form the basic data for steering control. Possible mechanizations of sensor and controller are outlined. Techniques for handling certain anomalous conditions, such as a missing marker, or loss of acquisition, and special maneuvers, such as u-turns and switching, are briefly discussed. A general analysis of the vehicle dynamics and the discrete control system is presented using the state variable formulation. Noise in both the sensor measurement and in the steering servo are accounted for. An optimal controller is simulated on a general purpose computer, and the resulting plots of vehicle path are presented. Parameters representing a small multipassenger tram were selected, and the simulation runs show response to an erroneous sensor measurement and acquisition following large initial path errors.

  1. Cell surface carbohydrates as prognostic markers in human carcinomas

    DEFF Research Database (Denmark)

    Dabelsteen, Erik

    1996-01-01

    Tumour development is usually associated with changes in cell surface carbohydrates. These are often divided into changes related to terminal carbohydrate structures, which include incomplete synthesis and modification of normally existing carbohydrates, and changes in the carbohydrate core struc...

  2. meta-analysis of Serum Tumor Markers in Lung Cancer

    Directory of Open Access Journals (Sweden)

    Xianfeng LU

    2010-12-01

    Full Text Available Background and objective The detection of serum tumor markers is of great value for early diagnosis of lung cancer. The aim of this study is to summarize the clinic significance characteristics of serum markers contributing to the detection of lung cancer. Methods References about serum markers of lung cancer were estimated using meta-analysis method. 712 references which included more than 20 cases, 20 controls, the serum markers of 52 832 patients with malignancies and 32 037 patients as controls were evaluated. Results Overall the detection of 13 markers play a significant part in lung cancer diagnosis. The sensitivity of CEA, CA125, CYFRA21-1, TPA, SCCAg, DKK1, NSE, ProGRP in the patients’ serum with lung cancer were 47.50%, 50.11%, 57.00%, 50.93%, 49.00%, 69.50%, 39.73%, 51.48% and the specificity were 92.34%, 80.19%, 90.16%, 88.41%, 91.07%, 92.20%, 89.11%, 94.89%. In the combined analysis of tumor markers: the sensitivity, specificity of NSE+ProGRP were 88.90% and 72.82% in diagnosis of small cell lung cancer, respectively. In diagnosis of squamous corcinoma, the sensitivity and specificity of TSGF+SCCAg+CYFRA21-1 were 95.30% and 74.20%. The the sensitivity and specificity of CA153+Ferrtin+CEA were 91.90% and 44.00% in diagnosis of lung cancer. Conclusion Although the assay of tumor markers in serum is useful for diagnosis of early lung cancer, the sensitivity and specificity are low. Combined detection of these tumor markers could increase sensitivity and specificity.

  3. Transference of surface markers in X-ray, CT- and MR-imaging

    International Nuclear Information System (INIS)

    Grevelhoerster, T.; Poetter, R.; Prott, F.J.; Dittrich, M.

    1995-01-01

    By using pharmacological capsules and plastic tubes filled with oily contrast medium contraining iodine (Lipiodol; Byk Gulden), marking aids were developed which can be seen in similar definite limits within the framework of MRI-, CT- and conventional X-ray-Imaging. A method to view these new, artificial markers in combination with individual, anatomical landmarks is introduced. The marking aid/surface marker, fixed on anatomical reference structures on the skin, does not result in an additional burden for the patient. The new, artificial markers are also useful for making other structures recognizable, such as anatomical relation lines, center of the portal and edges in planning imaging for radiotherapy treatments and are used as leading and reference structures to compare localisation and extent of lesions in X-ray-, CT- and MRI. Marking aids/surface markers do not have to be changed in different imaging methods. (orig./MG) [de

  4. Surface analysis the principal techniques

    CERN Document Server

    Vickerman, John C

    2009-01-01

    This completely updated and revised second edition of Surface Analysis: The Principal Techniques, deals with the characterisation and understanding of the outer layers of substrates, how they react, look and function which are all of interest to surface scientists. Within this comprehensive text, experts in each analysis area introduce the theory and practice of the principal techniques that have shown themselves to be effective in both basic research and in applied surface analysis. Examples of analysis are provided to facilitate the understanding of this topic and to show readers how they c

  5. Analysis of Molecular Marker Compounds from Vitexagnus cactus ...

    African Journals Online (AJOL)

    Analysis of Molecular Marker Compounds from Vitexagnus cactus Using the High Performance Liquid Chromatography and Evaporative Light Scattering Detector ... ELS detector is regarded as a valuable alternative to UV detection system for identification of the compounds that do not contain strong chromophores.

  6. 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.

  7. Two small lymphocyte subpopulations in human peripheral blood. I. Purification and surface marker profiles

    DEFF Research Database (Denmark)

    Hokland, M; Hokland, P; Heron, I

    1978-01-01

    By means of simple rosette sedimentation methods two subsets from human peripheral blood lymphocytes have been isolated: (1) (E, Fc)- and (2) (E, Ig)-. The first subset was obtained by centrifuging suspensions of macrophage-depleted PBL in which E and EA rosettes had been allowed to form...... simultaneously. The dominant marker of these E- Fc- cells was surface Ig, and during 4 days of culture this population did not alter its surface markers. Subset 2 was obtained in two ways following rosette centrifugation with AET-treated SRBC and rabbit anti-human Ig-coated autologous RBC. This 'Null cell...

  8. Gait Analysis Using Floor Markers and Inertial Sensors

    Directory of Open Access Journals (Sweden)

    Young Soo Suh

    2012-02-01

    Full Text Available In this paper, a gait analysis system which estimates step length and foot angles is proposed. A measurement unit, which consists of a camera and inertial sensors, is installed on a shoe. When the foot touches the floor, markers are recognized by the camera to obtain the current position and attitude. A simple planar marker with 4,096 different codes is used. These markers printed on paper are placed on the floor. When the foot is moving off the floor, the position and attitude are estimated using an inertial navigation algorithm. For accurate estimation, a smoother is proposed, where vision information and inertial sensor data are combined. Through experiments, it is shown that the proposed system can both track foot motion and estimate step length.

  9. Surface Markers for Chondrogenic Determination: A Highlight of Synovium-Derived Stem Cells

    Directory of Open Access Journals (Sweden)

    Douglas D. Campbell

    2012-11-01

    Full Text Available Cartilage tissue engineering is a promising field in regenerative medicine that can provide substantial relief to people suffering from degenerative cartilage disease. Current research shows the greatest chondrogenic potential for healthy articular cartilage growth with minimal hypertrophic differentiation to be from mesenchymal stem cells (MSCs of synovial origin. These stem cells have the capacity for differentiation into multiple cell lineages related to mesenchymal tissue; however, evidence exists for cell surface markers that specify a greater potential for chondrogenesis than other differentiation fates. This review will examine relevant literature to summarize the chondrogenic differentiation capacities of tested synovium-derived stem cell (SDSC surface markers, along with a discussion about various other markers that may hold potential, yet require further investigation. With this information, a potential clinical benefit exists to develop a screening system for SDSCs that will produce the healthiest articular cartilage possible.

  10. Proteomic analysis of fetal programming-related obesity markers.

    Science.gov (United States)

    Lee, Ji Hye; Yoo, Jae Young; You, Young-Ah; Kwon, Woo-Sung; Lee, Sang Mi; Pang, Myung-Geol; Kim, Young Ju

    2015-08-01

    The objectives of this study were to analyze fetal programming in rat brain using proteomic analysis and to identify fetal programming-related obesity markers. Sprague-Dawley rats were divided into four feeding groups: (i) the Ad Libitum (AdLib)/AdLib group was given a normal diet during pregnancy and the lactation period; (ii) the AdLib/maternal food restriction group (FR) was subjected to 50% FR during the lactation period; (iii) the FR/AdLib group was subjected to 50% FR during pregnancy; and (iv) the FR/FR group was subjected to 50% FR during pregnancy and the lactation period. Offspring from each group were sacrificed at 3 weeks of age and whole brains were dissected. To obtain a maximum number of protein markers related to obesity, 2DE and Pathway Studio bioinformatics analysis were performed. The identities of the markers among the selected and candidate proteins were confirmed by Western blotting and immunohistochemistry. Proteomic and bioinformatics analyses revealed that expression of ubiquitin carboxy-terminal hydrolase L1 (UCHL1) and Secernin 1 (SCRN1) were significantly different in the FR/AdLib group compared with the AdLib/AdLib group for both male and female offspring. These findings suggest that UCHL1 and SCRN1 may be used as fetal programming-related obesity markers. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Two small lymphocyte subpopulations in human peripheral blood. I. Purification and surface marker profiles

    DEFF Research Database (Denmark)

    Hokland, M; Hokland, P; Heron, I

    1978-01-01

    By means of simple rosette sedimentation methods two subsets from human peripheral blood lymphocytes have been isolated: (1) (E, Fc)- and (2) (E, Ig)-. The first subset was obtained by centrifuging suspensions of macrophage-depleted PBL in which E and EA rosettes had been allowed to form simultan......By means of simple rosette sedimentation methods two subsets from human peripheral blood lymphocytes have been isolated: (1) (E, Fc)- and (2) (E, Ig)-. The first subset was obtained by centrifuging suspensions of macrophage-depleted PBL in which E and EA rosettes had been allowed to form...... simultaneously. The dominant marker of these E- Fc- cells was surface Ig, and during 4 days of culture this population did not alter its surface markers. Subset 2 was obtained in two ways following rosette centrifugation with AET-treated SRBC and rabbit anti-human Ig-coated autologous RBC. This 'Null cell...... population' was shown to be highly variable as judged by the surface markers applied after 4 days of culture, and it is suggested that Null cells contain a number of immature lymphoid cells that may acquire their surface marker during culture. It is concluded that the methods described for purification...

  12. Stereotactic core needle breast biopsy marker migration: An analysis of factors contributing to immediate marker migration.

    Science.gov (United States)

    Jain, Ashali; Khalid, Maria; Qureshi, Muhammad M; Georgian-Smith, Dianne; Kaplan, Jonah A; Buch, Karen; Grinstaff, Mark W; Hirsch, Ariel E; Hines, Neely L; Anderson, Stephan W; Gallagher, Katherine M; Bates, David D B; Bloch, B Nicolas

    2017-11-01

    To evaluate breast biopsy marker migration in stereotactic core needle biopsy procedures and identify contributing factors. This retrospective study analyzed 268 stereotactic biopsy markers placed in 263 consecutive patients undergoing stereotactic biopsies using 9G vacuum-assisted devices from August 2010-July 2013. Mammograms were reviewed and factors contributing to marker migration were evaluated. Basic descriptive statistics were calculated and comparisons were performed based on radiographically-confirmed marker migration. Of the 268 placed stereotactic biopsy markers, 35 (13.1%) migrated ≥1 cm from their biopsy cavity. Range: 1-6 cm; mean (± SD): 2.35 ± 1.22 cm. Of the 35 migrated biopsy markers, 9 (25.7%) migrated ≥3.5 cm. Patient age, biopsy pathology, number of cores, and left versus right breast were not associated with migration status (P> 0.10). Global fatty breast density (P= 0.025) and biopsy in the inner region of breast (P = 0.031) were associated with marker migration. Superior biopsy approach (P= 0.025), locally heterogeneous breast density, and t-shaped biopsy markers (P= 0.035) were significant for no marker migration. Multiple factors were found to influence marker migration. An overall migration rate of 13% supports endeavors of research groups actively developing new biopsy marker designs for improved resistance to migration. • Breast biopsy marker migration is documented in 13% of 268 procedures. • Marker migration is affected by physical, biological, and pathological factors. • Breast density, marker shape, needle approach etc. affect migration. • Study demonstrates marker migration prevalence; marker design improvements are needed.

  13. Message development for surface markers at the Hanford Radwaste Disposal sites

    Energy Technology Data Exchange (ETDEWEB)

    Kaplan, M.F.

    1984-12-31

    At the Hanford Reservation in Washington, there are sites which received liquid and solid transuranic wastes from the late 1940`s until 1970. Rockwell Hanford Operations (Rockwell) is investigating the feasibility of several options for the permanent disposal of these wastes. One option is to stabilize the wastes in their present locations and to add barriers to minimize water infiltration and root penetration into the wastes. This report forms part of the project to develop a marking system for transuranic wastes on the Hanford Reservation. The focus of this report is the development of the message system to appear on the surface markers. A logical framework is developed to deduce what is required by the message system. Alternatives for each message component are evaluated and justification is provided for the choice of each component. The components are then laid out on the surface marker to provide a legible, comprehensible message system. The surface markers are tall, standing monoliths which ring the perimeter of each disposal area. Based on the logical framework, it is recommended that three domains of representation -- symbols, pictures, and language -- be used in the message system. The warning symbol chosen for the message system is the radiation trefoil. Two other options were considered, including the warning symbol developed by the Human Interference Task Force for a high-level waste repository. The trefoil was preferred because of the widespread usage and international acceptance which is already enjoys.

  14. Ideal, nonideal, and no-marker variables: The confirmatory factor analysis (CFA) marker technique works when it matters.

    Science.gov (United States)

    Williams, Larry J; O'Boyle, Ernest H

    2015-09-01

    A persistent concern in the management and applied psychology literature is the effect of common method variance on observed relations among variables. Recent work (i.e., Richardson, Simmering, & Sturman, 2009) evaluated 3 analytical approaches to controlling for common method variance, including the confirmatory factor analysis (CFA) marker technique. Their findings indicated significant problems with this technique, especially with nonideal marker variables (those with theoretical relations with substantive variables). Based on their simulation results, Richardson et al. concluded that not correcting for method variance provides more accurate estimates than using the CFA marker technique. We reexamined the effects of using marker variables in a simulation study and found the degree of error in estimates of a substantive factor correlation was relatively small in most cases, and much smaller than error associated with making no correction. Further, in instances in which the error was large, the correlations between the marker and substantive scales were higher than that found in organizational research with marker variables. We conclude that in most practical settings, the CFA marker technique yields parameter estimates close to their true values, and the criticisms made by Richardson et al. are overstated. (c) 2015 APA, all rights reserved).

  15. A method of surface marker location optimization for tumor motion estimation in lung stereotactic body radiation therapy

    International Nuclear Information System (INIS)

    Lu, Bo; Park, Justin C.; Fan, Qiyong; Kahler, Darren; Liu, Chihray; Chen, Yunmei

    2015-01-01

    Purpose: Accurately localizing lung tumor localization is essential for high-precision radiation therapy techniques such as stereotactic body radiation therapy (SBRT). Since direct monitoring of tumor motion is not always achievable due to the limitation of imaging modalities for treatment guidance, placement of fiducial markers on the patient’s body surface to act as a surrogate for tumor position prediction is a practical alternative for tracking lung tumor motion during SBRT treatments. In this work, the authors propose an innovative and robust model to solve the multimarker position optimization problem. The model is able to overcome the major drawbacks of the sparse optimization approach (SOA) model. Methods: The principle-component-analysis (PCA) method was employed as the framework to build the authors’ statistical prediction model. The method can be divided into two stages. The first stage is to build the surrogate tumor matrix and calculate its eigenvalues and associated eigenvectors. The second stage is to determine the “best represented” columns of the eigenvector matrix obtained from stage one and subsequently acquire the optimal marker positions as well as numbers. Using 4-dimensional CT (4DCT) and breath hold CT imaging data, the PCA method was compared to the SOA method with respect to calculation time, average prediction accuracy, prediction stability, noise resistance, marker position consistency, and marker distribution. Results: The PCA and SOA methods which were both tested were on all 11 patients for a total of 130 cases including 4DCT and breath-hold CT scenarios. The maximum calculation time for the PCA method was less than 1 s with 64 752 surface points, whereas the average calculation time for the SOA method was over 12 min with 400 surface points. Overall, the tumor center position prediction errors were comparable between the two methods, and all were less than 1.5 mm. However, for the extreme scenarios (breath hold), the

  16. The surface elevation table: marker horizon method for measuring wetland accretion and elevation dynamics

    Science.gov (United States)

    Callaway, John C.; Cahoon, Donald R.; Lynch, James C.

    2014-01-01

    Tidal wetlands are highly sensitive to processes that affect their elevation relative to sea level. The surface elevation table–marker horizon (SET–MH) method has been used to successfully measure these processes, including sediment accretion, changes in relative elevation, and shallow soil processes (subsidence and expansion due to root production). The SET–MH method is capable of measuring changes at very high resolution (±millimeters) and has been used worldwide both in natural wetlands and under experimental conditions. Marker horizons are typically deployed using feldspar over 50- by 50-cm plots, with replicate plots at each sampling location. Plots are sampled using a liquid N2 cryocorer that freezes a small sample, allowing the handling and measurement of soft and easily compressed soils with minimal compaction. The SET instrument is a portable device that is attached to a permanent benchmark to make high-precision measurements of wetland surface elevation. The SET instrument has evolved substantially in recent decades, and the current rod SET (RSET) is widely used. For the RSET, a 15-mm-diameter stainless steel rod is pounded into the ground until substantial resistance is achieved to establish a benchmark. The SET instrument is attached to the benchmark and leveled such that it reoccupies the same reference plane in space, and pins lowered from the instrument repeatedly measure the same point on the soil surface. Changes in the height of the lowered pins reflect changes in the soil surface. Permanent or temporary platforms provide access to SET and MH locations without disturbing the wetland surface.

  17. Prospective Isolation of Murine and Human Bone Marrow Mesenchymal Stem Cells Based on Surface Markers

    Directory of Open Access Journals (Sweden)

    Yo Mabuchi

    2013-01-01

    Full Text Available Mesenchymal stem cells (MSCs are currently defined as multipotent stromal cells that undergo sustained in vitro growth and can give rise to cells of multiple mesenchymal lineages, such as adipocytes, chondrocytes, and osteoblasts. The regenerative and immunosuppressive properties of MSCs have led to numerous clinical trials exploring their utility for the treatment of a variety of diseases (e.g., acute graft-versus-host disease, Crohn’s disease, multiple sclerosis, osteoarthritis, and cardiovascular diseases including heart failure and myocardial infarction. On the other hand, conventionally cultured MSCs reflect heterogeneous populations that often contain contaminating cells due to the significant variability in isolation methods and the lack of specific MSC markers. This review article focuses on recent developments in the MSC research field, with a special emphasis on the identification of novel surface markers for the in vivo localization and prospective isolation of murine and human MSCs. Furthermore, we discuss the physiological importance of MSC subtypes in vivo with specific reference to data supporting their contribution to HSC niche homeostasis. The isolation of MSCs using selective markers (combination of PDGFRα and Sca-1 is crucial to address the many unanswered questions pertaining to these cells and has the potential to enhance their therapeutic potential enormously.

  18. Marker development

    Energy Technology Data Exchange (ETDEWEB)

    Adams, M.R.

    1987-05-01

    This report is to discuss the marker development for radioactive waste disposal sites. The markers must be designed to last 10,000 years, and place no undue burdens on the future generations. Barriers cannot be constructed that preclude human intrusion. Design specifications for surface markers will be discussed, also marker pictograms will also be covered.

  19. Marker list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available Database Site Policy | Contact Us Marker list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ... ...switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods

  20. Parentage Reconstruction in Eucalyptus nitens Using SNPs and Microsatellite Markers: A Comparative Analysis of Marker Data Power and Robustness.

    Science.gov (United States)

    Telfer, Emily J; Stovold, Grahame T; Li, Yongjun; Silva-Junior, Orzenil B; Grattapaglia, Dario G; Dungey, Heidi S

    2015-01-01

    Pedigree reconstruction using molecular markers enables efficient management of inbreeding in open-pollinated breeding strategies, replacing expensive and time-consuming controlled pollination. This is particularly useful in preferentially outcrossed, insect pollinated Eucalypts known to suffer considerable inbreeding depression from related matings. A single nucleotide polymorphism (SNP) marker panel consisting of 106 markers was selected for pedigree reconstruction from the recently developed high-density Eucalyptus Infinium SNP chip (EuCHIP60K). The performance of this SNP panel for pedigree reconstruction in open-pollinated progenies of two Eucalyptus nitens seed orchards was compared with that of two microsatellite panels with 13 and 16 markers respectively. The SNP marker panel out-performed one of the microsatellite panels in the resolution power to reconstruct pedigrees and out-performed both panels with respect to data quality. Parentage of all but one offspring in each clonal seed orchard was correctly matched to the expected seed parent using the SNP marker panel, whereas parentage assignment to less than a third of the expected seed parents were supported using the 13-microsatellite panel. The 16-microsatellite panel supported all but one of the recorded seed parents, one better than the SNP panel, although there was still a considerable level of missing and inconsistent data. SNP marker data was considerably superior to microsatellite data in accuracy, reproducibility and robustness. Although microsatellites and SNPs data provide equivalent resolution for pedigree reconstruction, microsatellite analysis requires more time and experience to deal with the uncertainties of allele calling and faces challenges for data transferability across labs and over time. While microsatellite analysis will continue to be useful for some breeding tasks due to the high information content, existing infrastructure and low operating costs, the multi-species SNP resource

  1. Parentage Reconstruction in Eucalyptus nitens Using SNPs and Microsatellite Markers: A Comparative Analysis of Marker Data Power and Robustness.

    Directory of Open Access Journals (Sweden)

    Emily J Telfer

    Full Text Available Pedigree reconstruction using molecular markers enables efficient management of inbreeding in open-pollinated breeding strategies, replacing expensive and time-consuming controlled pollination. This is particularly useful in preferentially outcrossed, insect pollinated Eucalypts known to suffer considerable inbreeding depression from related matings. A single nucleotide polymorphism (SNP marker panel consisting of 106 markers was selected for pedigree reconstruction from the recently developed high-density Eucalyptus Infinium SNP chip (EuCHIP60K. The performance of this SNP panel for pedigree reconstruction in open-pollinated progenies of two Eucalyptus nitens seed orchards was compared with that of two microsatellite panels with 13 and 16 markers respectively. The SNP marker panel out-performed one of the microsatellite panels in the resolution power to reconstruct pedigrees and out-performed both panels with respect to data quality. Parentage of all but one offspring in each clonal seed orchard was correctly matched to the expected seed parent using the SNP marker panel, whereas parentage assignment to less than a third of the expected seed parents were supported using the 13-microsatellite panel. The 16-microsatellite panel supported all but one of the recorded seed parents, one better than the SNP panel, although there was still a considerable level of missing and inconsistent data. SNP marker data was considerably superior to microsatellite data in accuracy, reproducibility and robustness. Although microsatellites and SNPs data provide equivalent resolution for pedigree reconstruction, microsatellite analysis requires more time and experience to deal with the uncertainties of allele calling and faces challenges for data transferability across labs and over time. While microsatellite analysis will continue to be useful for some breeding tasks due to the high information content, existing infrastructure and low operating costs, the multi

  2. Dyes as bifunctional markers of DNA hybridization on surfaces and mutation detection.

    Science.gov (United States)

    García-Mendiola, Tania; Cerro, María Ramos; López-Moreno, José María; Pariente, Félix; Lorenzo, Encarnación

    2016-10-01

    The interaction of small molecules with DNA has found diagnostic and therapeutic applications. In this work, we propose the use of two different dyes, in particular Azure A and Safranine, as bifunctional markers of on-surface DNA hybridization and potent tools for screening of specific gene mutations directly in real DNA PCR amplicons extracted from blood cells. By combining spectroscopic and electrochemical methods we demonstrate that both dyes can interact with single and double stranded DNA to a different extent, allowing reliable hybridization detection. From these data, we have also elucidated the nature of the interaction. We conclude that the binding mode is fundamentally intercalative with an electrostatic component. The dye fluorescence allows their use as nucleic acid stains for the detection of on-surfaces DNA hybridization. Its redox activity is exploited in the development of selective electrochemical DNA biosensors. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Clinical use of computed tomography and surface markers to assist internal fixation within the equine hoof.

    Science.gov (United States)

    Gasiorowski, Janik C; Richardson, Dean W

    2015-02-01

    To describe clinical use of computed tomography (CT) and hoof surface markers to facilitate internal fixation within the confines of the hoof wall. Retrospective case series. Horses (n = 16) that had CT-guided internal fixation of the distal phalanx (DP) or distal sesamoid bone (DSB). Drill bit entry point and direction were planned from CT image series performed on hooves with grids of barium paste dots at proposed entry and projected exit sites. Post-implantation CT images were obtained to check screw position and length as well as fracture reduction. Imaging, reduction, and surgical and general anesthesia times were evaluated. Outcome was recorded. Screw position and length were considered near optimal in all horses, with no consequential malposition of bits or screws. Fracture reduction was evident in all cases. Preoperative planning times (at least 2 CT image acquisitions and grid creation) ranged from 10 to 20 minutes. Surgery time ranged from 45 to 90 minutes (mean, 61 minutes) and general anesthesia time ranged from 115 to 220 minutes (mean, 171 minutes). The combination of CT and surface marker grids allowed accurate positioning of screws in clinical DP and DSB fractures. The technique was simple and rapid. An aiming device is useful for the technique. © Copyright 2014 by The American College of Veterinary Surgeons.

  4. Surface analysis and techniques in biology

    CERN Document Server

    Smentkowski, Vincent S

    2014-01-01

    This book highlights state-of-the-art surface analytical instrumentation, advanced data analysis tools, and the use of complimentary surface analytical instrumentation to perform a complete analysis of biological systems.

  5. An Efficiency Analysis of Augmented Reality Marker Recognition Algorithm

    Directory of Open Access Journals (Sweden)

    Kurpytė Dovilė

    2014-05-01

    Full Text Available The article reports on the investigation of augmented reality system which is designed for identification and augmentation of 100 different square markers. Marker recognition efficiency was investigated by rotating markers along x and y axis directions in range from −90° to 90°. Virtual simulations of four environments were developed: a an intense source of light, b an intense source of light falling from the left side, c the non-intensive light source falling from the left side, d equally falling shadows. The graphics were created using the OpenGL graphics computer hardware interface; image processing was programmed in C++ language using OpenCV, while augmented reality was developed in Java programming language using NyARToolKit. The obtained results demonstrate that augmented reality marker recognition algorithm is accurate and reliable in the case of changing lighting conditions and rotational angles - only 4 % markers were unidentified. Assessment of marker recognition efficiency let to propose marker classification strategy in order to use it for grouping various markers into distinct markers’ groups possessing similar recognition properties.

  6. A CONTRASTIVE ANALYSIS OF ARABIC AND ENGLISH NOUN PLURAL MARKERS

    Directory of Open Access Journals (Sweden)

    Aliyatul Himmah

    2015-01-01

    Full Text Available This paper is attempting to explore the plural markers in both Arabic and English. The data collected qualitatively are sorted to meet the scope of this paper. Through contrastive analysis, it is discovered that there are numerous significant differences rather than similarities in terms of syllable count start, patterns of plural nouns in relation to gender, regularity, regular vs irregular plural and internal vowel change. Moreover, Arabic has some uniqueness in its plural marking system. Being well informed on all of these might pave the way for second or foreign language learners to comprehensively understand the plural marking system in Arabic and English.   Tulisan ini mencoba untuk mengeksplorasi penanda jamak dalam bahasa Arab dan bahasa Inggris. Data yang dikumpulkan secara kualitatif diurutkan untuk memenuhi cakupan makalah ini. Melalui analisis kontrastif, ditemukan banyak perbedaan yang signifikan daripada kesamaan dalam segi jumlah awal suku kata, pola kata benda jamak dalam kaitannya dengan gender, keteraturan dan ketidakteraturan jamak, serta perubahan vokal. Selain itu, bahasa Arab memiliki beberapa keunikan dalam sistem menandai jamaknya. Memahami informasi hal tersebut dengan baik mungkin memudahkan pembelajar bahasa kedua atau asing untuk memahami secara komprehensif sistem penanda jamak dalam bahasa Arab dan Inggris

  7. Results of a diabetic retinopathy screening. Risk markers analysis.

    Science.gov (United States)

    Ancochea, G; Martín Sánchez, M D

    2016-01-01

    To identify risk markers for retinopathy in patients from our geographic area, and to compare them with those published in other studies. To design a screening interval strategy, taking into account these results, and compare it with intervals suggested in published studies. Cross-sectional observational study on 383 diabetic patients with no previous retinopathy diagnosis, who were screened for diabetic retinopathy. An analysis was made on the possible association between patient factors and presence of retinopathy. A greater probability for finding retinopathy in diabetic patients was associated to insulin treatment in our study, with a statistical significance level of 95%. In patients with less than 10year onset of their diabetes, only mild retinopathy without macular oedema was found. Insulin treatment and time of onset of diabetes should be taken into account when designing efficient screening strategies for diabetic retinopathy. Copyright © 2015 Sociedad Española de Oftalmología. Published by Elsevier España, S.L.U. All rights reserved.

  8. 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.

  9. Analysis of morphological markers of chromosomal instability in ascitic fluid.

    Science.gov (United States)

    Tyagi, Ruchita; Dey, Pranab; Uppal, Radha; Rajwanshi, Arvind

    2015-10-01

    Chromosomal instability (CI) plays a major role in the carcinogenesis. Micronuclei, nuclear budding, chromatin bridges,and multipolar mitoses are the morphological markers of CI and have never been studied in routine cytological specimens. Aims of the study is to analyze the significance of morphological markers of CI in malignant and benign ascitic fluid smears. A total of sixty benign and 40 malignant ascitic fluid samples were selected for this study. All the cases with malignant ascitic fluid showed histopathological evidence of malignancy in ovary and omentum. Chromatin bridges, multipolar mitosis (MPM), micronuclei and nuclear budding were counted in 1000 cells in representative May Grunwald Giemsa (MGG) stained smears. The CI markers were correlated with the cytological diagnosis of effusion. The mean number of micronuclei, nuclear budding, chromatin bridge and multipolar mitoses found in malignant effusions were 13.2611.79, 10.1067.07, 2.5362.67, 1.964.5, respectively. The mean number of micronuclei, nuclear budding, anaphase bridges, and MPM found in benign effusion cases were 0.566761.07934, 0.516761.33, 0.66760.25, and 0, respectively. The student t test showed significant differences between malignant and benign ascitic fluid samples for each marker of CI. This is the first comprehensive study of morphological markers of CI in ascitic fluid smears. This study has shown strong correlation between markers of CI and cytological diagnosis of malignancy. In future, the knowledge of these markers can be applied to diagnose malignancy in suspected cases of effusion in difficult situations. © 2015 Wiley Periodicals, Inc.

  10. The Cell Surface Markers Expression in Postmenopausal Women and Relation to Obesity and Bone Status

    Directory of Open Access Journals (Sweden)

    Mira Horváthová

    2017-07-01

    Full Text Available The age-related changes and hormonal deprivation in postmenopausal women are associated with the immune response alteration. The excessive fat accumulation, local and systemic inflammation may lead to dysregulation in immune function and relevant health problems, including obesity and osteoporosis. We analyzed the expression of cell surface markers in the venous blood specimens, stained with fluorophores-conjugated monoclonal antibodies and analysed by multicolour flow cytometry. The significant changes of cytotoxic, naive, and memory T-lymphocytes, plasmacytoid dendritic cells (DCs were in postmenopausal women versus fertile women. Body mass index (BMI affected markedly the cell surface expression of CD265/RANK. Osteoporosis is linked to reduced percentage of plasmacytoid DCs, and elevated natural Treg cells (p < 0.05. The confounding factors such as women age, BMI, bone mineral density (BMD, waist size and tissue fat affect the expression of RANK on myeloid DCs and CD40L on T-lymphocytes that might be the immunophenotypic modulators after menopause.

  11. Intra-operative prostate motion tracking using surface markers for robot-assisted laparoscopic radical prostatectomy

    Science.gov (United States)

    Esteghamatian, Mehdi; Sarkar, Kripasindhu; Pautler, Stephen E.; Chen, Elvis C. S.; Peters, Terry M.

    2012-02-01

    Radical prostatectomy surgery (RP) is the gold standard for treatment of localized prostate cancer (PCa). Recently, emergence of minimally invasive techniques such as Laparoscopic Radical Prostatectomy (LRP) and Robot-Assisted Laparoscopic Radical Prostatectomy (RARP) has improved the outcomes for prostatectomy. However, it remains difficult for the surgeons to make informed decisions regarding resection margins and nerve sparing since the location of the tumor within the organ is not usually visible in a laparoscopic view. While MRI enables visualization of the salient structures and cancer foci, its efficacy in LRP is reduced unless it is fused into a stereoscopic view such that homologous structures overlap. Registration of the MRI image and peri-operative ultrasound image using a tracked probe can potentially be exploited to bring the pre-operative information into alignment with the patient coordinate system during the procedure. While doing so, prostate motion needs to be compensated in real-time to synchronize the stereoscopic view with the pre-operative MRI during the prostatectomy procedure. In this study, a point-based stereoscopic tracking technique is investigated to compensate for rigid prostate motion so that the same motion can be applied to the pre-operative images. This method benefits from stereoscopic tracking of the surface markers implanted over the surface of the prostate phantom. The average target registration error using this approach was 3.25+/-1.43mm.

  12. Neospora caninum surface antigen (p40) is a potential diagnostic marker for cattle neosporosis.

    Science.gov (United States)

    He, Pengfei; Li, Jianhua; Gong, Pengtao; Liu, Chengwu; Zhang, Guocai; Yang, Ju; Tuo, Wenbin; Yang, Bintong; Zhang, Xichen

    2013-05-01

    Neospora caninum is an intracellular protozoan that infects domestic and wild canids as well as many warm-blooded animals as shown by the isolation of viable parasites. The effectiveness of diagnostic tests for detecting specific antibodies against N. caninum is hampered by potential cross-reaction with other Coccidia. So, there is currently an urgent need for a sensitive and specific diagnostic assay for detecting N. caninum in animals. The N. caninum 40-kD surface antigen (p40), similar to NcSAG1 and NcSRS2, was shown to belong to surface antigen super family and thus represents an excellent marker for the diagnosis of neosporosis. In order to test the hypothesis, recombinant Ncp40 (rNcp40) was expressed in Escherichia coli, and an indirect ELISA test was developed using recombinant NCp40 antigen for N. caninum serodiagnosis. The antigen used in this study did not have cross-reactivity with anti-Toxoplasma gondii serum. Anti-p40 antibodies were detected by ELISA in the sera of Yellow cattle and were compared with (IFAT). Optimal sensitivity and specificity (98.2 and 98.6 %) were identified by IFAT. Additionally, 37 positive sera of T. gondii were detected and there was no significant difference with the negative serum of N. caninum. The rNcp40 ELISA developed here provides a specific and sensitive assay for detecting neosporosis in cattle.

  13. SSR markers associated to early leaf spot disease resistance through selective genotyping and single marker analysis in groundnut (Arachis hypogaea L.

    Directory of Open Access Journals (Sweden)

    Adama Zongo

    2017-09-01

    Full Text Available Groundnut (Arachis hypogaea L. is an important oilseed and food crop of the world. Breeding for disease resistance is one of major objectives in groundnut breeding. Early leaf spot (ELS is one of the major destructive diseases worldwide and in West Africa, particularly in Burkina Faso causing significant yield losses. Conventional breeding approaches have been employed to develop improved varieties resistant to ELS. Molecular dissection of resistance traits using QTL analysis can improve the efficiency of resistance breeding. In the present study, an ELS susceptible genotype QH243C and an ELS resistant genotype NAMA were crossed and the F2 population genotypic and F3 progenies phenotypic data were used for marker-trait association analysis. Parents were surveyed with 179 simple sequence repeat (SSR markers out of which 103 SSR markers were found to be polymorphic between the parents. These polymorphic markers were utilized to genotype the F2 population followed by marker-trait analysis through single marker analysis (SMA and selective genotyping of the population using 23 resistant and 23 susceptible genotypes. The SMA revealed 13 markers while the selective genotyping method identified 8 markers associated with ELS resistance. Four markers (GM1911, GM1883, GM1000 and Seq13E09 were found common between the two trait mapping methods. These four markers could be employed in genomics-assisted breeding for selection of ELS resistant genotypes in groundnut breeding.

  14. Global Analysis of Minimal Surfaces

    CERN Document Server

    Dierkes, Ulrich; Tromba, Anthony J

    2010-01-01

    Many properties of minimal surfaces are of a global nature, and this is already true for the results treated in the first two volumes of the treatise. Part I of the present book can be viewed as an extension of these results. For instance, the first two chapters deal with existence, regularity and uniqueness theorems for minimal surfaces with partially free boundaries. Here one of the main features is the possibility of 'edge-crawling' along free parts of the boundary. The third chapter deals with a priori estimates for minimal surfaces in higher dimensions and for minimizers of singular integ

  15. Gap Surface Plasmon Waveguide Analysis

    DEFF Research Database (Denmark)

    Nielsen, Michael Grøndahl; Bozhevolnyi, Sergey I.

    2014-01-01

    Plasmonic waveguides supporting gap surface plasmons (GSPs) localized in a dielectric spacer between metal films are investigated numerically and the waveguiding properties at telecommunication wavelengths are presented. Especially, we emphasize that the mode confinement can advantageously be con...

  16. Thin film surface reconstruction analysis

    International Nuclear Information System (INIS)

    Imperatori, P.

    1996-01-01

    The study of the atomic structure of surfaces and interfaces is a fundamental step in the knowledge and the development of new materials. Among the several surface-sensitive techniques employed to characterise the atomic arrangements, grazing incidence x-ray diffraction (GIXD) is one of the most powerful. With a simple data treatment, based on the kinematical theory, and using the classical methods of x-ray bulk structure determination, it gives the atomic positions of atoms at a surface or an interface and the atomic displacements of subsurface layers for a complete determination of the structure. In this paper the main features of the technique will be briefly reviewed and selected of application to semiconductor and metal surfaces will be discussed

  17. Thin film surface reconstruction analysis

    Energy Technology Data Exchange (ETDEWEB)

    Imperatori, P. [CNR, Monterotondo Stazione, Rome (Italy). Istituto di Chimica dei materiali

    1996-09-01

    The study of the atomic structure of surfaces and interfaces is a fundamental step in the knowledge and the development of new materials. Among the several surface-sensitive techniques employed to characterise the atomic arrangements, grazing incidence x-ray diffraction (GIXD) is one of the most powerful. With a simple data treatment, based on the kinematical theory, and using the classical methods of x-ray bulk structure determination, it gives the atomic positions of atoms at a surface or an interface and the atomic displacements of subsurface layers for a complete determination of the structure. In this paper the main features of the technique will be briefly reviewed and selected of application to semiconductor and metal surfaces will be discussed.

  18. Segregation analysis of microsatellite (SSR) markers in sugarcane polyploids

    Science.gov (United States)

    Although the microsatellite (SSR) DNA markers have been extensively used in sugarcane breeding research, little is known about its inheritance mechanism. To address this problem, a high throughput molecular genotyping experiment was conducted on 964 single pollen grains and a 288-self progeny S1 map...

  19. Analysis of genetic diversity in linseed using AFLP markers | Wakjira ...

    African Journals Online (AJOL)

    Linseed (Linum usitatissimum L.) is the second most important oilseed crop in the highlands of Ethiopia where it has been cultivated for its valuable seed-oil since antiquity. Sixty accessions of linseed predominantly from Ethiopia were analysed using amplified fragment length polymorphism (AFLP) markers to assess their ...

  20. FY11 Report on Metagenome Analysis using Pathogen Marker Libraries

    Energy Technology Data Exchange (ETDEWEB)

    Gardner, Shea N. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Allen, Jonathan E. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); McLoughlin, Kevin S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Slezak, Tom [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2011-06-02

    A method, sequence library, and software suite was invented to rapidly assess whether any member of a pre-specified list of threat organisms or their near neighbors is present in a metagenome. The system was designed to handle mega- to giga-bases of FASTA-formatted raw sequence reads from short or long read next generation sequencing platforms. The approach is to pre-calculate a viral and a bacterial "Pathogen Marker Library" (PML) containing sub-sequences specific to pathogens or their near neighbors. A list of expected matches comparing every bacterial or viral genome against the PML sequences is also pre-calculated. To analyze a metagenome, reads are compared to the PML, and observed PML-metagenome matches are compared to the expected PML-genome matches, and the ratio of observed relative to expected matches is reported. In other words, a 3-way comparison among the PML, metagenome, and existing genome sequences is used to quickly assess which (if any) species included in the PML is likely to be present in the metagenome, based on available sequence data. Our tests showed that the species with the most PML matches correctly indicated the organism sequenced for empirical metagenomes consisting of a cultured, relatively pure isolate. These runs completed in 1 minute to 3 hours on 12 CPU (1 thread/CPU), depending on the metagenome and PML. Using more threads on the same number of CPU resulted in speed improvements roughly proportional to the number of threads. Simulations indicated that detection sensitivity depends on both sequencing coverage levels for a species and the size of the PML: species were correctly detected even at ~0.003x coverage by the large PMLs, and at ~0.03x coverage by the smaller PMLs. Matches to true positive species were 3-4 orders of magnitude higher than to false positives. Simulations with short reads (36 nt and ~260 nt) showed that species were usually detected for metagenome coverage above 0.005x and coverage in the PML above 0.05x, and

  1. 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

    : 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...

  2. Isolation of Pancreatic Progenitor Cells with the Surface Marker of Hematopoietic Stem Cells

    Directory of Open Access Journals (Sweden)

    Fengxia Ma

    2012-01-01

    Full Text Available To isolate pancreatic progenitor cells with the surface markers of hematopoietic stem cells, the expression of stem cell antigen (Sca-1 and c-Kit and the coexpression of them with pancreatic duodenal homeobox-1 (PDX-1, neurogenin 3 (Ngn3, and insulin were examined in murine embryonic pancreas. Then different pancreatic cell subpopulations were isolated by magnet-activated cell sorting. Isolated cells were cultured overnight in hanging drops. When cells formed spheres, they were laid on floating filters at the air/medium interface. With this new culture system, pancreatic progenitor cells were induced to differentiate to endocrine and exocrine cells. It was shown that c-Kit and Sca-1 were expressed differently in embryonic pancreas at 12.5, 15.5, and 17.5 days of gestation. The expression of c-Kit and Sca-1 was the highest at 15.5 days of gestation. c-Kit rather than Sca-1 coexpressed with PDX-1, Ngn3, and insulin. Cells differentiated from c-Kit-positive cells contained more insulin-producing cells and secreted more insulin in response to glucose stimulation than that from c-Kit-negative cells. These results suggested that c-Kit could be used to isolate pancreatic progenitor cells and our new culture system permitted pancreatic progenitor cells to differentiate to mature endocrine cells.

  3. Biological Markers for Alcohol Withdrawal Seizures: A Retrospective Analysis

    OpenAIRE

    Karagülle, Deniz; Heberlein, Annemarie; Wilhelm, Julia; Frieling, Helge; Kornhuber, Johannes; Bleich, Stefan; Hillemacher, Thomas

    2013-01-01

    Aims: Alcohol withdrawal seizures (AWS) are among the most important possible complications during the detoxification treatment of alcohol-dependent patients. Pharmacological therapy is often used during detoxification, but can cause dangerous side effects [Eur Addict Res 2010;16:179– 184]. In separate studies several biological markers have been described as being associated with AWS risk. We investigated the role of homocysteine (HCT), carbohydrate-deficient transferrin (CDT) and prolactin ...

  4. (SSR) markers for analysis of genetic diversity in African rice ...

    African Journals Online (AJOL)

    Bonny Oloka

    2015-05-06

    May 6, 2015 ... 161/161. 194/196. 32 WAC 116. AfricaRice. 116/122. 121/121. 182/182. 146/146. 217/217. 210/210. 157/189. 231/257. 157/157. 174/177. 33 AER-75 ..... Life Technologies Inc., USA. Table 3. Estimated genetic diversity parameters obtained at each locus across 99 genotypes. Marker. No. of Alleles. He. Ho.

  5. In situ surface-enhanced Raman spectroelectrochemical analysis system with a hemin modified nanostructured gold surface.

    Science.gov (United States)

    Yuan, Tao; Le Thi Ngoc, Loan; van Nieuwkasteele, Jan; Odijk, Mathieu; van den Berg, Albert; Permentier, Hjalmar; Bischoff, Rainer; Carlen, Edwin T

    2015-03-03

    An integrated surface-enhanced Raman scattering (SERS) spectroelectrochemical (SEC) analysis system is presented that combines a small volume microfluidic sample chamber (Raman spectroelectrochemistry. The SEC system includes a nanostructured Au surface that serves dual roles as the electrochemical working electrode (WE) and SERS substrate, a microfabricated Pt counter electrode (CE), and an external Ag/AgCl reference electrode (RE). The nanostructured Au WE enables highly sensitive in situ SERS spectroscopy through large and reproducible SERS enhancements, which eliminates the need for resonant wavelength matching of the laser excitation source with the electronic absorption of the target molecule. The new SEC analysis system has the merits of wide applicability to target molecules, small sample volume, and a low detection limit. We demonstrate in situ SERS spectroelectrochemistry measurements of the metalloporphyrin hemin showing shifts of the iron oxidation marker band ν4 with the nanostructured Au working electrode under precise potential control.

  6. Establishment of Relational Model of Congenital Heart Disease Markers and GO Functional Analysis of the Association between Its Serum Markers and Susceptibility Genes

    OpenAIRE

    Liu, Min; Zhao, Luosha; Yuan, Jiaying

    2016-01-01

    Purpose. The purpose of present study was to construct the best screening model of congenital heart disease serum markers and to provide reference for further prevention and treatment of the disease. Methods. Documents from 2006 to 2014 were collected and meta-analysis was used for screening susceptibility genes and serum markers closely related to the diagnosis of congenital heart disease. Data of serum markers were extracted from 80 congenital heart disease patients and 80 healthy controls,...

  7. Surface computing and collaborative analysis work

    CERN Document Server

    Brown, Judith; Gossage, Stevenson; Hack, Chris

    2013-01-01

    Large surface computing devices (wall-mounted or tabletop) with touch interfaces and their application to collaborative data analysis, an increasingly important and prevalent activity, is the primary topic of this book. Our goals are to outline the fundamentals of surface computing (a still maturing technology), review relevant work on collaborative data analysis, describe frameworks for understanding collaborative processes, and provide a better understanding of the opportunities for research and development. We describe surfaces as display technologies with which people can interact directly, and emphasize how interaction design changes when designing for large surfaces. We review efforts to use large displays, surfaces or mixed display environments to enable collaborative analytic activity. Collaborative analysis is important in many domains, but to provide concrete examples and a specific focus, we frequently consider analysis work in the security domain, and in particular the challenges security personne...

  8. Development of a Prognostic Marker for Lung Cancer Using Analysis of Tumor Evolution

    Science.gov (United States)

    2017-08-01

    AWARD NUMBER: W81XWH-15-1-0243 TITLE: Development of a Prognostic Marker for Lung Cancer Using Analysis of Tumor Evolution PRINCIPAL...SUBTITLE 5a. CONTRACT NUMBER Development of a Prognostic Marker for Lung Cancer Using Analysis of Tumor Evolution 5b. GRANT NUMBER 5c. PROGRAM...derive a prognostic classifier. 15. SUBJECT TERMS NSCLC; tumor evolution ; whole exome sequencing 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF

  9. The Cell Surface Structure of Tumor Endothelial Marker 8 (TEM8) is Regulated by the Actin Cytoskeleton

    OpenAIRE

    Yang, Mi Young; Chaudhary, Amit; Seaman, Steven; Dunty, Jill; Stevens, Janine; Elzarrad, Mohammed K.; Frankel, Arthur E.; St. Croix, Brad

    2010-01-01

    Tumor Endothelial Marker 8 (TEM8) is an integrin-like cell surface protein upregulated on tumor blood vessels and a potential vascular target for cancer therapy. Here, we found that the ability of an anti-TEM8 antibody, clone SB5, to recognize the extracellular domain of TEM8 on the cell surface depends on other host-cell factors. By taking advantage of SB5’s ability to distinguish different forms of cell-surface TEM8, we identified alpha-smooth muscle actin and transgelin, an actin binding p...

  10. Identification of circulating fetal cell markers by microarray analysis

    DEFF Research Database (Denmark)

    Brinch, Marie; Hatt, Lotte; Singh, Ripudaman

    2012-01-01

    OBJECTIVE: Different fetal cell types have been found in the maternal blood during pregnancy in the past, but fetal cells are scarce, and the proportions of the different cell types are unclear. The objective of the present study was to identify specific fetal cell markers from fetal cells found...... identified by XY fluorescence in situ hybridization and confirmed by reverse-color fluorescence in situ hybridization were shot off microscope slides by laser capture microdissection. The expression pattern of a subset of expressed genes was compared between fetal cells and maternal blood cells using stem...

  11. Stem Cell Surface Marker Expression Defines Late Stages of Reprogramming to Pluripotency in Human Fibroblasts.

    Science.gov (United States)

    Pomeroy, Jordan E; Hough, Shelley R; Davidson, Kathryn C; Quaas, Alex M; Rees, Jordan A; Pera, Martin F

    2016-07-01

    Our current understanding of the induction of pluripotency by defined factors indicates that this process occurs in discrete stages characterized by specific alterations in the cellular transcriptome and epigenome. However, the final phase of the reprogramming process is incompletely understood. We sought to generate tools to characterize the transition to a fully reprogramed state. We used combinations of stem cell surface markers to isolate colonies emerging after transfection of human fibroblasts with reprogramming factors and then analyzed their expression of genes associated with pluripotency and early germ lineage specification. We found that expression of a subset of these genes, including the cell-cell adhesion molecule CDH3, characterized a late stage in the reprogramming process. Combined live-cell staining with the antibody GCTM-2 and anti-CDH3 during reprogramming identified colonies of cells that showed gene expression patterns very similar to those of embryonic stem cell or established induced pluripotent stem cell lines, and gave rise to stable induced pluripotent stem cell lines at high frequency. Our findings will facilitate studies of the final stages of reprogramming of human cells to pluripotency and will provide a simple means for prospective identification of fully reprogrammed cells. Reprogramming of differentiated cells back to an embryonic pluripotent state has wide ranging applications in understanding and treating human disease. However, how cells traverse the barriers on the journey to pluripotency still is not fully understood. This report describes tools to study the late stages of cellular reprogramming. The findings enable a more precise approach to dissecting the final phases of conversion to pluripotency, a process that is particularly poorly defined. The results of this study also provide a simple new method for the selection of fully reprogrammed cells, which could enhance the efficiency of derivation of cell lines for research

  12. Relationship of CD86 surface marker expression and cytotoxicity on dendritic cells exposed to chemical allergen

    International Nuclear Information System (INIS)

    Hulette, Ben C.; Ryan, Cindy A.; Gildea, Lucy A.; Gerberick, G. Frank

    2005-01-01

    Human peripheral blood-derived dendritic cells (DC) respond to a variety of chemical allergens by up-regulating expression of the co-stimulatory molecule CD86. It has been postulated that this measure might provide the basis for an in vitro alternative approach for the identification of skin sensitizing chemicals. We recently reported that DC, exposed in culture to the highest non-cytotoxic concentrations of various chemical allergens, displayed marginal up-regulation of membrane CD86 expression; the interpretation being that such changes were insufficiently sensitive for the purposes of hazard identification. For the work presented here, immature DC were derived from human monocytes and treated with the chemical allergens 2,4-dinitrobenzenesulfonic acid (DNBS), nickel sulfate (NiSO 4 ), p-phenylenediamine (PPD), Bandrowski's base (BB), hydroquinone (HQ) and propyl gallate (PG) for 48 h at concentrations which induced both no to slight to moderate cytotoxicity. For comparison, DC were treated with the irritants sodium dodecyl sulfate (SDS), benzoic acid (BA), and benzalkonium chloride (BZC) at concentrations resulting in comparable levels of cytotoxicity. CD86 expression, as measured by flow cytometry, was consistently up-regulated (ranging from 162 to 386% control) on DC treated with concentrations of chemical allergens that induced approximately 10-15% cytotoxicity. The irritants BA and BZC did not induce up-regulation of CD86 expression when tested at concentrations that induced similar levels of cytotoxicity. SDS, however, up-regulated CD86 expression to 125-138% of control in 2/4 preparations when tested at concentrations which induced similar toxicity. Our results confirm that chemical allergens up-regulate CD86 expression on blood-derived DC and illustrate further that up-regulation of CD86 surface marker expression is more robust when DC are treated with concentrations of chemical allergen that induce slight to moderate cytotoxicity

  13. Refrigerated storage of platelets initiates changes in platelet surface marker expression and localization of intracellular proteins.

    Science.gov (United States)

    Wood, Ben; Padula, Matthew P; Marks, Denese C; Johnson, Lacey

    2016-10-01

    Platelets (PLTs) are currently stored at room temperature (22°C), which limits their shelf life, primarily due to the risk of bacterial growth. Alternatives to room temperature storage include PLT refrigeration (2-6°C), which inhibits bacterial growth, thus potentially allowing an extension of shelf life. Additionally, refrigerated PLTs appear more hemostatically active than conventional PLTs, which may be beneficial in certain clinical situations. However, the mechanisms responsible for this hemostatic function are not well characterized. The aim of this study was to assess the protein profile of refrigerated PLTs in an effort to understand these functional consequences. Buffy coat PLTs were pooled, split, and stored either at room temperature (20-24°C) or under refrigerated (2-6°C) conditions (n = 8 in each group). PLTs were assessed for changes in external receptor expression and actin filamentation using flow cytometry. Intracellular proteomic changes were assessed using two-dimensional gel electrophoresis and Western blotting. PLT refrigeration significantly reduced the abundance of glycoproteins (GPIb, GPIX, GPIIb, and GPIV) on the external membrane. However, refrigeration resulted in the increased expression of high-affinity integrins (αIIbβ3 and β1) and activation and apoptosis markers (CD62P, CD63, and phosphatidylserine). PLT refrigeration substantially altered the abundance and localization of several cytoskeletal proteins and resulted in an increase in actin filamentation, as measured by phalloidin staining. Refrigerated storage of PLTs induces significant changes in the expression and localization of both surface-expressed and intracellular proteins. Understanding these proteomic changes may help to identify the mechanisms resulting in the refrigeration-associated alterations in PLT function and clearance. © 2016 AABB.

  14. Comparative Analysis of Genetic Diversity and Structure in Rice Using ILP and SSR Markers

    Directory of Open Access Journals (Sweden)

    Ming HUANG

    2010-12-01

    Full Text Available Genetic diversity of 36 rice entries from the United States Department of Agriculture (USDA rice collection was assessed using 103 ILP (intron length polymorphism and 54 SSR (simple sequence repeats markers. A total of 236 and 332 alleles were detected by the ILP and SSR markers, respectively. On average, the SSR markers produced higher polymorphism information content value and number of alleles than the ILP markers. Whereas the Nei's genetic distance measured using the SSR markers was much higher than that measured using the ILP markers. Mantel's test indicated that there was a statistically significant correlation (r=0.827, P<0.001 between the two marker systems. UPGMA clustering based on the ILP and SSR markers resulted in consensus dendrograms. The cophenetic correlation coefficient (r=0.918, 0.878 and 0.924, P<0.001 for the ILP, SSR and combined markers, respectively showed a highly accurate dendrogram represented the genetic distance among these entries. The 36 entries were divided into four groups. Four African Oryza glaberrima accessions were clustered within a distinct group (I, and the remaining entries were separated into three groups (II, III and IV. All the entries could be also clustered into two main groups: One was composed of III and IV, considered as indica group, and the other was composed of I (O. glaberrima and II (japonica-like. Model-based cluster analysis revealed that the japonica-like group maintained very pure ancestry while the indica group shared mixed ancestry, especially for group III, which had seven admixtures sharing from 19.5% to 30.0% of ancestry with group IV (based on SSR markers. It is suggested that ILP and SSR markers could be very useful for the genetic study and breeding in rice.

  15. Clinical Evaluation and Cost-Effectiveness Analysis of Serum Tumor Markers in Lung Cancer

    Directory of Open Access Journals (Sweden)

    Rong Wang

    2013-01-01

    Full Text Available The detection of serum tumor markers is valuable for the early diagnosis of lung cancer. Tumor markers are frequently used for the management of cancer patients. However, single markers are less efficient but marker combinations increase the cost, which is troublesome for clinics. To find an optimal serum marker combination panel that benefits the patients and the medical management system as well, four routine lung cancer serum markers (SCCA, NSE, CEA, and CYFRA21-1 were evaluated individually and in combination. Meanwhile, the costs and effects of these markers in clinical practice in China were assessed by cost-effectiveness analysis. As expected, combinations of these tumor markers improved their sensitivity for lung cancer and different combination panels had their own usefulness. NSE + CEA + CYFRA21-1 was the optimal combination panel with highest Youden’s index (0.64, higher sensitivity (75.76%, and specificity (88.57%, which can aid the clinical diagnosis of lung cancer. Nevertheless, the most cost-effective combination was SCCA + CEA, which can be used to screen the high-risk group.

  16. Surface imaging, portal imaging, and skin marker set-up vs. CBCT for radiotherapy of the thorax and pelvis

    International Nuclear Information System (INIS)

    Pallotta, Stefania; Bucciolini, Marta; Vanzi, Eleonora; Marrazzo, Livia; Simontacchi, Gabriele; Paiar, Fabiola; Ceroti, Marco; Livi, Lorenzo

    2015-01-01

    The aim of this study was to compare surface imaging, portal imaging, and skin marker set-up in radiotherapy of thoracic and pelvic regions, using cone beam computed tomography (CBCT) data as the gold standard. Twenty patients were included in this study. CBCT, surface acquisition (SA), and two orthogonal portal images (PI) were acquired during the first four treatment sessions. Patient set-up corrections, obtained by registering the planning CT with CBCT, were used as the gold standard. Registration results of the PI and SA were evaluated and compared with those obtained with CBCT. The advantage derived from using SA or PI verification systems over a skin marker set-up was also quantified. A statistically significant difference between PI and SA (in favour of PI) was observed in seven patients undergoing treatment of the pelvic region and in two patients undergoing treatment of the thoracic region. The use of SA or PI, compared with a skin marker set-up, improved patient positioning in 50% and 57 % of the thoracic fractions, respectively. For pelvic fractions, the use of PI was beneficial in 73 % of the cases, while the use of SA was beneficial in only 45 %. Patient positioning worsened with SA, particularly along longitudinal and vertical directions. PI yielded more accurate registration results than SA for both pelvic and thoracic fractions. Compared with the skin marker set-up, PI performances were superior to SA for pelvic fractions while comparable results were obtained for thoracic fractions. (orig.) [de

  17. Voice analysis as an objective state marker in bipolar disorder

    DEFF Research Database (Denmark)

    Faurholt-Jepsen, M.; Busk, Jonas; Frost, M.

    2016-01-01

    features with automatically generated objective smartphone data on behavioral activities (for example, number of text messages and phone calls per day) and electronic self-monitored data (mood) on illness activity would increase the accuracy as a marker of affective states. Using smartphones, voice...... features, automatically generated objective smartphone data on behavioral activities and electronic self-monitored data were collected from 28 outpatients with bipolar disorder in naturalistic settings on a daily basis during a period of 12 weeks. Depressive and manic symptoms were assessed using...... the Hamilton Depression Rating Scale 17-item and the Young Mania Rating Scale, respectively, by a researcher blinded to smartphone data. Data were analyzed using random forest algorithms. Affective states were classified using voice features extracted during everyday life phone calls. Voice features were found...

  18. Forensic Body Fluid Identification by Analysis of Multiple RNA Markers Using NanoString Technology

    Directory of Open Access Journals (Sweden)

    Jong-Lyul Park

    2013-12-01

    Full Text Available RNA analysis has become a reliable method of body fluid identification for forensic use. Previously, we developed a combination of four multiplex quantitative PCR (qRT-PCR probes to discriminate four different body fluids (blood, semen, saliva, and vaginal secretion. While those makers successfully identified most body fluid samples, there were some cases of false positive and negative identification. To improve the accuracy of the identification further, we tried to use multiple markers per body fluid and adopted the NanoString nCounter system instead of a multiplex qRT-PCR system. After measuring tens of RNA markers, we evaluated the accuracy of each marker for body fluid identification. For body fluids, such as blood and semen, each body fluid-specific marker was accurate enough for perfect identification. However, for saliva and vaginal secretion, no single marker was perfect. Thus, we designed a logistic regression model with multiple markers for saliva and vaginal secretion and achieved almost perfect identification. In conclusion, the NanoString nCounter is an efficient platform for measuring multiple RNA markers per body fluid and will be useful for forensic RNA analysis.

  19. Development and characterization of highly polymorphic long TC repeat microsatellite markers for genetic analysis of peanut

    Directory of Open Access Journals (Sweden)

    Macedo Selma E

    2012-02-01

    Full Text Available Abstract Background Peanut (Arachis hypogaea L. is a crop of economic and social importance, mainly in tropical areas, and developing countries. Its molecular breeding has been hindered by a shortage of polymorphic genetic markers due to a very narrow genetic base. Microsatellites (SSRs are markers of choice in peanut because they are co-dominant, highly transferrable between species and easily applicable in the allotetraploid genome. In spite of substantial effort over the last few years by a number of research groups, the number of SSRs that are polymorphic for A. hypogaea is still limiting for routine application, creating the demand for the discovery of more markers polymorphic within cultivated germplasm. Findings A plasmid genomic library enriched for TC/AG repeats was constructed and 1401 clones sequenced. From the sequences obtained 146 primer pairs flanking mostly TC microsatellites were developed. The average number of repeat motifs amplified was 23. These 146 markers were characterized on 22 genotypes of cultivated peanut. In total 78 of the markers were polymorphic within cultivated germplasm. Most of those 78 markers were highly informative with an average of 5.4 alleles per locus being amplified. Average gene diversity index (GD was 0.6, and 66 markers showed a GD of more than 0.5. Genetic relationship analysis was performed and corroborated the current taxonomical classification of A. hypogaea subspecies and varieties. Conclusions The microsatellite markers described here are a useful resource for genetics and genomics in Arachis. In particular, the 66 markers that are highly polymorphic in cultivated peanut are a significant step towards routine genetic mapping and marker-assisted selection for the crop.

  20. The thrombopoietin receptor, c-Mpl, is a selective surface marker for human hematopoietic stem cells

    Directory of Open Access Journals (Sweden)

    Kerr William G

    2006-02-01

    from mid-fetal through adult life. This study extends our previous work documenting human B-lineage, myeloid and CD34+ cell repopulation by c-mpl+ progenitors to show that c-mpl+ HSC/PC are also capable of significant T-lineage reconstitution in vivo. These results suggest that c-mpl merits consideration as a selective surface marker for the identification and isolation of human HSC in both basic research and clinical settings.

  1. The use of a spaceflight-compatible device to perform WBC surface marker staining and whole-blood mitogenic activation for cytokine detection by flow cytometry

    Science.gov (United States)

    Crucian, B. E.; Sams, C. F.

    1999-01-01

    Significant changes have recently been described regarding circulating peripheral immune cells immediately following spaceflight. Existing methods for immunophenotype staining of peripheral blood in terrestrial labs do not meet the constraints for flight on the Space Shuttle. We have recently described the development and use of the Whole Blood Staining Device (WBSD), a simple device for staining flow cytometry specimens during spaceflight. When preparing samples with the WBSD, all liquids are safely contained as the cells are moved through staining, lysis and fixation steps. Here we briefly review the use of the WBSD, and then describe another versatile adaptation, a modification to perform intracellular staining of cytokines for detection by flow cytometry. Alterations in cytokine production have been reported both in ground-based simulated microgravity culture and in astronaut samples returning from spaceflight. Data regarding microgravity effects on cytokine production for specific subpopulations of cells is lacking. Flow cytometric cytokine analysis offers the unique ability to perform simultaneous surface marker analysis and positively identity cytokine producing subsets of cells. The utilization of the WBSD provides the ability to perform rapid and routine mitogenic activation during spaceflight coupled with the ability to perform simultaneous surface marker analysis. The only external requirements for this procedure are an in-flight 37-degree incubator and the capacity for 4-degree storage.

  2. Evaluating a new marker for risk prediction: decision analysis to the rescue.

    Science.gov (United States)

    Baker, Stuart G; Kramer, Barnett S

    2012-09-01

    In many areas of medicine risk prediction models are used to identify high-risk persons to receive treatment, with the goal of maximizing the ratio of benefits to harms. Thus there is considerable interest in evaluating markers to improve risk prediction. Many measures to evaluate a new marker for risk prediction are based solely on predictive accuracy including the odds ratio, change in the area under the receiver operating characteristic curve, and net reclassification improvement. However, predictive accuracy measures do not capture important clinical implications. Decision analysis comes to the rescue by including the ratio of the anticipated harm ("cost") of a false positive to the anticipated benefit of a true positive, which is transformed into a risk threshold (T) of indifference between treatment and no treatment. A decision-analytic measure of the "value" of a new marker is the number needed to test at a particular risk threshold, denoted NNTest(T), the minimum number of marker tests per true positive needed for risk prediction to be worthwhile. If NNTest(T) is acceptable given the invasiveness and adverse consequences of the test for the new marker, the new marker is recommended for inclusion in risk prediction. We provide a simple review of the derivation and computation of NNTest(T) from risk stratification tables and compare the minimum of NNTest(T), over risk thresholds, with measures of predictive accuracy in six studies. The results illustrate the advantages of this decision-analytic approach for evaluating a new marker for risk prediction.

  3. Expression of epithelial markers by human umbilical cord stem cells. A topographical analysis.

    Science.gov (United States)

    Garzón, I; Alfonso-Rodríguez, C A; Martínez-Gómez, C; Carriel, V; Martin-Piedra, M A; Fernández-Valadés, R; Sánchez-Quevedo, M C; Alaminos, M

    2014-12-01

    Human umbilical cord stem cells have inherent differentiation capabilities and potential usefulness in regenerative medicine. However, the epithelial differentiation capability and the heterogeneity of these cells have not been fully explored to the date. We analyzed the expression of several undifferentiation and epithelial markers in cells located in situ in different zones of the umbilical cord -in situ analysis- and in primary ex vivo cell cultures of Wharton's jelly stem cells by microarray and immunofluorescence. Our results demonstrated that umbilical cord cells were heterogeneous and had intrinsic capability to express in situ stem cell markers, CD90 and CD105 and the epithelial markers cytokeratins 3, 4, 7, 8, 12, 13, 19, desmoplakin and zonula occludens 1 as determined by microarray and immunofluorescence, and most of these markers remained expressed after transferring the cells from the in situ to the ex vivo cell culture conditions. However, important differences were detected among some cell types in the umbilical cord, with subvascular zone cells showing less expression of stem cell markers and cells in Wharton's jelly and the amnioblastic zones showing the highest expression of stem cells and epithelial markers. These results suggest that umbilical cord mesenchymal cells have intrinsic potential to express relevant epithelial markers, and support the idea that they could be used as alternative cell sources for epithelial tissue engineering. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. SURFACE ENERGY BALANCE OVER ORANGE ORCHARD USING SURFACE RENEWAL ANALYSIS

    Directory of Open Access Journals (Sweden)

    Salvatore Barbagallo

    2009-12-01

    Full Text Available Reliable estimation of surface sensible and latent heat flux is the most important process to appraise energy and mass exchange among atmosphere and biosphere. In this study the surface energy fluxes were measured over an irrigated orange orchard during 2005-2008 monitoring periods using a Surface Renewal- Energy Balance approach. The experimental area is located in a representative orchard growing area of eastern Sicily (Italy. The performance of Surface Renewal (SR analysis for estimating sensible heat flux (H was analysed and evaluated in terms of correlation with H fluxes from the eddy covariance (EC method. Study revealed that the mean available energy (RN- G and latent heat flux (LE were of about 300 W m-2 and 237 W m-2, respectively, during dry periods and unstable-case atmospheric conditions. The estimated crop coefficient Kc values for the orchard crop averaged close to 0.80, which is considerably higher than previous FAO studies that found the value to be 0.65 for citrus with 70% of ground cover. The intercepted photosynthetically active radiation (LI PAR by the crop was measured and relationships between LAI and crop coefficient (Kc were established.

  5. Concomitant analysis of salivary tumor markers--a new diagnostic tool for oral cancer.

    Science.gov (United States)

    Nagler, Rafael; Bahar, Gideon; Shpitzer, Thomas; Feinmesser, Raphael

    2006-07-01

    Oral squamous cell carcinoma (OSCC) is a common human malignancy. Circulatory epithelial tumor markers were previously investigated in the serum of OSCC patients but almost never in their saliva, in spite of the fact that there is a direct contact between the saliva and the oral cancer lesion. The purpose of the current study was to examine tumor markers in the saliva of OSCC patients. We measured the concentrations of the six most studied epithelial serum circulatory tumor markers in the saliva of OSCC (tongue) patients. Significant increases (of 400%) in salivary concentrations of Cyfra 21-1, tissue polypeptide antigen, and CA125 were shown. Salivary concentrations of CA19-9, SCC, and carcinoembryonic antigen were increased without statistical significance. A concurrent analysis of the three significantly increased markers revealed sensitivity, specificity, and negative and positive predictive values of 71%, 75%, 71%, and 75%, respectively. The increase reported in salivary tumor markers may be used as a diagnostic tool, especially when a concurrent analysis for significantly increased markers is done. Salivary testing is noninvasive, making it an attractive, effective alternative to serum testing, and the possibility of developing home testing kits would further facilitate it as a diagnostic aid, enabling patients to monitor their own health at home and is important for those who live far from their treatment centers and especially for those at risk of developing OSCC.

  6. SECTION 6.2 SURFACE TOPOGRAPHY ANALYSIS

    DEFF Research Database (Denmark)

    Seah, M. P.; De Chiffre, Leonardo

    2005-01-01

    Surface physical analysis, i.e. topography characterisation, encompasses measurement, visualisation, and quantification. This is critical for both component form and for surface finish at macro-, micro- and nano-scales. The principal methods of surface topography measurement are stylus profilometry......, optical scanning techniques, and scanning probe microscopy (SPM). These methods, based on acquisition of topography data from point by point scans, give quantitative information of heights with respect to position. Based on a different approach, the so-called integral methods produce parameters...

  7. Use of SSR markers for DNA fingerprinting and diversity analysis of Pakistani sugarcane (Saccharum spp. hybrids) cultivars

    Science.gov (United States)

    In recent years SSR markers have been used widely for genetic analysis. The objective of this study was to use an SSR-based marker system to develop the molecular fingerprints and analyze the genetic relationship of sugarcane cultivars grown in Pakistan. Twenty-one highly polymorphic SSR markers wer...

  8. 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...... frequently (14 of 30 tumors, six of six CSF metastasis specimens); LOH of chromosomes 10q, 16q22, 11, 6, 9q22, and 1q31 was observed in 20.6%, 20%, 14.3%, 12%, 10%, and 0%, respectively. Eight of 32 tumors and CSF specimens showed amplification of c-myc. All tumors with amplification of c-myc were resistant...

  9. Smooth ROC curves and surfaces for markers subject to a limit of detection using monotone natural cubic splines.

    Science.gov (United States)

    Bantis, Leonidas E; Tsimikas, John V; Georgiou, Stelios D

    2013-09-01

    The use of ROC curves in evaluating a continuous or ordinal biomarker for the discrimination of two populations is commonplace. However, in many settings, marker measurements above or below a certain value cannot be obtained. In this paper, we study the construction of a smooth ROC curve (or surface in the case of three populations) when there is a lower or upper limit of detection. We propose the use of spline models that incorporate monotonicity constraints for the cumulative hazard function of the marker distribution. The proposed technique is computationally stable and simulation results showed a satisfactory performance. Other observed covariates can be also accommodated by this spline-based approach. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Analogy of ISSR and RAPD markers for comparative analysis of ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-12-03

    Dec 3, 2008 ... Yeh FC, Chong DKX, Yang RC (1995). RAPD variation within and among natural populations of Trembling Aspen (Populus tremuloides Michx.) from Alberta. J. Hered. 86: 454-460. Zhao WG, Zhang JQ, Wangi YH, Chen TT, Yin Y, Huang, YP, Pan. Y, Yang Y (2006). Analysis of Genetic Diversity in Wild.

  11. Simple sequence repeat (SSR) markers analysis of genetic diversity ...

    African Journals Online (AJOL)

    hope&shola

    2012-04-24

    Apr 24, 2012 ... eight groups according to the k-means cluster analysis based on seed quality characters. There were significant differences among different groups (P< 0.01). The characteristics of each group were as follows; group 1: yellow seed with high oil and protein content, group 2: yellow seed with low oil and high ...

  12. Surface analysis with low energy ion scattering

    International Nuclear Information System (INIS)

    Taglauer, E.; Heiland, W.

    1976-01-01

    Principles and applications of low energy ion scattering for surface analysis are presented. Basic features are the binary collision concept, the scattering cross-sections and the ion neutralization process. The potential and the limitations of the method are outlined. Some pertinent experimental aspects are considered. In a number of examples the performance of the technique is demonstrated for qualitative composition analysis and for studies of surface structures. Finally a few comparisons are made with other techniques, such as AES, LEED, or SIMS. (orig.) [de

  13. Endoscopy/EUS-guided fiducial marker placement in patients with esophageal cancer: a comparative analysis of 3 types of markers

    NARCIS (Netherlands)

    Machiels, Melanie; van Hooft, Jeanin; Jin, Peng; van Berge Henegouwen, Mark I.; van Laarhoven, Hanneke M.; Alderliesten, Tanja; Hulshof, Maarten C.

    2015-01-01

    Markers placed at the borders of esophageal tumors are potentially useful to facilitate radiotherapy (RT) target delineation, which offers the possibility of image-guided RT. To evaluate and compare the feasibility and technical benefit of endoscopy/EUS-guided marker placement of 3 different types

  14. Analysis of Genetic Variation of rs1542705 Marker in SMPD1 Gene Region as an Informative Marker for Molecular Diagnosis of Niemann-Pick Disease in Isfahan Population

    Directory of Open Access Journals (Sweden)

    Nasim Ebrahimi

    2016-09-01

    Full Text Available Abstract Background: Niemann-Pick disease (NPD refers to a group of lysosomal storage diseases that causes abnormal metabolism of lipids. One of the genes that play a role in the pathogenesis of this disease is SMPD1. To date, more than hundred disease- causing mutations have been identified in SMPD1 gene. Due to the large number of mutations in this gene, direct analysis of the mutations is costly and time-consuming. Therefore, indirect linkage analysis using polymorphic markers as an alternative method for molecular diagnosis of the mutations has been recommended. In the present study, allele frequency of rs1542705 genetic marker was analyzed in the Iranian population. The aim was to determine the polymorphic information content (PIC and the possibility of its application in indirect diagnosing of NPD. Materials and Methods: After bioinformatics analysis of the SMPD1 gene region, rs1542705 marker was selected for genotyping in Isfahan population. In order to calculate the allele and genotype frequency of the marker, molecular tests were done on 113 DNA samples of unrelated healthy individuals by using ARMS-PCR technique. Finally, the information related to the genotype of the individuals was statistically analyzed using Powermarker and Genepop software. Results: The analyses showed that the studied population was in accordance with Hardy-Weinberg equilibrium. Allele frequency of rs1542705 marker for T and C alleles was 71.24% and 28.76%, respectively, and the heterozygosity of the marker was 43.36%. Also, polymorphic information content (PIC was 0.325. Conclusion: The results of this study showed that rs1542705 marker could be considered as an informative marker for molecular diagnosis of Niemann- Pick disease using linkage analysis in the studied population.

  15. De novo transcriptomic analysis of cowpea (Vigna unguiculata L. Walp.) for genic SSR marker development.

    Science.gov (United States)

    Chen, Honglin; Wang, Lixia; Liu, Xiaoyan; Hu, Liangliang; Wang, Suhua; Cheng, Xuzhen

    2017-07-11

    Cowpea [Vigna unguiculata (L.) Walp.] is one of the most important legumes in tropical and semi-arid regions. However, there is relatively little genomic information available for genetic research on and breeding of cowpea. The objectives of this study were to analyse the cowpea transcriptome and develop genic molecular markers for future genetic studies of this genus. Approximately 54 million high-quality cDNA sequence reads were obtained from cowpea based on Illumina paired-end sequencing technology and were de novo assembled to generate 47,899 unigenes with an N50 length of 1534 bp. Sequence similarity analysis revealed 36,289 unigenes (75.8%) with significant similarity to known proteins in the non-redundant (Nr) protein database, 23,471 unigenes (49.0%) with BLAST hits in the Swiss-Prot database, and 20,654 unigenes (43.1%) with high similarity in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Further analysis identified 5560 simple sequence repeats (SSRs) as potential genic molecular markers. Validating a random set of 500 SSR markers yielded 54 polymorphic markers among 32 cowpea accessions. This transcriptomic analysis of cowpea provided a valuable set of genomic data for characterizing genes with important agronomic traits in Vigna unguiculata and a new set of genic SSR markers for further genetic studies and breeding in cowpea and related Vigna species.

  16. Establishment of Relational Model of Congenital Heart Disease Markers and GO Functional Analysis of the Association between Its Serum Markers and Susceptibility Genes.

    Science.gov (United States)

    Liu, Min; Zhao, Luosha; Yuan, Jiaying

    2016-01-01

    The purpose of present study was to construct the best screening model of congenital heart disease serum markers and to provide reference for further prevention and treatment of the disease. Documents from 2006 to 2014 were collected and meta-analysis was used for screening susceptibility genes and serum markers closely related to the diagnosis of congenital heart disease. Data of serum markers were extracted from 80 congenital heart disease patients and 80 healthy controls, respectively, and then logistic regression analysis and support vector machine were utilized to establish prediction models of serum markers and Gene Ontology (GO) functional annotation. Results showed that NKX2.5, GATA4, and FOG2 were susceptibility genes of congenital heart disease. CRP, BNP, and cTnI were risk factors of congenital heart disease (p heart disease (p markers' relational model established by support vector machine was only 85%. GO analysis suggested that NKX2.5, GATA4, and FOG2 were functionally related to Lp(a) and BNP. The combined markers model of BNP and cTnI had the highest accuracy rate, providing a theoretical basis for the diagnosis of congenital heart disease.

  17. Laboratory studies of spectroscopic markers for the characterization of surface erosion by plasmas

    International Nuclear Information System (INIS)

    Manos, D.M.; Bennett, T.; Herzer, M.; Schwarzmann, J.

    1992-01-01

    The erosion rates in portions of fusion plasma devices like the ITER tokamak are sufficiently high that nearly real-time information on cumulative removal is needed for control and machine safety. We are developing a digitally--encoded scheme to indicate the depth of erosion at numerous poloidal and toroidal locations around ITER. The scheme uses materials embedded in the walls and divertors, which, when uncovered, present remotely detectable signals. This paper reports laboratory experiments on prototype markers consisting of combinations of up to 5 elements (Au,Pd,Ag,In,Ga) along with Au,Pt, and Ta pure metals. The markers were bonded to 4-D carbon-carbon composite of the type proposed for use in the ITER first wall, and placed in the lower-hybrid-driven plasma of the atomic beam facility at PPL. The paper describes this device Light emission was characterized using a 1 meter Czerny-Turner vacuum ultraviolet monochromator. The samples were characterized both before and after plasma exposure by Auger spectroscopy. We report the time-dependent behavior of the spectra of the visible and ultraviolet light emitted by the plasma when the markers are uncovered by the erosion showing emission lines of the marker elements which are easily distinguished from the background plasma lines. The dependence of the light intensity on bias voltage is compared to the known sputtering yields of the elements. The optical detection method allows exploration of the threshold dependence of these multi-element targets. An exponential dependence of yield above threshold was observed for all of the elements studied

  18. A Human Pluripotent Stem Cell Surface N-Glycoproteome Resource Reveals Markers, Extracellular Epitopes, and Drug Targets

    Directory of Open Access Journals (Sweden)

    Kenneth R. Boheler

    2014-07-01

    Full Text Available Detailed knowledge of cell-surface proteins for isolating well-defined populations of human pluripotent stem cells (hPSCs would significantly enhance their characterization and translational potential. Through a chemoproteomic approach, we developed a cell-surface proteome inventory containing 496 N-linked glycoproteins on human embryonic (hESCs and induced PSCs (hiPSCs. Against a backdrop of human fibroblasts and 50 other cell types, >100 surface proteins of interest for hPSCs were revealed. The >30 positive and negative markers verified here by orthogonal approaches provide experimental justification for the rational selection of pluripotency and lineage markers, epitopes for cell isolation, and reagents for the characterization of putative hiPSC lines. Comparative differences between the chemoproteomic-defined surfaceome and the transcriptome-predicted surfaceome directly led to the discovery that STF-31, a reported GLUT-1 inhibitor, is toxic to hPSCs and efficient for selective elimination of hPSCs from mixed cultures.

  19. Powerful Tests for Multi-Marker Association Analysis Using Ensemble Learning.

    Directory of Open Access Journals (Sweden)

    Badri Padhukasahasram

    Full Text Available Multi-marker approaches have received a lot of attention recently in genome wide association studies and can enhance power to detect new associations under certain conditions. Gene-, gene-set- and pathway-based association tests are increasingly being viewed as useful supplements to the more widely used single marker association analysis which have successfully uncovered numerous disease variants. A major drawback of single-marker based methods is that they do not look at the joint effects of multiple genetic variants which individually may have weak or moderate signals. Here, we describe novel tests for multi-marker association analyses that are based on phenotype predictions obtained from machine learning algorithms. Instead of assuming a linear or logistic regression model, we propose the use of ensembles of diverse machine learning algorithms for prediction. We show that phenotype predictions obtained from ensemble learning algorithms provide a new framework for multi-marker association analysis. They can be used for constructing tests for the joint association of multiple variants, adjusting for covariates and testing for the presence of interactions. To demonstrate the power and utility of this new approach, we first apply our method to simulated SNP datasets. We show that the proposed method has the correct Type-1 error rates and can be considerably more powerful than alternative approaches in some situations. Then, we apply our method to previously studied asthma-related genes in 2 independent asthma cohorts to conduct association tests.

  20. Repository surface design site layout analysis

    International Nuclear Information System (INIS)

    Montalvo, H.R.

    1998-01-01

    The purpose of this analysis is to establish the arrangement of the Yucca Mountain Repository surface facilities and features near the North Portal. The analysis updates and expands the North Portal area site layout concept presented in the ACD, including changes to reflect the resizing of the Waste Handling Building (WHB), Waste Treatment Building (WTB), Carrier Preparation Building (CPB), and site parking areas; the addition of the Carrier Washdown Buildings (CWBs); the elimination of the Cask Maintenance Facility (CMF); and the development of a concept for site grading and flood control. The analysis also establishes the layout of the surface features (e.g., roads and utilities) that connect all the repository surface areas (North Portal Operations Area, South Portal Development Operations Area, Emplacement Shaft Surface Operations Area, and Development Shaft Surface Operations Area) and locates an area for a potential lag storage facility. Details of South Portal and shaft layouts will be covered in separate design analyses. The objective of this analysis is to provide a suitable level of design for the Viability Assessment (VA). The analysis was revised to incorporate additional material developed since the issuance of Revision 01. This material includes safeguards and security input, utility system input (size and location of fire water tanks and pump houses, potable water and sanitary sewage rates, size of wastewater evaporation pond, size and location of the utility building, size of the bulk fuel storage tank, and size and location of other exterior process equipment), main electrical substation information, redundancy of water supply and storage for the fire support system, and additional information on the storm water retention pond

  1. Repository Surface Design Site Layout Analysis

    International Nuclear Information System (INIS)

    Montalvo, H.R.

    1998-01-01

    The purpose of this analysis is to establish the arrangement of the Repository surface facilities and features near the North Portal. The analysis updates and expands the North Portal area site layout concept presented in the ACD (Reference 5.5), including changes to reflect the resizing of the Waste Handling Building (WHB), Waste Treatment Building (WTB), Carrier Preparation Building (CPB), and site parking areas; the addition of the Carrier Washdown Buildings (CWBs); the elimination of the Cask Maintenance Facility (CMF); and the development of a concept for site grading and flood control. The analysis also establishes the layout of the surface features (e.g., roads and utilities) that connect all the repository surface areas (North Portal Operations Area, South Portal Development Operations Area, Emplacement Shaft Surface Operations Area, and Development Shaft Surface Operations Area) and locates an area for a potential lag storage facility. Details of South Portal and shaft layouts will be covered in separate design analyses. The objective of this analysis is to provide a suitable level of design for the Viability Assessment (VA). The analysis was revised to incorporate additional material developed since the issuance of Revision 01. This material includes safeguards and security input, utility system input (size and location of fire water tanks and pump houses, potable water and sanitary sewage rates, size of wastewater evaporation pond, size and location of the utility building, size of the bulk fuel storage tank, and size and location of other exterior process equipment), main electrical substation information, redundancy of water supply and storage for the fire support system, and additional information on the storm water retention pond

  2. Proteomics Analysis for Finding Serum Markers of Ovarian Cancer

    Directory of Open Access Journals (Sweden)

    Yushan Cheng

    2014-01-01

    Full Text Available A combination of peptide ligand library beads (PLLB and 1D gel liquid chromatography-mass spectrometry/mass spectrometry (1DGel-LC-MS/MS was employed to analyze serum samples from patients with ovarian cancer and from healthy controls. Proteomic analysis identified 1200 serum proteins, among which 57 proteins were upregulated and 10 were downregulated in the sera from cancer patients. Retinol binding protein 4 (RBP4 is highly upregulated in the ovarian cancer serum samples. ELISA was employed to measure plasma concentrations of RBP4 in 80 samples from ovarian cancer patients, healthy individuals, myoma patients, and patients with benign ovarian tumor, respectively. The plasma concentrations of RBP4 ranging from 76.91 to 120.08 ng/mL with the mean value 89.13±1.67 ng/mL in ovarian cancer patients are significantly higher than those in healthy individuals (10.85±2.38 ng/mL. Results were further confirmed with immunohistochemistry, demonstrating that RBP4 expression levels in normal ovarian tissue were lower than those in ovarian cancer tissues. Our results suggested that RBP4 is a potential biomarker for diagnostic of screening ovarian cancer.

  3. SURFACE TEXTURE ANALYSIS FOR FUNCTIONALITY CONTROL

    DEFF Research Database (Denmark)

    De Chiffre, Leonardo; Andreasen, Jan Lasson; Tosello, Guido

    This document is used in connection with three exercises of 3 hours duration as a part of the course VISION ONLINE – One week course on Precision & Nanometrology. The exercises concern surface texture analysis for functionality control, in connection with three different case stories. This docume...... contains a short description of each case story, 3-D roughness parameters analysis and relation with the product’s functionality.......This document is used in connection with three exercises of 3 hours duration as a part of the course VISION ONLINE – One week course on Precision & Nanometrology. The exercises concern surface texture analysis for functionality control, in connection with three different case stories. This document...

  4. Analysis of inheritance mode in chrysanthemum using EST-derived SSR markers

    NARCIS (Netherlands)

    Park, Sang Kun; Arens, Paul; Esselink, Danny; Lim, Jin Hee; Shin, Hak Ki

    2015-01-01

    To study the inheritance mode of hexaploid chrysanthemum (random or preferential chromosome pairing), a segregation analysis was carried out using SSR markers derived from chrysanthemum ESTs in the public domain. A total of 248 EST-SSR primer pairs were screened in chrysanthemum cultivars

  5. SNP marker analysis for validating the authenticity of Tunisian olive oil

    Indian Academy of Sciences (India)

    1Centre of Biotechnology of Sfax, P.B. '1177', 3018 Sfax, Tunisia. 2Laboratory of Physics-Mathematics and Applications, Faculty of Sciences of Sfax, BP 1177, 3000 Sfax, Tunisia. [Ben Ayed R., Kallel I., Ben Hassen H. and Rebai A. 2014 SNP marker analysis for validating the authenticity of Tunisian olive oil. J. Genet.

  6. Gyral Folding Pattern Analysis via Surface Profiling

    Science.gov (United States)

    Li, Kaiming; Guo, Lei; Li, Gang; Nie, Jingxin; Faraco, Carlos; Cui, Guangbin; Zhao, Qun; Miller, L. Stephen; Liu, Tianming

    2010-01-01

    Folding is an essential shape characteristic of the human cerebral cortex. Descriptors of cortical folding patterns have been studied for decades. However, many previous studies are either based on local shape descriptors such as curvature, or based on global descriptors such as gyrification index or spherical wavelets. This paper proposes a gyrus-scale folding pattern analysis technique via cortical surface profiling. Firstly, we sample the cortical surface into 2D profiles and model them using a power function. This step provides both the flexibility of representing arbitrary shape by profiling and the compactness of representing shape by parametric modeling. Secondly, based on the estimated model parameters, we extract affine-invariant features on the cortical surface, and apply the affinity propagation clustering algorithm to parcellate the cortex into cortical regions with strict hierarchy and smooth transitions among them. Finally, a second-round surface profiling is performed on the parcellated cortical surface, and the number of hinges is detected to describe the gyral folding pattern. We have applied the surface profiling method to two normal brain datasets and a Schizophrenia patient dataset. The experimental results demonstrate that the proposed method can accurately classify human gyri into 2-hinge, 3-hinge and 4-hinge patterns. The distribution of these folding patterns on brain lobes and the relationship between fiber density and gyral folding patterns are further investigated. Results from the Schizophrenia dataset are consistent with commonly found abnormality in former studies by others, which demonstrates the potential clinical applications of the proposed technique. PMID:20472071

  7. Surface analysis with STM and AFM

    CERN Document Server

    Magonov, Sergi N

    1996-01-01

    Scanning tunneling microscopy (STM) and atomic force microscopy (AFM) are powerful tools for surface examination. In the past, many STM and AFM studies led to erroneous conclusions due to lack of proper theoretical considerations and of an understanding of how image patterns are affected by measurement conditions. For this book, two world experts, one on theoretical analysis and the other on experimental characterization, have joined forces to bring together essential components of STM and AFM studies: The practical aspects of STM, the image simulation by surface electron density plot calculat

  8. Paired Expression Analysis of Tumor Cell Surface Antigens

    Directory of Open Access Journals (Sweden)

    Rimas J. Orentas

    2017-08-01

    Full Text Available Adoptive immunotherapy with antibody-based therapy or with T cells transduced to express chimeric antigen receptors (CARs is useful to the extent that the cell surface membrane protein being targeted is not expressed on normal tissues. The most successful CAR-based (anti-CD19 or antibody-based therapy (anti-CD20 in hematologic malignancies has the side effect of eliminating the normal B cell compartment. Targeting solid tumors may not provide a similar expendable marker. Beyond antibody to Her2/NEU and EGFR, very few antibody-based and no CAR-based therapies have seen broad clinical application for solid tumors. To expand the way in which the surfaceome of solid tumors can be analyzed, we created an algorithm that defines the pairwise relative overexpression of surface antigens. This enables the development of specific immunotherapies that require the expression of two discrete antigens on the surface of the tumor target. This dyad analysis was facilitated by employing the Hotelling’s T-squared test (Hotelling–Lawley multivariate analysis of variance for two independent variables in comparison to a third constant entity (i.e., gene expression levels in normal tissues. We also present a unique consensus scoring mechanism for identifying transcripts that encode cell surface proteins. The unique application of our bioinformatics processing pipeline and statistical tools allowed us to compare the expression of two membrane protein targets as a pair, and to propose a new strategy based on implementing immunotherapies that require both antigens to be expressed on the tumor cell surface to trigger therapeutic effector mechanisms. Specifically, we found that, for MYCN amplified neuroblastoma, pairwise expression of ACVR2B or anaplastic lymphoma kinase (ALK with GFRA3, GFRA2, Cadherin 24, or with one another provided the strongest hits. For MYCN, non-amplified stage 4 neuroblastoma, neurotrophic tyrosine kinase 1, or ALK paired with GFRA2, GFRA3, SSK

  9. Tropomyosin is a nice marker gene for phylogenetic analysis of molluscs.

    Science.gov (United States)

    Wang, Xiaotong; Li, Li; Xu, Fei; Zhang, Guofan

    2011-10-01

    Molluscs are an extraordinarily diverse group of animals and to discriminate them based on one molecular marker/gene is very difficult because of the too fast or slow rate of nucleotide substitution. In the study, the tropomyosin cds (coding sequences) of 43 animal species were analyzed, the results of which suggested that the tropomyosin gene was a nice marker gene to phylogenetic analysis of molluscs, even for all the studied animals. In addition, InDels (insertions and deletions) in tropomyosin cds of turbo cornutus were also studied and one segment repeat, which probably happened recently and was of functional importance, was found.

  10. Immunohistochemical analysis of retinoblastoma cell phenotype using neuronal and glial cell markers.

    Science.gov (United States)

    Orellana, María Eugenia; Belfort, Rubens; Antecka, Emilia; Burnier, Miguel Noel

    2016-01-01

    The cellular origin of retinoblastoma is uncertain as constituent tumor cells heterogeneously express markers of both immature and mature retinal cells. An immunohistochemical analysis of cellular origin may yield valuable insights into disease progression and treatment options. This study aimed to determine the cellular origin of retinoblastoma in a large case series and correlate these findings with histopathological prognostic factors. Thirty-nine retinoblastoma cases were histopathologically diagnosed and analyzed by immunohistochemistry using monoclonal antibodies against the immature neural cell marker SRY-box containing gene 2 (SOX-2), the mature neuronal cell marker microtubule-associated protein 2 (MAP2), and the mature glial cell marker glial fibrillary acidic protein (GFAP). Histopathological features were also evaluated, including patterns of growth, differentiation, vitreous seeding, and choroidal/scleral, optic nerve, and anterior chamber invasion. Two retinoblastoma cell lines, WERI-1 and Y79, were studied by immunocytochemistry using the same antibodies. Expression of SOX-2 was strong in 97.4% of retinoblastoma cases, while MAP-2 was expressed in 59% of cases. Immunostaining for GFAP was positive only in reactive stromal astrocytes interspersed amongst tumor cells and in peritumoral tissue. There was no correlation between histopathological prognostic factors and immunohistochemical markers. Retinoblastoma cell lines showed strong positivity for SOX2 (90% of WERI-1 cells and 70% of Y79 cells) and MAP2 (90% of cells in both lines). GFAP was completely negative in both cell lines. The majority of retinoblastomas and both RB cell lines expressed an immature neural and/or a mature neuronal cell marker, but not a glial marker. These results indicate a typical neuroblast or neuronal origin and eliminate astrocyte differentiation from neural stem cells as the source of retinoblastoma.

  11. Immunohistochemical analysis of retinoblastoma cell phenotype using neuronal and glial cell markers

    Directory of Open Access Journals (Sweden)

    María Eugenia Orellana

    Full Text Available ABSTRACT Purpose: The cellular origin of retinoblastoma is uncertain as constituent tumor cells heterogeneously express markers of both immature and mature retinal cells. An immunohistochemical analysis of cellular origin may yield valuable insights into disease progression and treatment options. This study aimed to determine the cellular origin of retinoblastoma in a large case series and correlate these findings with histopathological prognostic factors. Methods: Thirty-nine retinoblastoma cases were histopathologically diagnosed and analyzed by immunohistochemistry using monoclonal antibodies against the immature neural cell marker SRY-box containing gene 2 (SOX-2, the mature neuronal cell marker microtubule-associated protein 2 (MAP2, and the mature glial cell marker glial fibrillary acidic protein (GFAP. Histopathological features were also evaluated, including patterns of growth, differentiation, vitreous seeding, and choroidal/scleral, optic nerve, and anterior chamber invasion. Two retinoblastoma cell lines, WERI-1 and Y79, were studied by immunocytochemistry using the same antibodies. Results: Expression of SOX-2 was strong in 97.4% of retinoblastoma cases, while MAP-2 was expressed in 59% of cases. Immunostaining for GFAP was positive only in reactive stromal astrocytes interspersed amongst tumor cells and in peritumoral tissue. There was no correlation between histopathological prognostic factors and immunohistochemical markers. Retinoblastoma cell lines showed strong positivity for SOX2 (90% of WERI-1 cells and 70% of Y79 cells and MAP2 (90% of cells in both lines. GFAP was completely negative in both cell lines. Conclusion: The majority of retinoblastomas and both RB cell lines expressed an immature neural and/or a mature neuronal cell marker, but not a glial marker. These results indicate a typical neuroblast or neuronal origin and eliminate astrocyte differentiation from neural stem cells as the source of retinoblastoma.

  12. Discovery and identification of quality markers of Chinese medicine based on pharmacokinetic analysis.

    Science.gov (United States)

    He, Jun; Feng, Xinchi; Wang, Kai; Liu, Changxiao; Qiu, Feng

    2018-02-28

    Quality control of Chinese medicine (CM) is an effective measure to ensure the safety and efficacy of CM in clinical practice, which is also a key factor to restrict the modernization process of CM. Various chemical components exist in CM and the determination of several chemical components is the main approach for quality control of vast majority of CM in the present. However, many components determined lack not only specificity, but also biological activities. This is bound to greatly reduce the actual value of quality standard of CM. Professor Changxiao Liu proposed the "quality marker" (Q-marker) concept to ensure the standardization and rationalization for the quality control of CM. As we all know, CMs are taken orally in most cases and could be extensively metabolized in vivo. Both prototype components and the metabolites could be the actual therapeutic material basis. Pharmacokinetic studies could benefit the elucidation of actual therapeutic material basis which is closely related to the identification of Q-markers. Therefore, a new strategy about Q-marker was proposed based on the pharmacokinetic analysis of CM, hoping to provide some ideas for the discovery and identification of Q-marker. The relationship between pharmacokinetic studies and the identification of Q-markers was demonstrated in this review and a new strategy was proposed. Starting from the pharmacokinetic analysis, reverse tracing of the prototype active components and the potential prodrugs in CM were conducted first and the therapeutic material basis were identified as Q-markers. Then, modern analytical techniques and methods were applied to obtain comprehensive quality control for these constituents. Several CMs including gingko biloba, ginseng, Periplocae Cortex, Mori Cortex, Bupleuri Radix and Scutellariae Radix were listed as examples to clarify how the new strategy could be applied. Pharmacokinetic studies play an important role for the elucidation of therapeutic material basis of CM

  13. Surface analysis methods in materials science

    CERN Document Server

    Sexton, Brett; Smart, Roger

    1992-01-01

    The idea for this book stemmed from a remark by Philip Jennings of Murdoch University in a discussion session following a regular meeting of the Australian Surface Science group. He observed that a text on surface analysis and applica­ tions to materials suitable for final year undergraduate and postgraduate science students was not currently available. Furthermore, the members of the Australian Surface Science group had the research experience and range of coverage of sur­ face analytical techniques and applications to provide a text for this purpose. A of techniques and applications to be included was agreed at that meeting. The list intended readership of the book has been broadened since the early discussions, particularly to encompass industrial users, but there has been no significant alter­ ation in content. The editors, in consultation with the contributors, have agreed that the book should be prepared for four major groups of readers: - senior undergraduate students in chemistry, physics, metallur...

  14. Microchemical surface analysis of two Numidian coins

    International Nuclear Information System (INIS)

    Mousser, Henia; Amri, Redha; Madani, Abdelghani; Darchen, Andre; Mousser, Abdelhamid

    2011-01-01

    This work is a contribution to the microchemical surface analysis of two Numidian coins. Numidia was an ancient kingdom of northern Algeria during 2nd and 1st century BC. Investigations were performed with scanning electron microscopy (SEM) coupled with energy dispersive spectrometry (EDS), energy dispersive X-ray fluorescence spectrometry (EDXRF) and X-ray diffraction (XRD). The identification of the coins was done thanks to the name initials and effigy of King Massinissa. SEM observations of coins showed heterogeneous surfaces. SEM and EDXRF analyses showed an alloy structure with copper (65%), antimony (19%) and lead (16%). The XRD identified a metal structure and corrosion products which were on the coin surfaces: Litharge (PbO), Hydrocerussite (Pb 3 (CO 3 ) 2 (OH) 2 ), Bindheimite (Pb 2 Sb 2 O 7 ) and Bystromite (MgSb 2 O 6 ).

  15. Identification of genetic markers linked to anthracnose resistance in sorghum using association analysis.

    Science.gov (United States)

    Upadhyaya, Hari D; Wang, Yi-Hong; Sharma, Rajan; Sharma, Shivali

    2013-06-01

    Anthracnose in sorghum caused by Colletotrichum sublineolum is one of the most destructive diseases affecting sorghum production under warm and humid conditions. Markers and genes linked to resistance to the disease are important for plant breeding. Using 14,739 SNP markers, we have mapped eight loci linked to resistance in sorghum through association analysis of a sorghum mini-core collection consisting of 242 diverse accessions evaluated for anthracnose resistance for 2 years in the field. The mini-core was representative of the International Crops Research Institute for the Semi-Arid Tropics' world-wide sorghum landrace collection. Eight marker loci were associated with anthracnose resistance in both years. Except locus 8, disease resistance-related genes were found in all loci based on their physical distance from linked SNP markers. These include two NB-ARC class of R genes on chromosome 10 that were partially homologous to the rice blast resistance gene Pib, two hypersensitive response-related genes: autophagy-related protein 3 on chromosome 1 and 4 harpin-induced 1 (Hin1) homologs on chromosome 8, a RAV transcription factor that is also part of R gene pathway, an oxysterol-binding protein that functions in the non-specific host resistance, and homologs of menthone:neomenthol reductase (MNR) that catalyzes a menthone reduction to produce the antimicrobial neomenthol. These genes and markers may be developed into molecular tools for genetic improvement of anthracnose resistance in sorghum.

  16. Analysis of polymer surfaces and thin-film coatings with Raman and surface enhanced Raman scattering

    International Nuclear Information System (INIS)

    McAnally, Gerard David

    2001-01-01

    This thesis investigates the potential of surface-enhanced Raman scattering (SERS) for the analysis and characterisation of polymer surfaces. The Raman and SERS spectra from a PET film are presented. The SERS spectra from the related polyester PBT and from the monomer DMT are identical to PET, showing that only the aromatic signals are enhanced. Evidence from other compounds is presented to show that loss of the carbonyl stretch (1725 cm -1 ) from the spectra is due to a chemical interaction between the silver and surface carbonyl groups. The interaction of other polymer functional groups with silver is discussed. A comparison of Raman and SERS spectra collected from three faces of a single crystal shows the SERS spectra are depolarised. AFM images of the silver films used to obtain SERS are presented. They consist of regular islands of silver, fused together to form a complete film. The stability and reproducibility and of these surfaces is assessed. Band assignments for the SERS spectrum of PET are presented. A new band in the spectrum (1131 cm -1 ) is assigned to a complex vibration using a density functional calculation. Depth profiling through a polymer film on to the silver layer showed the SERS signals arise from the silver surface only. The profiles show the effects of refraction on the beam, and the adverse affect on the depth resolution. Silver films were used to obtain SERS spectra from a 40 nm thin-film coating on PET, without interference from the PET layer. The use of an azo dye probe as a marker to detect the coating is described. Finally, a novel method for the synthesis of a SERS-active vinyl-benzotriazole monomer is reported. The monomer was incorporated into a thin-film coating and the SERS spectrum obtained from the polymer. (author)

  17. Advanced wettability analysis of implant surfaces

    Directory of Open Access Journals (Sweden)

    Jennissen Herbert P.

    2016-09-01

    Full Text Available New methodologies are a major driving force of scientific progress. In this case the finding that contact angles can be expressed as complex numbers offers the possibility of a much refined analysis beyond zero degrees of rough ultra-/superhydrophilic, (now called hyperhydrophilic, metal surfaces, which play a distinct role in dental and orthopedic implantology. The approaches, a short theoretical introduction and examples from medical applications are given.

  18. The Mesenchymal Precursor Cell Marker Antibody STRO-1 Binds to Cell Surface Heat Shock Cognate 70.

    Science.gov (United States)

    Fitter, Stephen; Gronthos, Stan; Ooi, Soo Siang; Zannettino, Andrew C W

    2017-04-01

    Since its discovery more than 25 years ago, the STRO-1 antibody has played a fundamental role in defining the hierarchical nature of mesenchymal precursor cells (MPC) and their progeny. STRO-1 antibody binding remains a hallmark of immature pluripotent MPC. Despite the significance of STRO-1 in the MPC field, the identity of the antigen has remained elusive. Using a combination of two-dimensional gel electrophoresis, coupled with Western blotting and Tandem mass spectroscopy, we have identified the STRO-1 antigen as heat shock cognate 70 (HSC70;HSPA8). STRO-1 binds to immune-precipitated HSC70 and siRNA-mediated knock down of HSPA8 reduced STRO-1 binding. STRO-1 surface binding does not correlate with HSC70 expression and sequestration of cholesterol reduces STRO-1 surface binding, suggesting that the plasma membrane lipid composition may be an important determinant in the presentation of HSC70 on the cell surface. HSC70 is present on the surface of STRO-1 + but not STRO-1 - cell lines as assessed by cell surface biotinylation and recombinant HSC70 blocks STRO-1 binding to the cell surface. The STRO-1 epitope on HSC70 was mapped to the ATPase domain using a series of deletion mutants in combination with peptide arrays. Deletion of the first four amino acids of the consensus epitope negated STRO-1 binding. Notably, in addition to HSC70, STRO-1 cross-reacts with heat shock protein 70 (HSP70), however all the clonogenic cell activity is restricted to the STRO-1 BRIGHT /HSP70 - fraction. These results provide important insight into the properties that define multipotent MPC and provide the impetus to explore the role of cell surface HSC70 in MPC biology. Stem Cells 2017;35:940-951. © 2016 AlphaMed Press.

  19. Genetic Diversity Analysis of South and East Asian Duck Populations Using Highly Polymorphic Microsatellite Markers

    Directory of Open Access Journals (Sweden)

    Dongwon Seo

    2016-04-01

    Full Text Available Native duck populations have lower productivity, and have not been developed as much as commercials duck breeds. However, native ducks have more importance in terms of genetic diversity and potentially valuable economic traits. For this reason, population discriminable genetic markers are needed for conservation and development of native ducks. In this study, 24 highly polymorphic microsatellite (MS markers were investigated using commercial ducks and native East and South Asian ducks. The average polymorphic information content (PIC value for all MS markers was 0.584, indicating high discrimination power. All populations were discriminated using 14 highly polymorphic MS markers by genetic distance and phylogenetic analysis. The results indicated that there were close genetic relationships among populations. In the structure analysis, East Asian ducks shared more haplotypes with commercial ducks than South Asian ducks, and they had more independent haplotypes than others did. These results will provide useful information for genetic diversity studies in ducks and for the development of duck traceability systems in the market.

  20. Surface analysis of stone and bone tools

    Science.gov (United States)

    Stemp, W. James; Watson, Adam S.; Evans, Adrian A.

    2016-03-01

    Microwear (use-wear) analysis is a powerful method for identifying tool use that archaeologists and anthropologists employ to determine the activities undertaken by both humans and their hominin ancestors. Knowledge of tool use allows for more accurate and detailed reconstructions of past behavior, particularly in relation to subsistence practices, economic activities, conflict and ritual. It can also be used to document changes in these activities over time, in different locations, and by different members of society, in terms of gender and status, for example. Both stone and bone tools have been analyzed using a variety of techniques that focus on the observation, documentation and interpretation of wear traces. Traditionally, microwear analysis relied on the qualitative assessment of wear features using microscopes and often included comparisons between replicated tools used experimentally and the recovered artifacts, as well as functional analogies dependent upon modern implements and those used by indigenous peoples from various places around the world. Determination of tool use has also relied on the recovery and analysis of both organic and inorganic residues of past worked materials that survived in and on artifact surfaces. To determine tool use and better understand the mechanics of wear formation, particularly on stone and bone, archaeologists and anthropologists have increasingly turned to surface metrology and tribology to assist them in their research. This paper provides a history of the development of traditional microwear analysis in archaeology and anthropology and also explores the introduction and adoption of more modern methods and technologies for documenting and identifying wear on stone and bone tools, specifically those developed for the engineering sciences to study surface structures on micro- and nanoscales. The current state of microwear analysis is discussed as are the future directions in the study of microwear on stone and bone tools.

  1. Surface Properties of TNOs: Preliminary Statistical Analysis

    Science.gov (United States)

    Antonieta Barucci, Maria; Fornasier, S.; Alvarez-Cantal, A.; de Bergh, C.; Merlin, F.; DeMeo, F.; Dumas, C.

    2009-09-01

    An overview of the surface properties based on the last results obtained during the Large Program performed at ESO-VLT (2007-2008) will be presented. Simultaneous high quality visible and near-infrared spectroscopy and photometry have been carried out on 40 objects with various dynamical properties, using FORS1 (V), ISAAC (J) and SINFONI (H+K bands) mounted respectively at UT2, UT1 and UT4 VLT-ESO telescopes (Cerro Paranal, Chile). For spectroscopy we computed the spectral slope for each object and searched for possible rotational inhomogeneities. A few objects show features in their visible spectra such as Eris, whose spectral bands are displaced with respect to pure methane-ice. We identify new faint absorption features on 10199 Chariklo and 42355 Typhon, possibly due to the presence of aqueous altered materials. The H+K band spectroscopy was performed with the new instrument SINFONI which is a 3D integral field spectrometer. While some objects show no diagnostic spectral bands, others reveal surface deposits of ices of H2O, CH3OH, CH4, and N2. To investigate the surface properties of these bodies, a radiative transfer model has been applied to interpret the entire 0.4-2.4 micron spectral region. The diversity of the spectra suggests that these objects represent a substantial range of bulk compositions. These different surface compositions can be diagnostic of original compositional diversity, interior source and/or different evolution with different physical processes affecting the surfaces. A statistical analysis is in progress to investigate the correlation of the TNOs’ surface properties with size and dynamical properties.

  2. Surface plasmon resonance biosensor for the detection of VEGFR-1-a protein marker of myelodysplastic syndromes

    Czech Academy of Sciences Publication Activity Database

    Pimková, K.; Bocková, Markéta; Hegnerová, Kateřina; Suttnar, J.; Čermák, J.; Homola, Jiří; Dyr, J. E.

    2012-01-01

    Roč. 402, č. 1 (2012), s. 381-387 ISSN 1618-2642 R&D Projects: GA AV ČR KAN200670701 Institutional research plan: CEZ:AV0Z20670512 Keywords : surface plasmon resonance * myelodysplastic syndromes * vascular endothelial growth factor Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering Impact factor: 3.659, year: 2012

  3. Lactobacilli differentially modulate expression of cytokines and maturation surface markers in murine dendritic cells

    DEFF Research Database (Denmark)

    Christensen, Hanne Risager; Frøkiær, Hanne; Pestka, J.J.

    2002-01-01

    in the capacity to induce IL-12 and TNF-a production in the DC. Similar but less pronounced differences were observed among lactobacilli in the induction of IL-6 and IL-10. Although all strains up-regulated surface MHC class II and B7-2 (CD86), which is indicative of DC maturation, those lactobacilli...

  4. Radiation Response of Cancer Stem-Like Cells From Established Human Cell Lines After Sorting for Surface Markers

    International Nuclear Information System (INIS)

    Al-Assar, Osama; Muschel, Ruth J.; Mantoni, Tine S.; McKenna, W. Gillies; Brunner, Thomas B.

    2009-01-01

    Purpose: A subpopulation of cancer stem-like cells (CSLC) is hypothesized to exist in different cancer cell lines and to mediate radioresistance in solid tumors. Methods and Materials: Cells were stained for CSLC markers and sorted (fluorescence-activated cell sorter/magnetic beads) to compare foci and radiosensitivity of phosphorylated histone H2AX at Ser 139 (γ-H2AX) in sorted vs. unsorted populations in eight cell lines from different organs. CSLC properties were examined using anchorage-independent growth and levels of activated Notch1. Validation consisted of testing tumorigenicity and postirradiation enrichment of CSLC in xenograft tumors. Results: The quantity of CSLC was generally in good agreement with primary tumors. CSLC from MDA-MB-231 (breast) and Panc-1 and PSN-1 (both pancreatic) cells had fewer residual γ-H2AX foci than unsorted cells, pointing to radioresistance of CSLC. However, only MDA-MB-231 CSLC were more radioresistant than unsorted cells. Furthermore, MDA-MB-231 CSLC showed enhanced anchorage-independent growth and overexpression of activated Notch1 protein. The expression of cancer stem cell surface markers in the MDA-MB-231 xenograft model was increased after exposure to fractionated radiation. In contrast to PSN-1 cells, a growth advantage for MDA-MB-231 CSLC xenograft tumors was found compared to tumors arising from unsorted cells. Conclusions: CSLC subpopulations showed no general radioresistant phenotype, despite the quantities of CSLC subpopulations shown to correspond relatively well in other reports. Likewise, CSLC characteristics were found in some but not all of the tested cell lines. The reported problems in testing for CSLC in cell lines may be overcome by additional techniques, beyond sorting for markers.

  5. Analysis of effectiveness of R1-nj anthocyanin marker for in vivo haploid identification in maize and molecular markers for predicting the inhibition of R1-nj expression.

    Science.gov (United States)

    Chaikam, Vijay; Nair, Sudha K; Babu, Raman; Martinez, Leocadio; Tejomurtula, Jyothsna; Boddupalli, Prasanna M

    2015-01-01

    R1-nj anthocyanin marker inhibition is highly frequent in tropical maize germplasm considerably affecting efficiency of haploid identification. Molecular markers reliably differentiating germplasm with anthocyanin color inhibitor have been identified in this study. The R1-Navajo (R1-nj) color marker facilitates easy and quick identification of haploid kernels at the seed stage during in vivo haploid induction process in maize. However, the Navajo phenotype can be completely suppressed or poorly expressed in some germplasm, making it impossible or inefficient to identify haploids at the seed stage. In this study, we characterized the expression of R1-nj marker in a large array of tropical/subtropical inbred lines, breeding populations and landraces by crossing with the R1-nj-based tropicalized haploid inducer. There was a high frequency of inhibition of the Navajo phenotype in the maize inbred lines, which are used in tropical breeding programs. Genome-wide association mapping showed that the C1 anthocyanin regulatory locus is the most significant genetic factor influencing inhibition of the Navajo phenotype. Molecular marker assays were designed based on polymorphism in the C1 vs C1-I alleles. Analysis of a set of 714 inbred lines demonstrated that a combination of two gene-specific markers--8 bp C1-I InDel and C1-I SNP--could predict with high accuracy the presence of anthocyanin color inhibition in the germplasm analyzed. Information generated in this study aids in making informed decisions on the constitution of source populations for doubled haploid (DH) line development in tropical germplasm, particularly those derived from elite maize lines from CIMMYT. The C1-I gene-specific molecular markers identified and validated will facilitate high-throughput and cost-effective evaluation of a large pool of germplasm for the presence of the dominant color inhibitor in maize germplasm.

  6. Isolation and characterization of microsatellite markers and analysis of genetic variability in Curculigo latifolia Dryand.

    Science.gov (United States)

    Babaei, Nahid; Abdullah, Nur Ashikin Psyquay; Saleh, Ghizan; Abdullah, Thohirah Lee

    2012-11-01

    Curculin, a sweet protein found in Curculigo latifolia fruit has great potential for the pharmaceutical industry. This protein interestingly has been found to have both sweet taste and taste-modifying capacities comparable with other natural sweeteners. According to our knowledge this is the first reported case on the isolation of microsatellite loci in this genus. Hence, the current development of microsatellite markers for C. latifolia will facilitate future population genetic studies and breeding programs for this valuable plant. In this study 11 microsatellite markers were developed using 3' and 5' ISSR markers. The primers were tested on 27 accessions from all states of Peninsular Malaysia. The number of alleles per locus ranged from three to seven, with allele size ranging from 141 to 306 bp. The observed and expected heterozygosity ranged between 0.00-0.65 and 0.38-0.79, respectively. The polymorphic information content ranged from 0.35 to 0.74 and the Shannon's information index ranged from 0.82 to 1.57. These developed polymorphic microsatellites were used for constructing a dendrogram by unweighted pair group method with arithmetic mean cluster analysis using the Dice's similarity coefficient. Accessions association according to their geographical origin was observed. Based on characteristics of isolated microsatellites for C. latifolia accessions all genotype can be distinguished using these 11 microsatellite markers. These polymorphic markers could also be applied to studies on uniformity determination and somaclonal variation of tissue culture plantlets, varieties identification, genetic diversity, analysis of phylogenetic relationship, genetic linkage maps and quantitative trait loci in C. latifolia.

  7. Cell-Surface Proteomics Identifies Lineage-Specific Markers of Embryo-Derived Stem Cells

    OpenAIRE

    Rugg-Gunn, Peter J.; Cox, Brian J.; Lanner, Fredrik; Sharma, Parveen; Ignatchenko, Vladimir; McDonald, Angela C.H.; Garner, Jodi; Gramolini, Anthony O.; Rossant, Janet; Kislinger, Thomas

    2012-01-01

    Summary The advent of reprogramming and its impact on stem cell biology has renewed interest in lineage restriction in mammalian embryos, the source of embryonic (ES), epiblast (EpiSC), trophoblast (TS), and extraembryonic endoderm (XEN) stem cell lineages. Isolation of specific cell types during stem cell differentiation and reprogramming, and also directly from embryos, is a major technical challenge because few cell-surface proteins are known that can distinguish each cell type. We provide...

  8. An evaluation of sequence tagged microsatellite site markers for genetic analysis within Citrus and related species.

    Science.gov (United States)

    Kijas, J M; Fowler, J C; Thomas, M R

    1995-04-01

    Microsatellites, also called sequence tagged microsatellite sites (STMSs), have become important markers for genome analysis but are currently little studied in plants. To assess the value of STMSs for analysis within the Citrus plant species, two example STMSs were isolated from an intergeneric cross between rangpur lime (Citrus x limonia Osbeck) and trifoliate orange (Poncirus trifoliata (L.) Raf.). Unique flanking primers were constructed for polymerase chain reaction amplification both within the test cross and across a broad range of citrus and related species. Both loci showed length variation between test cross parents with alleles segregating in a Mendelian fashion to progeny. Amplification across species showed the STMS flanking primers to be conserved in every genome tested. The traits of polymorphism, inheritance, and conservation across species mean that STMS markers are ideal for genome mapping within Citrus, which contains high levels of genetic variability.

  9. Analysis of cell surface antigens by Surface Plasmon Resonance imaging

    NARCIS (Netherlands)

    Stojanovic, Ivan; Schasfoort, Richardus B.M.; Terstappen, Leonardus Wendelinus Mathias Marie

    2013-01-01

    Surface Plasmon Resonance (SPR) is most commonly used to measure bio-molecular interactions. SPR is used significantly less frequent for measuring whole cell interactions. Here we introduce a method to measure whole cells label free using the specific binding of cell surface antigens expressed on

  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. Genetic diversity analysis of tropical sugar beet (Beta vulgaris L.) varieties in Bangladesh using RAPD markers

    OpenAIRE

    Saclain Saidin; Latif Abdul; Bala Babul; Mallik Mithun; Islam Shahidul

    2016-01-01

    Knowledge on intra-specific genetic variation of an organism is important for its genetic improvement and conservation. In order to estimate genetic variation and relatedness in eleven tropical Sugar beet varieties we used randomly amplified polymorphic DNA (RAPD) markers. The RAPD analysis was performed using six decamer random primers, which amplified a total of 63 DNA fragments of which 43 (68.25%) were found polymorphic. The average polymorphic bands pe...

  12. Wipe sampling for nicotine as a marker of thirdhand tobacco smoke contamination on surfaces in homes, cars, and hotels.

    Science.gov (United States)

    Quintana, Penelope J E; Matt, Georg E; Chatfield, Dale; Zakarian, Joy M; Fortmann, Addie L; Hoh, Eunha

    2013-09-01

    Secondhand smoke contains a mixture of pollutants that can persist in air, dust, and on surfaces for months or longer. This persistent residue is known as thirdhand smoke (THS). Here, we detail a simple method of wipe sampling for nicotine as a marker of accumulated THS on surfaces. We analyzed findings from 5 real-world studies to investigate the performance of wipe sampling for nicotine on surfaces in homes, cars, and hotels in relation to smoking behavior and smoking restrictions. The intraclass correlation coefficient for side-by-side samples was 0.91 (95% CI: 0.87-0.94). Wipe sampling for nicotine reliably distinguished between private homes, private cars, rental cars, and hotels with and without smoking bans and was significantly positively correlated with other measures of tobacco smoke contamination such as air and dust nicotine. The sensitivity and specificity of possible threshold values (0.1, 1, and 10 μg/m(2)) were evaluated for distinguishing between nonsmoking and smoking environments. Sensitivity was highest at a threshold of 0.1 μg/m(2), with 74%-100% of smoker environments showing nicotine levels above threshold. Specificity was highest at a threshold of 10 μg/m(2), with 81%-100% of nonsmoker environments showing nicotine levels below threshold. The optimal threshold will depend on the desired balance of sensitivity and specificity and on the types of smoking and nonsmoking environments. Surface wipe sampling for nicotine is a reliable, valid, and relatively simple collection method to quantify THS contamination on surfaces across a wide range of field settings and to distinguish between nonsmoking and smoking environments.

  13. MIDAS: software for analysis and visualisation of interallelic disequilibrium between multiallelic markers

    Directory of Open Access Journals (Sweden)

    Day Ian NM

    2006-04-01

    Full Text Available Abstract Background Various software tools are available for the display of pairwise linkage disequilibrium across multiple single nucleotide polymorphisms. The HapMap project also presents these graphics within their website. However, these approaches are limited in their use of data from multiallelic markers and provide limited information in a graphical form. Results We have developed a software package (MIDAS – Multiallelic Interallelic Disequilibrium Analysis Software for the estimation and graphical display of interallelic linkage disequilibrium. Linkage disequilibrium is analysed for each allelic combination (of one allele from each of two loci, between all pairwise combinations of any type of multiallelic loci in a contig (or any set of many loci (including single nucleotide polymorphisms, microsatellites, minisatellites and haplotypes. Data are presented graphically in a novel and informative way, and can also be exported in tabular form for other analyses. This approach facilitates visualisation of patterns of linkage disequilibrium across genomic regions, analysis of the relationships between different alleles of multiallelic markers and inferences about patterns of evolution and selection. Conclusion MIDAS is a linkage disequilibrium analysis program with a comprehensive graphical user interface providing novel views of patterns of linkage disequilibrium between all types of multiallelic and biallelic markers. Availability Available from http://www.genes.org.uk/software/midas and http://www.sgel.humgen.soton.ac.uk/midas

  14. Gold nanoparticles as markers for fluorinated surfaces containing embedded amide groups

    Science.gov (United States)

    Ballarin, Barbara; Barreca, Davide; Bertola, Maurizio; Cristina Cassani, Maria; Carraro, Giorgio; Maccato, Chiara; Mignani, Adriana; Nanni, Daniele; Parise, Chiara; Ranieri, Silvia

    2018-05-01

    Indium tin oxide (ITO) substrates were functionalized with fluoroalkylsilanes (FAS) having formula RFC(O)N(R)(CH2)3Si(OMe)3 (1, R = H, RF = C5F11; 2, R = CH3, RF = C5F11;3, R = H, RF = C3F7) and containing embedded amide moieties between the perfluoroalkyl chain and the syloxanic moiety. Subsequently, Au nanoparticle deposition (AuNP) onto the ITO-FAS functionalized surfaces was carried out by immersion into a solution of citrate-stabilized AuNP. The ITO-FAS and AuNP/ITO-FAS modified systems were characterized by various complementary techniques and compared with AuNP/ITO modified with RF(CH2)2Si(OEt)3 (4, RF = C6F13), free from functional groups between the fluorinated tail and the syloxanic moiety. The results showed that only ITO glasses modified with 1, 2 and 3 displayed an oleophobic, as well as hydrophobic, behaviour and that the AuNP Surface Coverage (SC %) directly depended on the fluoroalkylsilane nature with the following trend: 60% ITO-2 > 16% ITO-3 > 9% ITO-1 > 3% ITO-4. The obtained results revealed that, in organosilane 2, the presence of a methyl group on the amide nitrogen increases the steric hindrance in the rotation around the Nsbnd CO bond, resulting in the co-presence of two stable conformers in comparable amounts. Their co-presence in solution, combined with the lack of intermolecular Nsbnd H⋯OCsbnd N hydrogen bonds among the anchored molecules, has dramatic influences on the functionalized ITO, yielding a disorderedly packed coating able to accommodate a large quantity of AuNP. These results indicate that AuNP can act as excellent probes to evaluate the coating layer quality but, at the same time, it is possible to tune the gold loading on electroactive surfaces depending on the chemical structure of the used fluorinated silane.

  15. Surface Preparation for Microdebonding Analysis of Composites

    International Nuclear Information System (INIS)

    Kahraman, Ramazan; Mandell, J. F.

    1999-01-01

    The bond strength between fibers and matrix is an essential property of all composite materials and it must be measured accurately to be able to correlate it with the composite behavior. There are several factors affecting its measurement. This paper discusses the polishing and load application aspects of the indentation test technique for fibre-matrix bond strength determination in polymer and ceramic matrix composites. Different polishing procedures are suggested for polymer and ceramic surfaces for obtaining a smooth surface which is a must for the test results to be reliable. The geometry of the fibers tested was also found to affect the analysis results. For best results, fibers with similar size and which are similarly surrounded by other fibers should be tested. Care should be taken during load application on a fiber for the loading probe not to approach the fiber circumference. The force should be applied in a small increments as possible, however starting from a high enough level to prevent fiber breakage due to surface damage from several loading steps. (Author)

  16. Role of peripheral inflammatory markers in postoperative cognitive dysfunction (POCD: a meta-analysis.

    Directory of Open Access Journals (Sweden)

    Linying Peng

    Full Text Available BACKGROUND: Postoperative cognitive dysfunction (POCD is common following cardiac and non-cardiac surgery, but the pathogenic mechanisms remain unknown. Many studies suggest that an inflammatory response is a key contributor to POCD. The current meta-analysis shows that the levels of peripheral inflammatory markers are associated with POCD. METHODS: An online search was performed to identify peer-reviewed studies without language restriction that measured peripheral inflammatory markers of patients with and without POCD, using PubMed, ScienceDirect, SinoMed and the National Knowledge Infrastructure database. Extracted data were analyzed with STATA (version 12.The standardized mean difference (SMD and the 95% confidence interval (95%CI were calculated for each outcome using a random effect model. Tests of heterogeneity assessment of bias, and meta-regression were performed in the meta-analysis. RESULTS: A total of 13 studies that measured the concentrations of peripheral inflammatory markers were included. The current meta-analysis found significantly higher concentrations of S-100β(SMD[95%CI] (1.377 [0.423, 2.331], p-value < 0.001, N [POCD/non-POCD] =178/391, 7 studies, and interleukin(IL-6 (SMD[95%CI] (1.614 [0.603,2.624], p-value < 0.001, N[POCD/non-POCD] = 91/99, 5 studies, but not of neuron specific enolase, interleukin-1β, or tumor necrosis factor-α , in POCD compared with patients without POCD. In meta-regression analyses, a significant positive association was found between the SMD and the preoperative interleukin-6 peripheral blood concentration in patients with POCD (Coef.= 0.0587, p-value=0.038, 5 studies. CONCLUSIONS: This study shows that POCD is indeed correlated with the concentrations of peripheral inflammatory markers, particularly interleukin-6 and S-100β.

  17. Generation and analysis of expressed sequence tags (ESTs) for marker development in yam (Dioscorea alata L.)

    Science.gov (United States)

    2011-01-01

    Background Anthracnose (Colletotrichum gloeosporioides) is a major limiting factor in the production of yam (Dioscorea spp.) worldwide. Availability of high quality sequence information is necessary for designing molecular markers associated with resistance. However, very limited sequence information pertaining to yam is available at public genome databases. Therefore, this collaborative project was developed for genetic improvement and germplasm characterization of yams using molecular markers. The current investigation is focused on studying gene expression, by large scale generation of ESTs, from one susceptible (TDa 95-0310) and two resistant yam genotypes (TDa 87-01091, TDa 95-0328) challenged with the fungus. Total RNA was isolated from young leaves of resistant and susceptible genotypes and cDNA libraries were sequenced using Roche 454 technology. Results A total of 44,757 EST sequences were generated from the cDNA libraries of the resistant and susceptible genotypes. Greater than 56% of ESTs were annotated using MapMan Mercator tool and Blast2GO search tools. Gene annotations were used to characterize the transcriptome in yam and also perform a differential gene expression analysis between the resistant and susceptible EST datasets. Mining for SSRs in the ESTs revealed 1702 unique sequences containing SSRs and 1705 SSR markers were designed using those sequences. Conclusion We have developed a comprehensive annotated transcriptome data set in yam to enrich the EST information in public databases. cDNA libraries were constructed from anthracnose fungus challenged leaf tissues for transcriptome characterization, and differential gene expression analysis. Thus, it helped in identifying unique transcripts in each library for disease resistance. These EST resources provide the basis for future microarray development, marker validation, genetic linkage mapping and QTL analysis in Dioscorea species. PMID:21303556

  18. Generation and analysis of expressed sequence tags (ESTs for marker development in yam (Dioscorea alata L.

    Directory of Open Access Journals (Sweden)

    Robert Asiedu

    2011-02-01

    Full Text Available Abstract Background Anthracnose (Colletotrichum gloeosporioides is a major limiting factor in the production of yam (Dioscorea spp. worldwide. Availability of high quality sequence information is necessary for designing molecular markers associated with resistance. However, very limited sequence information pertaining to yam is available at public genome databases. Therefore, this collaborative project was developed for genetic improvement and germplasm characterization of yams using molecular markers. The current investigation is focused on studying gene expression, by large scale generation of ESTs, from one susceptible (TDa 95-0310 and two resistant yam genotypes (TDa 87-01091, TDa 95-0328 challenged with the fungus. Total RNA was isolated from young leaves of resistant and susceptible genotypes and cDNA libraries were sequenced using Roche 454 technology. Results A total of 44,757 EST sequences were generated from the cDNA libraries of the resistant and susceptible genotypes. Greater than 56% of ESTs were annotated using MapMan Mercator tool and Blast2GO search tools. Gene annotations were used to characterize the transcriptome in yam and also perform a differential gene expression analysis between the resistant and susceptible EST datasets. Mining for SSRs in the ESTs revealed 1702 unique sequences containing SSRs and 1705 SSR markers were designed using those sequences. Conclusion We have developed a comprehensive annotated transcriptome data set in yam to enrich the EST information in public databases. cDNA libraries were constructed from anthracnose fungus challenged leaf tissues for transcriptome characterization, and differential gene expression analysis. Thus, it helped in identifying unique transcripts in each library for disease resistance. These EST resources provide the basis for future microarray development, marker validation, genetic linkage mapping and QTL analysis in Dioscorea species.

  19. Surface imaging, portal imaging, and skin marker set-up vs. CBCT for radiotherapy of the thorax and pelvis

    Energy Technology Data Exchange (ETDEWEB)

    Pallotta, Stefania; Bucciolini, Marta [Universita degli Studi di Firenze, Dipartimento di Scienze Biomediche Sperimentali e Cliniche, Florence (Italy); AOU Careggi, Sezione di Fisica Medica, Florence (Italy); Vanzi, Eleonora; Marrazzo, Livia [AOU Careggi, Sezione di Fisica Medica, Florence (Italy); Simontacchi, Gabriele; Paiar, Fabiola [AOU Careggi, Sezione di Radioterapia, Florence (Italy); Ceroti, Marco [ISPO, U.O. Epidemiologia Molecolare e Nutrizionale, Florence (Italy); Livi, Lorenzo [Universita degli Studi di Firenze, Dipartimento di Scienze Biomediche Sperimentali e Cliniche, Florence (Italy); AOU Careggi, Sezione di Radioterapia, Florence (Italy)

    2015-09-15

    The aim of this study was to compare surface imaging, portal imaging, and skin marker set-up in radiotherapy of thoracic and pelvic regions, using cone beam computed tomography (CBCT) data as the gold standard. Twenty patients were included in this study. CBCT, surface acquisition (SA), and two orthogonal portal images (PI) were acquired during the first four treatment sessions. Patient set-up corrections, obtained by registering the planning CT with CBCT, were used as the gold standard. Registration results of the PI and SA were evaluated and compared with those obtained with CBCT. The advantage derived from using SA or PI verification systems over a skin marker set-up was also quantified. A statistically significant difference between PI and SA (in favour of PI) was observed in seven patients undergoing treatment of the pelvic region and in two patients undergoing treatment of the thoracic region. The use of SA or PI, compared with a skin marker set-up, improved patient positioning in 50% and 57 % of the thoracic fractions, respectively. For pelvic fractions, the use of PI was beneficial in 73 % of the cases, while the use of SA was beneficial in only 45 %. Patient positioning worsened with SA, particularly along longitudinal and vertical directions. PI yielded more accurate registration results than SA for both pelvic and thoracic fractions. Compared with the skin marker set-up, PI performances were superior to SA for pelvic fractions while comparable results were obtained for thoracic fractions. (orig.) [German] Ziel dieser Studie ist der Vergleich der Patientenpositionierung mittels der 3-D/4-D-Erfassung der Patientenoberflaeche durch ein Abtastsystem, kV/MV-Verifikationsaufnahmen mit Hochenergiebildsystemen und Markierungen auf der Haut bei Bestrahlungen im Thorax- bzw. Beckenbereich. Als Goldstandard zum Vergleich dienten CBCT(''cone beam computed tomography'')-Aufnahmen. Die Studie basiert auf Untersuchungen an 20 Patienten. Es wurden

  20. The Proteomic Analysis of Pancreatic Exocrine Insufficiency Protein Marker in Type 2 Diabetes Mellitus Patients

    Science.gov (United States)

    Srihardyastutie, Arie; Soeatmadji, DW; Fatchiyah; Aulanni'am

    2018-01-01

    Type 2 Diabetes Mellitus (T2D) is the vast majority case of diabetes. Patient with T2D is at higher risk for developing acute or chronic pancreatitis. Prolonged hyperglycemia results in damages to tissue, which also causes dysfunctions of some organ systems, including enzyme or hormone secretions. Commonly, dysfunction or insufficiency of pancreatic exocrine is evaluated by increasing activity of serum pancreatic enzyme, such as amylase and lipase. Although incidence of pancreatitis was found in Indonesian T2D, the pathogenic mechanism still unclear. The aim of this study was to characterize the marker protein that indicated the correlation of pancreatic exocrine insufficiency with progression of T2D. Proteomic analysis using LC-MS/MS was used in identification and characterization of protein marker which indicates insufficiency pancreatic exocrine. First step, protein profile was analyzed by SDS-PAGE methods using serum sample of T2D compared with normal or healthy control, as negative control, and pancreatitis patients, as positive control. Protein with 18 kDa was found as a candidate protein marker which indicated the pancreatic exocrine insufficiency in T2D. The further identification of that protein using LC-MS/MS showed 4 peptide fragments. In silico analysis of the peptide fragment indicated the correlation of pancreatic exocrine insufficiency with progression of T2D was METTL10 - methyltransferase like protein-10.

  1. Implementation and application of real-time motion analysis based on passive markers.

    Science.gov (United States)

    Baroni, G; Ferrigno, G; Pedotti, A

    1998-11-01

    A method for real-time motion analysis based on passive markers is presented. An opto-electronic automatic motion analyser was used as hardware platform and the real-time operation was based on the interfacing between two levels of the system architecture. True real-time acquisition, processing and representation of two-dimensional and three-dimensional kinematics data were implemented through a newly conceived data acquisition procedure and high speed optimisation of the kinematics data processing. The method allows one to operate the motion analysis system in real-time; even when the data elaboration unit is required to perform other processing functions, the only consequence is a decrease in system sampling rate. The maximum number of processed and plotted markers in three dimensions at the highest system sampling rate (100 Hz) turned out to be suitable for the implementation of analytical and visual kinematics biofeedback. An example of the achievable level of complexity in terms of marker disposition model and graphic representation is reported by describing a demonstration of the real-time representation of human face movements. A clinical application of the method for patient position definition and control at radiotherapy units is presented.

  2. Complete 1H NMR spectral analysis of ten chemical markers of Ginkgo biloba

    OpenAIRE

    Napolitano, José G.; Lankin, David C.; Chen, Shao-Nong; Pauli, Guido F.

    2012-01-01

    The complete and unambiguous 1H NMR assignments of ten marker constituents of Ginkgo biloba are described. The comprehensive 1H NMR profiles (fingerprints) of ginkgolide A, ginkgolide B, ginkgolide C, ginkgolide J, bilobalide, quercetin, kaempferol, isorhamnetin, isoquercetin, and rutin in DMSO-d6 were obtained through the examination of 1D 1H NMR and 2D 1H,1H-COSY data, in combination with 1H iterative Full Spin Analysis (HiFSA). The computational analysis of discrete spin systems allowed a ...

  3. Analysis of new microsatellite markers developed from reported sequences of Japanese flounder Paralichthys olivaceus

    Science.gov (United States)

    Yu, Haiyang; Jiang, Liming; Chen, Wei; Wang, Xubo; Wang, Zhigang; Zhang, Quanqi

    2010-12-01

    The expressed sequence tags (ESTs) of Japanese flounder, Paralichthys olivaceus, were selected from GenBank to identify simple sequence repeats (SSRs) or microsatellites. A bioinformatic analysis of 11111 ESTs identified 751 SSR-containing ESTs, including 440 dinucleotide, 254 trinucleotide, 53 tetranucleotide, 95 pentanucleotide and 40 hexanucleotide microsatellites respectively. The CA/TG and GA/TC repeats were the most abundant microsatellites. AT-rich types were predominant among trinucleotide and tetranucleotide microsatellites. PCR primers were designed to amplify 10 identified microsatellites loci. The PCR results from eight pairs of primers showed polymorphisms in wild populations. In 30 wild individuals, the mean observed and expected heterozygosities of these 8 polymorphic SSRs were 0.71 and 0.83 respectively and the average PIC value was 0.8. These microsatellite markers should prove to be a useful addition to the microsatellite markers that are now available for this species.

  4. [Determining mitochondrial molecular markers suitable for genetic diversity analysis of Cordyceps militaris].

    Science.gov (United States)

    Zhang, Yongjie; Guo, Lihong; Zhang, Shu; Liu, Xingzhong

    2015-07-04

    To screen efficient molecular markers suitable for genetic diversity analysis of Cordyceps militaris from mitochondrial DNA. We amplified 12 mitochondrial DNA fragments and 3 nuclear DNA fragments from each of 20 C. militaris isolates and analyzed nucleotide variations on these DNA fragments. We revealed a greatly higher genetic variation in mitochondrial DNA fragments than in nuclear DNA fragments. Specifically, C. militaris isolates exhibited intron presence/absence diversity in some mitochondrial fragments, and more variable sites were found in mitochondrial fragments than in nuclear fragments. The extent of nucleotide variations also varied by mitochondrial fragment, and intronic proteins seemed to be more vulnerable to amino acid changes than exonic proteins. Genetic diversity increased with the number of molecular markers used. We recommended using (in order) nad3-cox2. cox2-nad5, cox2, cox3, cob, and cox1 for future genetic diversity and population genetic studies of C. militaris.

  5. A radiation analysis of lunar surface habitats

    International Nuclear Information System (INIS)

    De Angelis, G.; Wilson, J.W.; Tripathi, R.K.; Clowdsley, M.S.; Nealy, J.E.

    2003-01-01

    An analysis is performed on the radiation environment found on the surface of the Moon, and applied to different possible lunar base mission scenarios. An optimization technique has been used to minimize the astronaut radiation exposure and at the same time control the effect of shielding, in terms of mass addition and material choice, as a mission cost driver. The optimization process performs minimization of mass along all phases of a mission scenario, considered in terms of time frame, equipment, location, crew characteristics and performance required, radiation exposure annual and career limit constraints (those proposed in NCRP 132), and implementation of the ALARA principle. In the lunar environment manned habitats are to host future crews involved in the construction and/or in the utilization of moon based infrastructure. Three different kinds of lunar missions are considered in the analysis, Moon Base Construction Phase, during which astronauts are on the surface just to build an outpost for future resident crews, Moon Base Outpost Phase, during which astronaut crews are resident but continuing exploration and installation activities, and Moon Base Routine Phase, with shifting resident crews. In each scenario various kinds of habitats, from very simple shelters to more complex bases, are considered in detail (e.g. shape, thickness, materials, etc) with considerations of various shielding strategies. The results for all scenarios clearly showed that the direct exposure to the space environment like in transfers and EVAs phases gives the most of the dose, with the proposed shielded habitats and shelters giving quite a good protection from radiation. Operational constraints on hardware and scenarios have all been considered by the optimization techniques. Within the limits of this preliminary analysis, the three Moon Base related mission scenarios are perfectly feasible from the astronaut radiation safety point of view with the currently adopted and proposed

  6. Genetic molecular analysis of Coffea arabica (Rubiaceae hybrids using SRAP markers

    Directory of Open Access Journals (Sweden)

    Manoj Kumar Mishra

    2011-06-01

    Full Text Available In Coffea arabica (arabica coffee, the phenotypic as well as genetic variability has been found low because of the narrow genetic basis and self fertile nature of the species. Because of high similarity in phenotypic appearance among the majority of arabica collections, selection of parental lines for inter-varietals hybridization and identification of resultant hybrids at an early stage of plant growth is difficult. DNA markers are known to be reliable in identifying closely related cultivars and hybrids. Sequence Related Amplified Polymorphism (SRAP is a new molecular marker technology developed based on PCR. In this paper, sixty arabica-hybrid progenies belonging to six crosses were analyzed using 31 highly polymorphic SRAP markers. The analysis revealed seven types of SRAP marker profiles which are useful in discriminating the parents and hybrids. The number of bands amplified per primer pair ranges from 6.13 to 8.58 with average number of seven bands. Among six hybrid combinations, percentage of bands shared between hybrids and their parents ranged from 66.29% to 85.71% with polymorphic bands varied from 27.64% to 60.0%. Percentage of hybrid specific fragments obtained in various hybrid combinations ranged from 0.71% to 10.86% and ascribed to the consequence of meiotic recombination. Based on the similarity index calculation, it was observed that F1 hybrids share maximum number of bands with the female parent compared to male parent. The results obtained in the present study revealed the effectiveness of SRAP technique in cultivar identification and hybrid analysis in this coffee species. Rev. Biol. Trop. 59 (2: 607-617. Epub 2011 June 01.

  7. Surface renewal analysis for estimating turbulent surface fluxes

    International Nuclear Information System (INIS)

    Castellvi, F.

    2009-01-01

    A decade ago, the need for a long-term surface monitoring was recognized to better understand the soil-vegetation-atmosphere scalar exchange and interaction processes. the AmeriFlux concept emerged in the IGBP workshop (La Thuile, IT, 1995). Continuous acquisition of surface fluxes for different species such as temperature, water vapour, CO x , halocarbon, ozone, etc.,) and momentum allows determination of the influence of local (canopy) exchanges, fossil fuel emission, large-scale biotic exchange on ambient concentrations which are crucial to take decisions for protecting natural environments and water resources, to develop new perspective for modern agriculture and forest management and to better understand the global climate change. (Author)

  8. Statistical strategies to reveal potential vibrational markers for in vivo analysis by confocal Raman spectroscopy

    Science.gov (United States)

    Oliveira Mendes, Thiago de; Pinto, Liliane Pereira; Santos, Laurita dos; Tippavajhala, Vamshi Krishna; Téllez Soto, Claudio Alberto; Martin, Airton Abrahão

    2016-07-01

    The analysis of biological systems by spectroscopic techniques involves the evaluation of hundreds to thousands of variables. Hence, different statistical approaches are used to elucidate regions that discriminate classes of samples and to propose new vibrational markers for explaining various phenomena like disease monitoring, mechanisms of action of drugs, food, and so on. However, the technical statistics are not always widely discussed in applied sciences. In this context, this work presents a detailed discussion including the various steps necessary for proper statistical analysis. It includes univariate parametric and nonparametric tests, as well as multivariate unsupervised and supervised approaches. The main objective of this study is to promote proper understanding of the application of various statistical tools in these spectroscopic methods used for the analysis of biological samples. The discussion of these methods is performed on a set of in vivo confocal Raman spectra of human skin analysis that aims to identify skin aging markers. In the Appendix, a complete routine of data analysis is executed in a free software that can be used by the scientific community involved in these studies.

  9. [Biological markers for the prognosis of neuroblastoma: proposal of a method of analysis].

    Science.gov (United States)

    Combaret, V; Delattre, O; Bénard, J; Favrot, M C

    1998-03-01

    The prognosis of pediatric neuroblastoma depends both on clinical presentation and on certain cellular and molecular characteristics. At the present time, two hypotheses can be drawn to explain both clinical and biological heterogeneity. In the first hypothesis, neuroblastoma progresses from early to late clinical stages through a classical multistep process linked to an accumulation of molecular abnormalities. In the second hypothesis, neuroblastoma represents an heterogeneous group of unrelated diseases, where most of stages I and II or stage IVS neuroblastomas can rather be considered as benign tumors, and stage IV neuroblastoma as a true malignant proliferation. To ascertain relevant biological factors for the prognosis of the disease, it is uppermost important that all investigators agree on biological criteria for analysis when neuroblastoma tissue is available in screened and unscreened populations. This paper reviews the biological tools available for prognosis in neuroblastoma, the priority for analysis of biological markers according to reliability, feasibility, and reproducibility of analysis procedure, and the conditions of tissue storage for further analysis of these biological markers. The standardized biological evaluation of neuroblastoma will allow, first, to collect sufficient data for multivariate analysis of prognostic factors and, second, to better define the putative links between various forms of the disease.

  10. Surface and interface analysis an electrochemists toolbox

    CERN Document Server

    Holze, Rudolf

    2009-01-01

    A broad, almost encyclopedic overview of spectroscopic and other analytical techniques useful for investigations of phase boundaries in electrochemistry is presented. The analysis of electrochemical interfaces and interphases on a microscopic, even molecular level, is of central importance for an improved understanding of the structure and dynamics of these phase boundaries. The gained knowledge will be needed for improvements of methods and applications reaching from electrocatalysis, electrochemical energy conversion, biocompatibility of metals, corrosion protection to galvanic surface treatment and finishing. The book provides an overview as complete as possible and enables the reader to choose methods most suitable for tackling his particular task. It is nevertheless compact and does not flood the reader with the details of review papers.

  11. Surface Management System Departure Event Data Analysis

    Science.gov (United States)

    Monroe, Gilena A.

    2010-01-01

    This paper presents a data analysis of the Surface Management System (SMS) performance of departure events, including push-back and runway departure events.The paper focuses on the detection performance, or the ability to detect departure events, as well as the prediction performance of SMS. The results detail a modest overall detection performance of push-back events and a significantly high overall detection performance of runway departure events. The overall detection performance of SMS for push-back events is approximately 55%.The overall detection performance of SMS for runway departure events nears 100%. This paper also presents the overall SMS prediction performance for runway departure events as well as the timeliness of the Aircraft Situation Display for Industry data source for SMS predictions.

  12. Multivariate analysis for the estimation of target localization errors in fiducial marker-based radiotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Takamiya, Masanori [Department of Nuclear Engineering, Graduate School of Engineering, Kyoto University, Kyoto 606-8501, Japan and Department of Radiation Oncology and Image-applied Therapy, Graduate School of Medicine, Kyoto University, Kyoto 606-8507 (Japan); Nakamura, Mitsuhiro, E-mail: m-nkmr@kuhp.kyoto-u.ac.jp; Akimoto, Mami; Ueki, Nami; Yamada, Masahiro; Matsuo, Yukinori; Mizowaki, Takashi; Hiraoka, Masahiro [Department of Radiation Oncology and Image-applied Therapy, Graduate School of Medicine, Kyoto University, Kyoto 606-8507 (Japan); Tanabe, Hiroaki [Division of Radiation Oncology, Institute of Biomedical Research and Innovation, Kobe 650-0047 (Japan); Kokubo, Masaki [Division of Radiation Oncology, Institute of Biomedical Research and Innovation, Kobe 650-0047, Japan and Department of Radiation Oncology, Kobe City Medical Center General Hospital, Kobe 650-0047 (Japan); Itoh, Akio [Department of Nuclear Engineering, Graduate School of Engineering, Kyoto University, Kyoto 606-8501 (Japan)

    2016-04-15

    Purpose: To assess the target localization error (TLE) in terms of the distance between the target and the localization point estimated from the surrogates (|TMD|), the average of respiratory motion for the surrogates and the target (|aRM|), and the number of fiducial markers used for estimating the target (n). Methods: This study enrolled 17 lung cancer patients who subsequently underwent four fractions of real-time tumor tracking irradiation. Four or five fiducial markers were implanted around the lung tumor. The three-dimensional (3D) distance between the tumor and markers was at maximum 58.7 mm. One of the markers was used as the target (P{sub t}), and those markers with a 3D |TMD{sub n}| ≤ 58.7 mm at end-exhalation were then selected. The estimated target position (P{sub e}) was calculated from a localization point consisting of one to three markers except P{sub t}. Respiratory motion for P{sub t} and P{sub e} was defined as the root mean square of each displacement, and |aRM| was calculated from the mean value. TLE was defined as the root mean square of each difference between P{sub t} and P{sub e} during the monitoring of each fraction. These procedures were performed repeatedly using the remaining markers. To provide the best guidance on the answer with n and |TMD|, fiducial markers with a 3D |aRM ≥ 10 mm were selected. Finally, a total of 205, 282, and 76 TLEs that fulfilled the 3D |TMD| and 3D |aRM| criteria were obtained for n = 1, 2, and 3, respectively. Multiple regression analysis (MRA) was used to evaluate TLE as a function of |TMD| and |aRM| in each n. Results: |TMD| for n = 1 was larger than that for n = 3. Moreover, |aRM| was almost constant for all n, indicating a similar scale for the marker’s motion near the lung tumor. MRA showed that |aRM| in the left–right direction was the major cause of TLE; however, the contribution made little difference to the 3D TLE because of the small amount of motion in the left–right direction. The TLE

  13. Multidisciplinary design optimization using response surface analysis

    Science.gov (United States)

    Unal, Resit

    1992-01-01

    Aerospace conceptual vehicle design is a complex process which involves multidisciplinary studies of configuration and technology options considering many parameters at many values. NASA Langley's Vehicle Analysis Branch (VAB) has detailed computerized analysis capabilities in most of the key disciplines required by advanced vehicle design. Given a configuration, the capability exists to quickly determine its performance and lifecycle cost. The next step in vehicle design is to determine the best settings of design parameters that optimize the performance characteristics. Typical approach to design optimization is experience based, trial and error variation of many parameters one at a time where possible combinations usually number in the thousands. However, this approach can either lead to a very long and expensive design process or to a premature termination of the design process due to budget and/or schedule pressures. Furthermore, one variable at a time approach can not account for the interactions that occur among parts of systems and among disciplines. As a result, vehicle design may be far from optimal. Advanced multidisciplinary design optimization (MDO) methods are needed to direct the search in an efficient and intelligent manner in order to drastically reduce the number of candidate designs to be evaluated. The payoffs in terms of enhanced performance and reduced cost are significant. A literature review yields two such advanced MDO methods used in aerospace design optimization; Taguchi methods and response surface methods. Taguchi methods provide a systematic and efficient method for design optimization for performance and cost. However, response surface method (RSM) leads to a better, more accurate exploration of the parameter space and to estimated optimum conditions with a small expenditure on experimental data. These two methods are described.

  14. Genetic variability analysis of Byrsonima crassifolia germplasm collected in Pará State using ISSR markers.

    Science.gov (United States)

    Rodrigues, S M; Moura, E F; Ramos, G K S; Oliveira, M S P

    2016-10-17

    Native of the Amazon, the nanche (Byrsonima crassifolia) is a fruit cultivated by family farmers and used in cooking; as such, it represents an opportunity for regional agribusiness. The Embrapa Eastern Amazon set up an active germplasm bank (BAG) consisting of 22 accessions sampled in 11 municipalities of Pará State. Due to its economic potential, there is an interest to advance the genetic breeding program of this species. The aim of this study was to characterize the BAG nanche collection using inter-simple sequence repeat (ISSR) markers. Accessions were genotyped using 23 pre-selected ISSR primers resulting in 109 amplified polymorphic and 51 monomorphic bands. With eight polymorphic bands each, the most polymorphic primers were UBC 809 and UBC 848. An unweighted pair-group method with arithmetic average cluster analysis based on Jaccard's coefficient indicated that the individuals clustered into two distinct groups. Accessions Igarapé Açu-2 and Augusto Corrêa-Pl 1 were most similar. The genetic dissimilarity values ranged from 0.10 to 0.59. We conclude that the ISSR markers were efficient in detecting polymorphisms in the nanche accessions, and that it is possible to infer the genetic variability among accessions of the collection. This demonstrate the importance of using molecular markers in poorly studied species and the advantages that this information can bring to the genetic improvement of such species.

  15. Imaging Markers of Post-Stroke Depression and Apathy: a Systematic Review and Meta-Analysis.

    Science.gov (United States)

    Douven, Elles; Köhler, Sebastian; Rodriguez, Maria M F; Staals, Julie; Verhey, Frans R J; Aalten, Pauline

    2017-09-01

    Several brain imaging markers have been studied in the development of post-stroke depression (PSD) and post-stroke apathy (PSA), but inconsistent associations have been reported. This systematic review and meta-analysis aims to provide a comprehensive and up-to-date evaluation of imaging markers associated with PSD and PSA. Databases (Medline, Embase, PsycINFO, CINAHL, and Cochrane Database of Systematic Reviews) were searched from inception to July 21, 2016. Observational studies describing imaging markers of PSD and PSA were included. Pooled odds ratios (OR) and 95% confidence intervals (CI) were calculated to examine the association between PSD or PSA and stroke lesion laterality, type, and location, also stratified by study phase (acute, post-acute, chronic). Other imaging markers were reviewed qualitatively. The search retrieved 4502 studies, of which 149 studies were included in the review and 86 studies in the meta-analyses. PSD in the post-acute stroke phase was significantly associated with frontal (OR 1.72, 95% CI 1.34-2.19) and basal ganglia lesions (OR 2.25, 95% CI 1.33-3.84). Hemorrhagic stroke related to higher odds for PSA in the acute phase (OR 2.58, 95% CI 1.18-5.65), whereas ischemic stroke related to higher odds for PSA in the post-acute phase (OR 0.20, 95% CI 0.06-0.69). Frequency of PSD and PSA is modestly associated with stroke type and location and is dependent on stroke phase. These findings have to be taken into consideration for stroke rehabilitation programs, as this could prevent stroke patients from developing PSD and PSA, resulting in better clinical outcome.

  16. Comparative mitogenomic analysis of mirid bugs (Hemiptera: Miridae and evaluation of potential DNA barcoding markers

    Directory of Open Access Journals (Sweden)

    Juan Wang

    2017-08-01

    Full Text Available The family Miridae is one of the most species-rich families of insects. To better understand the diversity and evolution of mirids, we determined the mitogenome of Lygus pratenszs and re-sequenced the mitogenomes of four mirids (i.e., Apolygus lucorum, Adelphocoris suturalis, Ade. fasciaticollis and Ade. lineolatus. We performed a comparative analysis for 15 mitogenomic sequences representing 11 species of five genera within Miridae and evaluated the potential of these mitochondrial genes as molecular markers. Our results showed that the general mitogenomic features (gene content, gene arrangement, base composition and codon usage were well conserved among these mirids. Four protein-coding genes (PCGs (cox1, cox3, nad1 and nad3 had no length variability, where nad5 showed the largest size variation; no intraspecific length variation was found in PCGs. Two PCGs (nad4 and nad5 showed relatively high substitution rates at the nucleotide and amino acid levels, where cox1 had the lowest substitution rate. The Ka/Ks values for all PCGs were far lower than 1 (<0.59, but the Ka/Ks values of cox1-barcode sequences were always larger than 1 (1.34 –15.20, indicating that the 658 bp sequences of cox1 may be not the appropriate marker due to positive selection or selection relaxation. Phylogenetic analyses based on two concatenated mitogenomic datasets consistently supported the relationship of Nesidiocoris + (Trigonotylus + (Adelphocoris + (Apolygus + Lygus, as revealed by nad4, nad5, rrnL and the combined 22 transfer RNA genes (tRNAs, respectively. Taken sequence length, substitution rate and phylogenetic signal together, the individual genes (nad4, nad5 and rrnL and the combined 22 tRNAs could been used as potential molecular markers for Miridae at various taxonomic levels. Our results suggest that it is essential to evaluate and select suitable markers for different taxa groups when performing phylogenetic, population genetic and species identification

  17. Isolation and differentiation of chondrocytic cells derived from human embryonic stem cells using dlk1/FA1 as a novel surface marker

    DEFF Research Database (Denmark)

    Harkness, Linda; Taipaleenmaki, Hanna; Mahmood, Amer

    2009-01-01

    Few surface markers are available to monitor lineage differentiation during chondrogenesis. Recently, delta-like1/fetal antigen1 (dlk1/FA1), a transmembrane protein of the Notch/Delta/Serrata family, was shown to be essential for inducing early chondrogenesis. Thus, we investigated the possible use...... of dlk1/FA1 as a novel surface marker for chondroprogenitor cells during hESC differentiation. We found that, Dlk1/FA1 is expressed specifically in cells undergoing transition from proliferating to prehypertrophic chondrocytes during endochondral ossification of the mouse limb. In hESC cells, dlk1/FA1...... was not expressed by undifferentiated hESC, but expressed during in vitro embryoid bodies (hEBs) formation upon down-regulation of undifferentiated markers e.g. Oct 3/4. Similarly, dlk1/FA1 was expressed in chondrocytic cells during in vivo teratoma formation. Interestingly, treatment of hEBs with Activin B...

  18. Cereal Crop Proteomics: Systemic Analysis of Crop Drought Stress Responses Towards Marker-Assisted Selection Breeding

    Directory of Open Access Journals (Sweden)

    Arindam Ghatak

    2017-06-01

    Full Text Available Sustainable crop production is the major challenge in the current global climate change scenario. Drought stress is one of the most critical abiotic factors which negatively impact crop productivity. In recent years, knowledge about molecular regulation has been generated to understand drought stress responses. For example, information obtained by transcriptome analysis has enhanced our knowledge and facilitated the identification of candidate genes which can be utilized for plant breeding. On the other hand, it becomes more and more evident that the translational and post-translational machinery plays a major role in stress adaptation, especially for immediate molecular processes during stress adaptation. Therefore, it is essential to measure protein levels and post-translational protein modifications to reveal information about stress inducible signal perception and transduction, translational activity and induced protein levels. This information cannot be revealed by genomic or transcriptomic analysis. Eventually, these processes will provide more direct insight into stress perception then genetic markers and might build a complementary basis for future marker-assisted selection of drought resistance. In this review, we survey the role of proteomic studies to illustrate their applications in crop stress adaptation analysis with respect to productivity. Cereal crops such as wheat, rice, maize, barley, sorghum and pearl millet are discussed in detail. We provide a comprehensive and comparative overview of all detected protein changes involved in drought stress in these crops and have summarized existing knowledge into a proposed scheme of drought response. Based on a recent proteome study of pearl millet under drought stress we compare our findings with wheat proteomes and another recent study which defined genetic marker in pearl millet.

  19. Occurrence and suitability of pharmaceuticals and personal care products as molecular markers for raw wastewater contamination in surface water and groundwater.

    Science.gov (United States)

    Tran, Ngoc Han; Li, Jinhua; Hu, Jiangyong; Ong, Say Leong

    2014-03-01

    This study aimed to provide the first and comprehensive data on the occurrence of 17 target pharmaceuticals and personal care products (PPCPs) in urban water environment in Singapore. Meanwhile, this study also verified the suitability of these PPCPs as specific markers of raw wastewater contamination in receiving water bodies in highly urbanized areas where both surface water and groundwater are not impacted by the discharge of treated wastewater effluents. Analytical results of wastewater showed that among 17 target PPCPs examined, only 5 PPCPs were detected in 100 % of raw wastewater samples, including acetaminophen (ACT), carbamazepine (CBZ), caffeine (CF), diethyltoluamide (DEET), and salicylic acid (SA). Similarly, these PPCPs were found in most surface water and groundwater. Interestingly, the three PPCPs (ACT, CBZ, and SA) were only detected in surface water and groundwater in the sampling sites close to relatively older sewer systems, while they were absent in background samples that were collected from the catchment with no known wastewater sources. This suggests that ACT, CBZ, and SA can be used as specific molecular markers of raw wastewater in surface water and groundwater. This study also confirmed that CF and DEET were not really associated with wastewater sources, thus cannot serve well as specific molecular markers of wastewater contamination in receiving water bodies. To the best knowledge of the authors, the use of ACT and SA as specific molecular markers of raw wastewater contamination in urban surface waters and groundwater was first reported. Further studies on the use of ACT, CBZ, and SA along with other chemical/microbial markers are recommended to identify and differentiate contamination sources of surface waters/groundwater.

  20. Genetic variation of space flight carried rice and mutant analysis by AFLP molecular marker

    International Nuclear Information System (INIS)

    Pu Zhigang; Zhang Zhiyong; Xiang Yuewu; Zhang Zhixiong; Cai Pingzhong; Wen Chunmiao; Zheng Jiakui

    2006-01-01

    Rice seeds were carried by 'Shenzhou No.3' space shuttle, a mutant with golden chaff, stem and leaf was selected and named Golden 1 after the seeds returned to the earth. Except the golden color, other traits of Golden 1 are no obviously different with its original material H9808. Genetic analysis identified that color variation was control by a pair of recessive gene. The DNA fragments of the mutant were compared with its parent by AFLP molecular markers. Five specific bands were found through a serial selection. (authors)

  1. Analysis of Fluid Flow over a Surface

    Science.gov (United States)

    McCloud, Peter L. (Inventor)

    2013-01-01

    A method, apparatus, and computer program product for modeling heat radiated by a structure. The flow of a fluid over a surface of a model of the structure is simulated. The surface has a plurality of surface elements. Heat radiated by the plurality of surface elements in response to the fluid flowing over the surface of the model of the structure is identified. An effect of heat radiated by at least a portion of the plurality of surface elements on each other is identified. A model of the heat radiated by the structure is created using the heat radiated by the plurality of surface elements and the effect of the heat radiated by at least a portion of the plurality of surface elements on each other.

  2. Global Surface Warming Hiatus Analysis Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were used to conduct the study of the global surface warming hiatus, an apparent decrease in the upward trend of global surface temperatures since 1998....

  3. Computer simulation, nuclear techniques and surface analysis

    Directory of Open Access Journals (Sweden)

    Reis, A. D.

    2010-02-01

    Full Text Available This article is about computer simulation and surface analysis by nuclear techniques, which are non-destructive. The “energy method of analysis” for nuclear reactions is used. Energy spectra are computer simulated and compared with experimental data, giving target composition and concentration profile information. Details of prediction stages are given for thick flat target yields. Predictions are made for non-flat targets having asymmetric triangular surface contours. The method is successfully applied to depth profiling of 12C and 18O nuclei in thick targets, by deuteron (d,p and proton (p,α induced reactions, respectively.

    Este artículo trata de simulación por ordenador y del análisis de superficies mediante técnicas nucleares, que son no destructivas. Se usa el “método de análisis en energía” para reacciones nucleares. Se simulan en ordenador espectros en energía que se comparan con datos experimentales, de lo que resulta la obtención de información sobre la composición y los perfiles de concentración de la muestra. Se dan detalles de las etapas de las predicciones de espectros para muestras espesas y planas. Se hacen predicciones para muestras no planas que tienen contornos superficiales triangulares asimétricos. Este método se aplica con éxito en el cálculo de perfiles en profundidad de núcleos de 12C y de 18O en muestras espesas a través de reacciones (d,p y (p,α inducidas por deuterones y protones, respectivamente.

  4. Multiplexed Analysis of Serum Breast and Ovarian Cancer Markers by Means of Suspension Bead-quantum Dot Microarrays

    Science.gov (United States)

    Brazhnik, Kristina; Sokolova, Zinaida; Baryshnikova, Maria; Bilan, Regina; Nabiev, Igor; Sukhanova, Alyona

    Multiplexed analysis of cancer markers is crucial for early tumor diagnosis and screening. We have designed lab-on-a-bead microarray for quantitative detection of three breast cancer markers in human serum. Quantum dots were used as bead-bound fluorescent tags for identifying each marker by means of flow cytometry. Antigen-specific beads reliably detected CA 15-3, CEA, and CA 125 in serum samples, providing clear discrimination between the samples with respect to the antigen levels. The novel microarray is advantageous over the routine single-analyte ones due to the simultaneous detection of various markers. Therefore the developed microarray is a promising tool for serum tumor marker profiling.

  5. Molecular marker analysis as a guide to the sources of fine organic aerosols

    International Nuclear Information System (INIS)

    Rogge, W.F.; Cass, G.R.; Hildemann, L.M.; Simoneit, B.R.T.

    1992-07-01

    The molecular composition of fine particulate (D p ≥ 2 μm) organic aerosol emissions from the most important sources in the Los Angeles area has been determined. Likewise, ambient concentration patterns for more than 80 single organic compounds have been measured at four urban sites (West Los Angeles, Downtown Los Angeles, Pasadena, and Rubidoux) and at one remote offshore site (San Nicolas Island). It has been found that cholesterol serves as a marker compound for emissions from charbroilers and other meat cooking operations. Vehicular exhaust being emitted from diesel and gasoline powered engines can be traced in the Los Angeles atmosphere using fossil petroleum marker compounds such as steranes and pentacyclic triterpanes (e.g., hopanes). Biogenic fine particle emission sources such as plant fragments abraded from leaf surfaces by wind and weather can be traced in the urban atmosphere. Using distinct and specific source organic tracers or assemblages of organic compounds characteristic for the sources considered it is possible to estimate the influence of different source types at any urban site where atmospheric data are available

  6. Surface analysis of selected hydrophobic materials

    Science.gov (United States)

    Wisniewska, Sylwia Katarzyna

    This dissertation contains a series of studies on hydrophobic surfaces by various surface sensitive techniques such as contact angle measurements, Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), and atomic force microscopy (AFM). Hydrophobic surfaces have been classified as mineral surfaces, organic synthetic surfaces, or natural biological surfaces. As a model hydrophobic mineral surface, elemental sulfur has been selected. The sulfur surface has been characterized for selected allotropic forms of sulfur such as rhombic, monoclinic, plastic, and cyclohexasulfur. Additionally, dextrin adsorption at the sulfur surface was measured. The structure of a dextrin molecule showing hydrophobic sites has been presented to support the proposed hydrophobic bonding nature of dextrin adsorption at the sulfur surface. As a model organic hydrophobic surface, primary fatty amines such as dodecylamine, hexadecylamine, and octadecylamine were chosen. An increase of hydrophobicity, significant changes of infrared bands, and surface topographical changes with time were observed for each amine. Based on the results it was concluded that hydrocarbon chain rearrangement associated with recrystallization took place at the surface during contact with air. A barley straw surface was selected as a model of biological hydrophobic surfaces. The differences in the contact angles for various straw surfaces were explained by the presence of a wax layer. SEM images confirmed the heterogeneity and complexity of the wax crystal structure. AFM measurements provided additional structural details including a measure of surface roughness. Additionally, straw degradation as a result of conditioning in an aqueous environment was studied. Significant contact angle changes were observed as soon as one day after conditioning. FTIR studies showed a gradual wax layer removal due to straw surface decomposition. SEM and AFM images revealed topographical changes and biological

  7. UGT1A1 gene linkage analysis: application of polymorphic markers rs4148326/rs4124874 in the Iranian population

    Directory of Open Access Journals (Sweden)

    Zakiye Nadeali

    2017-08-01

    Full Text Available Objective(s: Mutations in the UGT1A1 gene are responsible for hyperbilirubinemia syndromes including Crigler-Najjar type 1 and 2 and Gilbert syndrome. In view of the genetic heterogeneity and involvement of large numbers of the disease causing mutations, the application of polymorphic markers in the UGTA1 gene could be useful in molecular diagnosis of the disease. Materials and Methods: In the present study, two polymorphic markers including rs4148326 and rs4124874 in the UGT1A1 gene region were characterized. The markers were selected using bioinformatics analysis of the UGT1A1 gene region and genotyped in 212 unrelated healthy individuals and 13 family trios in the Iranian population using Tetra-Primer ARMS PCR technique. The allele frequency and population status of the alleles were estimated using GENEPOP, FBAT, PowerMarker and Arlequin software. Results: The results indicated that in the case of rs4148326 marker, allele frequency for T and C allele was 66.04% and 33.96%, respectively. For rs4124874 marker, allele frequency for G and T alleles was 39.4% and 60.6%, respectively. The values of heterozygosity index for the markers examined were 64.1 for rs4148326 and 72.1 for rs4124874, respectively. The haplotype estimation analysis of the markers resulted in three informative haplotypes with frequencies ≥0.05. Moreover, the results suggested the presence of linkage disequilibrium between two markers. Conclusion: Altogether, the data suggested that rs4148326 and rs4124874 could be introduced as informative markers for molecular diagnosis of Crigler-Najjar type 1 and 2 and Gilbert syndrome in the Iranian population.

  8. Are Urinary Tubular Injury Markers Useful in Chronic Kidney Disease? A Systematic Review and Meta Analysis.

    Science.gov (United States)

    Zhou, Le-Ting; Lv, Lin-Li; Pan, Ming-Ming; Cao, Yu-Han; Liu, Hong; Feng, Ye; Ni, Hai-Feng; Liu, Bi-Cheng

    2016-01-01

    Adverse outcome of chronic kidney disease, such as end stage renal disease, is a significant burden on personal health and healthcare costs. Urinary tubular injury markers, such as NGAL, KIM-1 and NAG, could provide useful prognostic value for the early identification of high-risk patients. However, discrepancies between recent large prospective studies have resulted in controversy regarding the potential clinical value of these markers. Therefore, we conducted the first meta-analysis to provide a more persuasive argument to this debate. In the current meta-analysis, based on ten prospective studies involving 29366 participants, we evaluated the role of urinary tubular injury markers (NGAL, KIM-1 and NAG) in predicting clinical outcomes including CKD stage 3, end stage renal disease and mortality. The prognostic values of these biomarkers were estimated using relative risks and 95% confidence interval in adjusted models. All risk estimates were normalized to those of 1 standard deviation increase in log-scale concentrations to minimize heterogeneity. Fixed-effects models were adopted to combine risk estimates. The quality of the research and between-study heterogeneity were evaluated. The level of research evidence was identified according to the GRADE profiler. uNGAL was identified as an independent risk predictor of ESRD (pooled adjusted relative risk: 1.40[1.21 to 1.61], pchronic kidney disease. A borderline significance of uKIM-1 in predicting CKD stage 3 independently in the community-based population was observed (pooled adjusted relative risk: 1.13[1.00 to 1.27], p = 0.057). Only the prognostic value of uNGAL for ESRD was supported by a grade B level of evidence. The concentration of uNGAL can be used in practice as an independent predictor of end stage renal disease among patients with chronic kidney disease, but it may be not useful in predicting disease progression to CKD stage 3 among community-based population.

  9. Validation of tumor protein marker quantification by two independent automated immunofluorescence image analysis platforms

    Science.gov (United States)

    Peck, Amy R; Girondo, Melanie A; Liu, Chengbao; Kovatich, Albert J; Hooke, Jeffrey A; Shriver, Craig D; Hu, Hai; Mitchell, Edith P; Freydin, Boris; Hyslop, Terry; Chervoneva, Inna; Rui, Hallgeir

    2016-01-01

    Protein marker levels in formalin-fixed, paraffin-embedded tissue sections traditionally have been assayed by chromogenic immunohistochemistry and evaluated visually by pathologists. Pathologist scoring of chromogen staining intensity is subjective and generates low-resolution ordinal or nominal data rather than continuous data. Emerging digital pathology platforms now allow quantification of chromogen or fluorescence signals by computer-assisted image analysis, providing continuous immunohistochemistry values. Fluorescence immunohistochemistry offers greater dynamic signal range than chromogen immunohistochemistry, and combined with image analysis holds the promise of enhanced sensitivity and analytic resolution, and consequently more robust quantification. However, commercial fluorescence scanners and image analysis software differ in features and capabilities, and claims of objective quantitative immunohistochemistry are difficult to validate as pathologist scoring is subjective and there is no accepted gold standard. Here we provide the first side-by-side validation of two technologically distinct commercial fluorescence immunohistochemistry analysis platforms. We document highly consistent results by (1) concordance analysis of fluorescence immunohistochemistry values and (2) agreement in outcome predictions both for objective, data-driven cutpoint dichotomization with Kaplan–Meier analyses or employment of continuous marker values to compute receiver-operating curves. The two platforms examined rely on distinct fluorescence immunohistochemistry imaging hardware, microscopy vs line scanning, and functionally distinct image analysis software. Fluorescence immunohistochemistry values for nuclear-localized and tyrosine-phosphorylated Stat5a/b computed by each platform on a cohort of 323 breast cancer cases revealed high concordance after linear calibration, a finding confirmed on an independent 382 case cohort, with concordance correlation coefficients >0

  10. Reconstruction Accuracy Assessment of Surface and Underwater 3D Motion Analysis: A New Approach

    Directory of Open Access Journals (Sweden)

    Kelly de Jesus

    2015-01-01

    Full Text Available This study assessed accuracy of surface and underwater 3D reconstruction of a calibration volume with and without homography. A calibration volume (6000 × 2000 × 2500 mm with 236 markers (64 above and 88 underwater control points—with 8 common points at water surface—and 92 validation points was positioned on a 25 m swimming pool and recorded with two surface and four underwater cameras. Planar homography estimation for each calibration plane was computed to perform image rectification. Direct linear transformation algorithm for 3D reconstruction was applied, using 1600000 different combinations of 32 and 44 points out of the 64 and 88 control points for surface and underwater markers (resp.. Root Mean Square (RMS error with homography of control and validations points was lower than without it for surface and underwater cameras (P≤0.03. With homography, RMS errors of control and validation points were similar between surface and underwater cameras (P≥0.47. Without homography, RMS error of control points was greater for underwater than surface cameras (P≤0.04 and the opposite was observed for validation points (P≤0.04. It is recommended that future studies using 3D reconstruction should include homography to improve swimming movement analysis accuracy.

  11. Autonomous Aerobraking Using Thermal Response Surface Analysis

    Science.gov (United States)

    Prince, Jill L.; Dec, John A.; Tolson, Robert H.

    2007-01-01

    Aerobraking is a proven method of significantly increasing the science payload that can be placed into low Mars orbits when compared to an all propulsive capture. However, the aerobraking phase is long and has mission cost and risk implications. The main cost benefit is that aerobraking permits the use of a smaller and cheaper launch vehicle, but additional operational costs are incurred during the long aerobraking phase. Risk is increased due to the repeated thermal loading of spacecraft components and the multiple attitude and propulsive maneuvers required for successful aerobraking. Both the cost and risk burdens can be significantly reduced by automating the aerobraking operations phase. All of the previous Mars orbiter missions that have utilized aerobraking have increasingly relied on onboard calculations during aerobraking. Even though the temperature of spacecraft components has been the limiting factor, operational methods have relied on using a surrogate variable for mission control. This paper describes several methods, based directly on spacecraft component maximum temperature, for autonomously predicting the subsequent aerobraking orbits and prescribing apoapsis propulsive maneuvers to maintain the spacecraft within specified temperature limits. Specifically, this paper describes the use of thermal response surface analysis in predicting the temperature of the spacecraft components and the corresponding uncertainty in this temperature prediction.

  12. Analysis of genetic diversity identified by amplified fragment length polymorphism marker in hybrid wheat.

    Science.gov (United States)

    Ejaz, M; Qidi, Z; Gaisheng, Z; Na, N; Huiyan, Z; Qunzhu, W

    2015-08-07

    Amplified fragment length polymorphism markers were used to assess genetic diversity in 10 male sterile wheat crop lines (hetero-cytoplasm with the same nucleus) in relation to a restorer wheat line. These male sterile lines were evaluated using 64 amplified fragment length polymorphism primer combinations, and 13 primers produced polymorphic bands, generating a total 682 fragments. Of the 682 fragments, 113 were polymorphic. The polymorphic information content and marker index values demonstrated the utility of the primer combinations used in the present study. Unweighted pair group method with arithmetic mean and principal coordinate analysis of the genotypic data revealed clustering of accessions based on genetic relationships, and accessions were separated into 2 groups with their restorer line. Jaccard's similarity coefficient values suggested good variability among the male sterile lines, indicating their utility in breeding programs. The fallouts of analysis of molecular variance showed large within-group population variation, accounting for 77% of variation, while among-group comparison accounted for 23% of the total molecular variation, which was statistically significant. The molecular diversity observed in this study will be useful for selecting appropriate accessions for plant improvement and hybridization through molecular-breeding approaches and for developing suitable conservation strategies.

  13. 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.

  14. Genetic Variability Analysis of the Polyploid Complex of Acacia nilotica (L. Willd. Using RAPD Markers

    Directory of Open Access Journals (Sweden)

    Chevallier, MH.

    2008-01-01

    Full Text Available The genetic variability of nine Acacia nilotica subspecies of various origins was analyzed by thirty-six RAPD primers. Sixteen among them produced polymorphic bands and generated 166 polymorphic markers. The amplified bands were separated by electrophoresis on 1.8% agarose gel. The analysis of 166 RAPD markers allowed to distinguish essentially three main groups in Acacia nilotica complex: (i The first group comprised subspecies, indica, cupressiformis, nilotica, tomentosa. Subspecies subalata and jacquemontii of which the systematic position is unclear seems to belong to this group. (ii The second group comprised subspecies adstringens and leiocarpa. (iii Kraussiana subspecies distinguishes itself from first two groups. The genetic variability within populations (H was calculated through Shannon index. Subspecies adstringens presents the lowest within population variability (H= 0.015 while kraussiana and leiocarpa subspecies showed high variation index (H= 0.095 and (H= 0.096 respectively. The genetic variability analysis of Acacia nilotica revealed large differences between subspecies but no correlation between geographic distances and genetic distances could be established. Subspecies native of east Africa presented higher allelic richness than west African and Indian ones.

  15. Genome-Wide Association Analysis of Diverse Soybean Genotypes Reveals Novel Markers for Nitrogen Traits

    Directory of Open Access Journals (Sweden)

    Arun Prabhu Dhanapal

    2015-11-01

    Full Text Available Nitrogen is a primary plant nutrient that plays a major role in achieving maximum economic yield. Insufficient availability most often limits soybean [ (L. Merr.] crop growth. Symbiotic N fixation in soybean is highly sensitive to limited water availability, and breeding for reduced N fixation sensitivity to drought is considered an important objective to improve yields under drought. The objective of this study was to identify single nucleotide polymorphism (SNP markers associated with N traits. A collection of 373 diverse soybean genotypes were grown in four field environments (2 yr and two locations and characterized for N derived from atmosphere (Ndfa, N concentration ([N], and C/N ratio. The population structure of 373 soybean genotypes was assessed based on 31,145 SNPs and genome-wide association analysis using a unified mixed model identified SNPs associated with Ndfa, [N], and C/N ratio. Although the Ndfa, [N], and C/N ratio values were significantly different between the two locations in both years, results were consistent among genotypes across years and locations. While numerous SNPs were identified by association analysis for each trait in only one of the four environments, 17, 19, and 24 SNPs showed a significant association with Ndfa, [N], and C/N ratio, respectively, in at least two environments as well as with the average across all four environments. These markers represent an important resource for pyramiding favorable alleles for drought tolerance and for identifying extremes for comparative physiological studies.

  16. Development of CACTA transposon derived SCAR markers and their use in population structure analysis in Zea mays.

    Science.gov (United States)

    Roy, Neha Samir; Park, Kyong-Cheul; Lee, Sung-Il; Im, Min-Ji; Ramekar, Rahul Vasudeo; Kim, Nam-Soo

    2018-02-01

    Molecular marker technologies have proven to be an important breakthrough for genetic studies, construction of linkage maps and population genetics analysis. Transposable elements (TEs) constitute major fractions of repetitive sequences in plants and offer a wide range of possible areas to be explored as molecular markers. Sequence characterized amplified region (SCAR) marker development provides us with a simple and time saving alternative approach for marker development. We employed the CACTA-TD to develop SCARs and then integrated them into linkage map and used them for population structure and genetic diversity analysis of corn inbred population. A total of 108 dominant SCAR markers were designed out of which, 32 were successfully integrated in to the linkage map of maize RIL population and the remaining were added to a physical map for references to check the distribution throughout all chromosomes. Moreover, 76 polymorphic SCARs were used for diversity analysis of corn accessions being used in Korean corn breeding program. The overall average polymorphic information content (PIC) was 0.34, expected heterozygosity was 0.324 and Shannon's information index was 0.491 with a percentage of polymorphism of 98.67%. Further analysis by associating with desirable traits may also provide some accurate trait specific tagged SCAR markers. TE linked SCARs can provide an added level of polymorphism as well as improved discriminating ability and therefore can be useful in further breeding programs to develop high yielding germplasm.

  17. Surface Operations Data Analysis and Adaptation Tool, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — This effort undertook the creation of a Surface Operations Data Analysis and Adaptation (SODAA) tool to store data relevant to airport surface research and...

  18. Migration of radio-opaque markers injected into tendon grafts: a study using roentgen stereophotogrammetric analysis (RSA).

    Science.gov (United States)

    Smith, Conrad Kay; Hull, M L; Howell, S M

    2005-10-01

    An increase in anterior laxity following reconstruction of the anterior cruciate ligament (ACL) can result from lengthening of the graft construct either at the sites of fixation and/or between the sites of fixation (i.e., graft substance). Roentgen stereophotogrammetric analysis (RSA), which requires that radio-opaque markers be attached to the graft, has been shown to be a useful technique in determining lengthening in these regions. Previous methods have been used for attaching radio-opaque markers to the graft, but they all have limitations particularly for single-loop grafts. Therefore, the objective of this study was to evaluate injecting markers directly into the substance of a tendon as a viable method for measuring lengthening of single-loop graft constructs by determining the maximum amount of migration after cyclic loading. Tantalum spheres of 0.8 mm diameter were used as tendon markers. Ten single-loop tendon grafts were passed through tibial tunnels drilled in calf tibias and fixed with a tibial fixation device. Two tendon markers were inserted in one tendon bundle of each graft and the grafts were cyclically loaded for 225,000 cycles from 20 N to 170 N. At specified intervals, simultaneous radiographs were obtained of the tendon markers. Marker migration was computed as the change in distance between the two tendon markers parallel to the axis of the tibial tunnel. Marker migration had a root mean square (RMS) value of less than 0.1 mm. Because the RMS value indicates the error introduced into measurements of lengthening and because this error is negligible, the method described for attaching markers to single-loop ACL grafts has the potential to be useful for determining lengthening of single-loop ACL graft constructs in in vivo studies in humans.

  19. Oxidative and Anti-Oxidative Stress Markers in Chronic Glaucoma: A Systematic Review and Meta-Analysis

    OpenAIRE

    Benoist d?Azy, C?dric; Pereira, Bruno; Chiambaretta, Fr?d?ric; Dutheil, Fr?d?ric

    2016-01-01

    Chronic glaucoma is a multifactorial disease among which oxidative stress may play a major pathophysiological role. We conducted a systematic review and meta-analysis to evaluate the levels of oxidative and antioxidative stress markers in chronic glaucoma compared with a control group. The PubMed, Cochrane Library, Embase and Science Direct databases were searched for studies reporting oxidative and antioxidative stress markers in chronic glaucoma and in healthy controls using the following k...

  20. Identification of Potential Transcriptomic Markers in Developing Ankylosing Spondylitis: A Meta-Analysis of Gene Expression Profiles

    OpenAIRE

    Fang, Fang; Pan, Jian; Xu, Lixiao; Li, Gang; Wang, Jian

    2015-01-01

    The goal of this study was to identify potential transcriptomic markers in developing ankylosing spondylitis by a meta-analysis of multiple public microarray datasets. Using the INMEX (integrative meta-analysis of expression data) program, we performed the meta-analysis to identify consistently differentially expressed (DE) genes in ankylosing spondylitis and further performed functional interpretation (gene ontology analysis and pathway analysis) of the DE genes identified in the meta-analys...

  1. Genetic diversity analysis of Valencia and Navel group sweet orange cultivars by SSR markers

    Directory of Open Access Journals (Sweden)

    İlknur POLAT

    2015-06-01

    Full Text Available Sweet orange [Citrus sinensis (L. Osbeck] fruit is one of the main citrus fruits, Navel and Valencia group sweet orange being the most representative and recognizable species of this species. The aims of this study were to determine genetic relationships and diversity of 84 Navel and 36 Valencia groups of sweet orange using SSR (simple sequence repeat molecular markers. Twenty-six SSR primers were tested on these accessions. Seven SSR primers produced thirteen polymorphic fragments, eight SSR primers produced monomorphic fragments, and eleven SSR primers produced no scorable fragments. Thirteen SSR primers produced a total of 29 fragments and 13 of them were polymorphic. The number of average polymorphic fragments per primer was 1.93. The mean polymorphism information content (PIC and marker index (MI are 0.16 and 11.74, respectively. The Dice’s similarity coefficient among Navel and Valencia group sweet oranges ranged from 0.42 to 1.00 and matrix correlation (r was 0.79. In the cluster analysis, Navel group sweet oranges were indicated as a separate group from Valencia group sweet oranges. ‘Antalya (40’ was most distinct accessions from the others.

  2. Analysis of water soluble polysaccharides as a potential chemotaxonomic marker for landraces in Bixa orellana.

    Science.gov (United States)

    Parimalan, Rangan; Mahendranath, Gondi; Giridhar, Parvatam

    2014-02-01

    Annatto tree (Bixa orellana L.) is native to Brazil and is now under cultivation in many parts of world for its reddish orange 'annatto' dye. There are three types of landraces in annatto and they are distinguished based on fruit shape i.e., ovate, conical and hemispherical, whose pigment yield differs. Since annatto pigment yield varies with landrace, it is necessary to characterize markers towards the identification of landraces. In this study, we characterized water soluble polysaccharides (WSP) of twigs from three landraces using size-exclusion chromatography (SEC), Fourier-transform Infrared spectroscopy (FT-IR), nuclear magnetic resonance spectroscopy (NMR) and gas liquid chromatography (GLC) for their potential use as chemotaxonomic markers to distinguish the landraces. GLC analysis on WSP showed hemispherical type contained 38% rhamnose, while conical and ovate types contained 17% and 34% glucose, respectively. Thus, glucose and rhamnose content of WSP could be used to distinguish the three landraces. Further, differences in calculated molecular weight as revealed by SEC (281.8, 151.3 and 79.4 kDa for conical, hemispherical and ovate types, respectively) could also be used to distinguish the three landraces.

  3. A New Cluster Analysis-Marker-Controlled Watershed Method for Separating Particles of Granular Soils

    Directory of Open Access Journals (Sweden)

    Md Ferdous Alam

    2017-10-01

    Full Text Available An accurate determination of particle-level fabric of granular soils from tomography data requires a maximum correct separation of particles. The popular marker-controlled watershed separation method is widely used to separate particles. However, the watershed method alone is not capable of producing the maximum separation of particles when subjected to boundary stresses leading to crushing of particles. In this paper, a new separation method, named as Monash Particle Separation Method (MPSM, has been introduced. The new method automatically determines the optimal contrast coefficient based on cluster evaluation framework to produce the maximum accurate separation outcomes. Finally, the particles which could not be separated by the optimal contrast coefficient were separated by integrating cuboid markers generated from the clustering by Gaussian mixture models into the routine watershed method. The MPSM was validated on a uniformly graded sand volume subjected to one-dimensional compression loading up to 32 MPa. It was demonstrated that the MPSM is capable of producing the best possible separation of particles required for the fabric analysis.

  4. Genetic diversity analysis among collected purslane (Portulaca oleracea L.) accessions using ISSR markers.

    Science.gov (United States)

    Alam, M Amirul; Juraimi, Abdul Shukor; Rafii, Mohd Yusop; Hamid, Azizah Abdul; Arolu, Ibrahim Wasiu; Abdul Latif, M

    2015-01-01

    Genetic diversity and relationships among 45 collected purslane accessions were evaluated using ISSR markers. The 28 primers gave a total of 167 bands, among which 163 were polymorphic (97.6%). The genetic diversity as estimated by Shannon's information index was 0.513, revealing a quite high level of genetic diversity in the germplasm. The average number of observed allele, effective allele, expected heterozygosity, polymorphic information content (PIC) and Nei's index were 5.96, 1.59, 0.43, 0.35 and 0.35, respectively. The UPGMA dendrogram based on Nei's genetic distance grouped the whole germplasm into 7 distinct clusters. The analysis of molecular variance (AMOVA) revealed that 89% of total variation occurred within population, while 11% were found among populations. Based on the constructed dendrogram using ISSR markers those accessions that are far from each other by virtue of genetic origin and diversity index (like Ac1 and Ac42; Ac19 and Ac45; Ac9 and Ac23; Ac18 and A25; Ac24 and Ac18) are strongly recommended to select as parent for future breeding program to develop high yielding and stress tolerant purslane variety in contribution to global food security. Copyright © 2014 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  5. Atomic force microscopy analysis of different surface treatments of Ti dental implant surfaces

    International Nuclear Information System (INIS)

    Bathomarco, R.V.; Solorzano, G.; Elias, C.N.; Prioli, R.

    2004-01-01

    The surface of commercial unalloyed titanium, used in dental implants, was analyzed by atomic force microscopy. The morphology, roughness, and surface area of the samples, submitted to mechanically-induced erosion, chemical etching and a combination of both, were compared. The results show that surface treatments strongly influence the dental implant physical and chemical properties. An analysis of the length dependence of the implant surface roughness shows that, for scan sizes larger than 50 μm, the average surface roughness is independent of the scanning length and that the surface treatments lead to average surface roughness in the range of 0.37 up to 0.48 μm. It is shown that the implant surface energy is sensitive to the titanium surface area. As the area increases there is a decrease in the surface contact angle

  6. Atomic force microscopy analysis of different surface treatments of Ti dental implant surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Bathomarco, R.V.; Solorzano, G.; Elias, C.N.; Prioli, R

    2004-06-30

    The surface of commercial unalloyed titanium, used in dental implants, was analyzed by atomic force microscopy. The morphology, roughness, and surface area of the samples, submitted to mechanically-induced erosion, chemical etching and a combination of both, were compared. The results show that surface treatments strongly influence the dental implant physical and chemical properties. An analysis of the length dependence of the implant surface roughness shows that, for scan sizes larger than 50 {mu}m, the average surface roughness is independent of the scanning length and that the surface treatments lead to average surface roughness in the range of 0.37 up to 0.48 {mu}m. It is shown that the implant surface energy is sensitive to the titanium surface area. As the area increases there is a decrease in the surface contact angle.

  7. Effects of Coenzyme Q10 on Markers of Inflammation: A Systematic Review and Meta-Analysis.

    Directory of Open Access Journals (Sweden)

    Junya Zhai

    Full Text Available Chronic inflammation contributes to the onset and development of metabolic diseases. Clinical evidence has suggested that coenzyme Q10 (CoQ10 has some effects on inflammatory markers. However, these results are equivocal. The aim of this systematic review was to assess the effects of CoQ10 on serum levels of inflammatory markers in people with metabolic diseases.Electronic databases were searched up to February 2016 for randomized controlled trials (RCTs. The outcome parameters were related to inflammatory factors, including interleukin-6 (IL-6, tumor necrosis factor-alpha (TNF-α and C reactive protein (CRP. RevMan software was used for meta-analysis. Meta-regression analysis, Egger line regression test and Begg rank correlation test were performed by STATA software.Nine trials involving 428 subjects were included in this meta-analysis. The results showed that compared with control group, CoQ10 supplementation has significantly improved the serum level of CoQ10 by 1.17μg/ml [MD = 1.17, 95% CI (0.47 to 1.87 μg/ml, I2 = 94%]. Meanwhile, it has significantly decreased TNF-α by 0.45 pg/ml [MD = -0.45, 95% CI (-0.67 to -0.24 pg/ml, I2 = 0%]. No significant difference was observed between CoQ10 and placebo with regard to CRP [MD = -0.21, 95% CI (-0.60 to 0.17 mg/L, I2 = 21%] and IL-6 [MD = -0.89, 95% CI (-1.95 to 0.16 pg/ml, I2 = 84%].CoQ10 supplementation may partly improve the process of inflammatory state. The effects of CoQ10 on inflammation should be further investigated by conducting larger sample size and well-defined trials of long enough duration.

  8. Identification of the intestinal type gastric adenocarcinoma transcriptomic markers using bioinformatic and gene expression analysis

    Directory of Open Access Journals (Sweden)

    V. V. Volkomorov

    2017-01-01

    Full Text Available Introduction. Searching for specific and sensitive molecular tumor markers is one of the important tasks of modern oncology. These markers can be used for early tumor diagnosis and prognosis as well as for prediction of therapeutic response, estimation of tumor volume or to assess disease recurrence through monitoring. Gene expression data base mining followed by experimental validation of results obtained is one of the promising approaches for searching of that kind.Objective: to identify several membrane proteins which can be used for serum diagnosis of intestinal type of gastric adenocarcinoma.Materials and methods. We used bioinformatic-driven search using Gene Ontology and The Cancer Genome Atlas (TCGA data to identify mRNA up-regulated in gastric cancer (GC. Then, the expression levels of the mRNAs in 55 pare clinical specimens were investigated using reverse transcription polymerase chain reaction.Results. Comparative analysis of the mRNA levels in normal and tumor tissues using a new bioinformatics algorithm allowed to identify 3 high-copy transcripts (SULF1, PMEPA1 and SPARC, intracellular content of which markedly increased in GC. Expression analysis of these genes in clinical specimens showed significantly higher mRNA levels of PMEPA1 and SPARC in tumor as compared to normal gastric tissue. Interestingly more than twofold increase in expression level of these genes was observed in 75 % of intestinal-type GC. The same results were found only in 25 and 38 % of diffuse-type GC respectively.Conclusions. As a result of original bioinforamtic analysis using TCGA data base two genes (PMEPA1 and SPARC were shown to be significantly upregulated in intestinal-type gastric adenocarcinoma. The findings show the importance of further investigation to clarify the clinical value of their expression level in stomach tumors as well as their role in carcinogenesis.

  9. Cell surface profiling using high-throughput flow cytometry: a platform for biomarker discovery and analysis of cellular heterogeneity.

    Directory of Open Access Journals (Sweden)

    Craig A Gedye

    Full Text Available Cell surface proteins have a wide range of biological functions, and are often used as lineage-specific markers. Antibodies that recognize cell surface antigens are widely used as research tools, diagnostic markers, and even therapeutic agents. The ability to obtain broad cell surface protein profiles would thus be of great value in a wide range of fields. There are however currently few available methods for high-throughput analysis of large numbers of cell surface proteins. We describe here a high-throughput flow cytometry (HT-FC platform for rapid analysis of 363 cell surface antigens. Here we demonstrate that HT-FC provides reproducible results, and use the platform to identify cell surface antigens that are influenced by common cell preparation methods. We show that multiple populations within complex samples such as primary tumors can be simultaneously analyzed by co-staining of cells with lineage-specific antibodies, allowing unprecedented depth of analysis of heterogeneous cell populations. Furthermore, standard informatics methods can be used to visualize, cluster and downsample HT-FC data to reveal novel signatures and biomarkers. We show that the cell surface profile provides sufficient molecular information to classify samples from different cancers and tissue types into biologically relevant clusters using unsupervised hierarchical clustering. Finally, we describe the identification of a candidate lineage marker and its subsequent validation. In summary, HT-FC combines the advantages of a high-throughput screen with a detection method that is sensitive, quantitative, highly reproducible, and allows in-depth analysis of heterogeneous samples. The use of commercially available antibodies means that high quality reagents are immediately available for follow-up studies. HT-FC has a wide range of applications, including biomarker discovery, molecular classification of cancers, or identification of novel lineage specific or stem cell

  10. Cell surface profiling using high-throughput flow cytometry: a platform for biomarker discovery and analysis of cellular heterogeneity.

    Science.gov (United States)

    Gedye, Craig A; Hussain, Ali; Paterson, Joshua; Smrke, Alannah; Saini, Harleen; Sirskyj, Danylo; Pereira, Keira; Lobo, Nazleen; Stewart, Jocelyn; Go, Christopher; Ho, Jenny; Medrano, Mauricio; Hyatt, Elzbieta; Yuan, Julie; Lauriault, Stevan; Meyer, Mona; Kondratyev, Maria; van den Beucken, Twan; Jewett, Michael; Dirks, Peter; Guidos, Cynthia J; Danska, Jayne; Wang, Jean; Wouters, Bradly; Neel, Benjamin; Rottapel, Robert; Ailles, Laurie E

    2014-01-01

    Cell surface proteins have a wide range of biological functions, and are often used as lineage-specific markers. Antibodies that recognize cell surface antigens are widely used as research tools, diagnostic markers, and even therapeutic agents. The ability to obtain broad cell surface protein profiles would thus be of great value in a wide range of fields. There are however currently few available methods for high-throughput analysis of large numbers of cell surface proteins. We describe here a high-throughput flow cytometry (HT-FC) platform for rapid analysis of 363 cell surface antigens. Here we demonstrate that HT-FC provides reproducible results, and use the platform to identify cell surface antigens that are influenced by common cell preparation methods. We show that multiple populations within complex samples such as primary tumors can be simultaneously analyzed by co-staining of cells with lineage-specific antibodies, allowing unprecedented depth of analysis of heterogeneous cell populations. Furthermore, standard informatics methods can be used to visualize, cluster and downsample HT-FC data to reveal novel signatures and biomarkers. We show that the cell surface profile provides sufficient molecular information to classify samples from different cancers and tissue types into biologically relevant clusters using unsupervised hierarchical clustering. Finally, we describe the identification of a candidate lineage marker and its subsequent validation. In summary, HT-FC combines the advantages of a high-throughput screen with a detection method that is sensitive, quantitative, highly reproducible, and allows in-depth analysis of heterogeneous samples. The use of commercially available antibodies means that high quality reagents are immediately available for follow-up studies. HT-FC has a wide range of applications, including biomarker discovery, molecular classification of cancers, or identification of novel lineage specific or stem cell markers.

  11. Comparative analysis of disease-linked single nucleotide polymorphic markers from Brassica rapa for their applicability to Brassica oleracea.

    Science.gov (United States)

    Cho, Young-Il; Ahn, Yul-Kyun; Tripathi, Swati; Kim, Jeong-Ho; Lee, Hye-Eun; Kim, Do-Sun

    2015-01-01

    Numerous studies using single nucleotide polymorphisms (SNPs) have been conducted in humans, and other animals, and in major crops, including rice, soybean, and Chinese cabbage. However, the number of SNP studies in cabbage is limited. In this present study, we evaluated whether 7,645 SNPs previously identified as molecular markers linked to disease resistance in the Brassica rapa genome could be applied to B. oleracea. In a BLAST analysis using the SNP sequences of B. rapa and B. oleracea genomic sequence data registered in the NCBI database, 256 genes for which SNPs had been identified in B. rapa were found in B. oleracea. These genes were classified into three functional groups: molecular function (64 genes), biological process (96 genes), and cellular component (96 genes). A total of 693 SNP markers, including 145 SNP markers [BRH--developed from the B. rapa genome for high-resolution melt (HRM) analysis], 425 SNP markers (BRP--based on the B. rapa genome that could be applied to B. oleracea), and 123 new SNP markers (BRS--derived from BRP and designed for HRM analysis), were investigated for their ability to amplify sequences from cabbage genomic DNA. In total, 425 of the SNP markers (BRP-based on B. rapa genome), selected from 7,645 SNPs, were successfully applied to B. oleracea. Using PCR, 108 of 145 BRH (74.5%), 415 of 425 BRP (97.6%), and 118 of 123 BRS (95.9%) showed amplification, suggesting that it is possible to apply SNP markers developed based on the B. rapa genome to B. oleracea. These results provide valuable information that can be utilized in cabbage genetics and breeding programs using molecular markers derived from other Brassica species.

  12. Comparative Analysis of Disease-Linked Single Nucleotide Polymorphic Markers from Brassica rapa for Their Applicability to Brassica oleracea

    Science.gov (United States)

    Cho, Young-Il; Ahn, Yul-Kyun; Tripathi, Swati; Kim, Jeong-Ho; Lee, Hye-Eun; Kim, Do-Sun

    2015-01-01

    Numerous studies using single nucleotide polymorphisms (SNPs) have been conducted in humans, and other animals, and in major crops, including rice, soybean, and Chinese cabbage. However, the number of SNP studies in cabbage is limited. In this present study, we evaluated whether 7,645 SNPs previously identified as molecular markers linked to disease resistance in the Brassica rapa genome could be applied to B. oleracea. In a BLAST analysis using the SNP sequences of B. rapa and B. oleracea genomic sequence data registered in the NCBI database, 256 genes for which SNPs had been identified in B. rapa were found in B. oleracea. These genes were classified into three functional groups: molecular function (64 genes), biological process (96 genes), and cellular component (96 genes). A total of 693 SNP markers, including 145 SNP markers [BRH—developed from the B. rapa genome for high-resolution melt (HRM) analysis], 425 SNP markers (BRP—based on the B. rapa genome that could be applied to B. oleracea), and 123 new SNP markers (BRS—derived from BRP and designed for HRM analysis), were investigated for their ability to amplify sequences from cabbage genomic DNA. In total, 425 of the SNP markers (BRP-based on B. rapa genome), selected from 7,645 SNPs, were successfully applied to B. oleracea. Using PCR, 108 of 145 BRH (74.5%), 415 of 425 BRP (97.6%), and 118 of 123 BRS (95.9%) showed amplification, suggesting that it is possible to apply SNP markers developed based on the B. rapa genome to B. oleracea. These results provide valuable information that can be utilized in cabbage genetics and breeding programs using molecular markers derived from other Brassica species. PMID:25790283

  13. Comparative analysis of disease-linked single nucleotide polymorphic markers from Brassica rapa for their applicability to Brassica oleracea.

    Directory of Open Access Journals (Sweden)

    Young-Il Cho

    Full Text Available Numerous studies using single nucleotide polymorphisms (SNPs have been conducted in humans, and other animals, and in major crops, including rice, soybean, and Chinese cabbage. However, the number of SNP studies in cabbage is limited. In this present study, we evaluated whether 7,645 SNPs previously identified as molecular markers linked to disease resistance in the Brassica rapa genome could be applied to B. oleracea. In a BLAST analysis using the SNP sequences of B. rapa and B. oleracea genomic sequence data registered in the NCBI database, 256 genes for which SNPs had been identified in B. rapa were found in B. oleracea. These genes were classified into three functional groups: molecular function (64 genes, biological process (96 genes, and cellular component (96 genes. A total of 693 SNP markers, including 145 SNP markers [BRH--developed from the B. rapa genome for high-resolution melt (HRM analysis], 425 SNP markers (BRP--based on the B. rapa genome that could be applied to B. oleracea, and 123 new SNP markers (BRS--derived from BRP and designed for HRM analysis, were investigated for their ability to amplify sequences from cabbage genomic DNA. In total, 425 of the SNP markers (BRP-based on B. rapa genome, selected from 7,645 SNPs, were successfully applied to B. oleracea. Using PCR, 108 of 145 BRH (74.5%, 415 of 425 BRP (97.6%, and 118 of 123 BRS (95.9% showed amplification, suggesting that it is possible to apply SNP markers developed based on the B. rapa genome to B. oleracea. These results provide valuable information that can be utilized in cabbage genetics and breeding programs using molecular markers derived from other Brassica species.

  14. Identification of new serum markers of pathological states by bioinformatic tools for the analysis of serum proteomics expression profiles

    International Nuclear Information System (INIS)

    Malorni, A.; Facchiano, A.

    2009-01-01

    We have developed new bioinformatic tools and strategies, aimed to the identification and characterization of proteins as markers of pathological states, for the analysis of data derived from protein expression profiles obtained by mass spectrometry techniques, for the study of structural and functional properties of the proteins, and for the analysis of data from omics approaches

  15. Glucose transporter-1 as an independent prognostic marker for cancer: a meta-analysis

    Science.gov (United States)

    Zhao, Zheng-Xiao; Lu, Lin-Wei; Qiu, Jian; Li, Qiu-Ping; Xu, Fei; Liu, Bao-Jun; Dong, Jing-Cheng; Gong, Wei-Yi

    2018-01-01

    Objective Glucose transporter-1 (GLUT-1) as the major glucose transporter present in human cells is found overexpressed in a proportion of human malignancies. This meta-analysis is attempted to assess the prognostic significance of GLUT-1 for survival in various cancers. Materials and Methods We conducted an electronic search using the databases PubMed, Embase and Web of Science, from inception to Oct 20th, 2016. Pooled hazard ratios (HRs) and 95% confidence intervals (CIs) were calculated. Results Fourty-one studies with a total of 4794 patients were included. High GLUT-1 expression was significantly associated with poorer prognosis [overall survival: HR = 1.833 (95% CI: 1.597–2.069, P GLUT-1 expression may be an independent prognostic marker to predict poor survival in various types of cancers. Further clinical trials with high quality need to be conducted to confirm our conclusion. PMID:29416806

  16. 2nd international conference on ion beam surface layer analysis

    International Nuclear Information System (INIS)

    1975-01-01

    The papers of this conference are concerned with the fundamental aspects and with the application of surface layer analysis. It is reported amongst others about backscattering analysis, Auger electron spectroscopy, channelling and microprobe. (HPOE) [de

  17. Inverse analysis of inner surface temperature history from outer surface temperature measurement of a pipe

    International Nuclear Information System (INIS)

    Kubo, S; Ioka, S; Onchi, S; Matsumoto, Y

    2010-01-01

    When slug flow runs through a pipe, nonuniform and time-varying thermal stresses develop and there is a possibility that thermal fatigue occurs. Therefore it is necessary to know the temperature distributions and the stress distributions in the pipe for the integrity assessment of the pipe. It is, however, difficult to measure the inner surface temperature directly. Therefore establishment of the estimation method of the temperature history on inner surface of pipe is needed. As a basic study on the estimation method of the temperature history on the inner surface of a pipe with slug flow, this paper presents an estimation method of the temperature on the inner surface of a plate from the temperature on the outer surface. The relationship between the temperature history on the outer surface and the inner surface is obtained analytically. Using the results of the mathematical analysis, the inverse analysis method of the inner surface temperature history estimation from the outer surface temperature history is proposed. It is found that the inner surface temperature history can be estimated from the outer surface temperature history by applying the inverse analysis method, even when it is expressed by the multiple frequency components.

  18. Genetic Diversity Analysis of Iranian Jujube Ecotypes (Ziziphus spp. Using RAPD Molecular Marker

    Directory of Open Access Journals (Sweden)

    S Abbasi

    2012-12-01

    Full Text Available Jujube (Ziziphus jujuba Mill. is a valuable medicinal plant which is important in Iranian traditional medicines. Although the regional plants such as jujube play an important role in our economy, but they are forgotten in research and technology. Considering the economic and medicinal importance of jujube, the first step in breeding programs is determination of the genetic diversity among the individuals. 34 ecotypes of jujube, which have been collected from eight provinces of Iran, were used in this study. The genetic relationships of Iranian jujube ecotypes were analyzed using Random Amplified Polymorphic DNA (RAPD marker. Six out of 15 random decamer primers applied for RAPD analysis, showed an informative polymorphism. According to clustering analysis using UPGMA's methods, the ecotypes were classified into two major groups at the 0.81 level of genetic similarity. The highest value of similarity coefficient (0.92 was detected between Mazandaran and Golestan ecotypes and the most genetic diversity was observed in ecotypes of Khorasan-Jonoubi. The affinity of Khorasan-Jonoubi and Esfahan ecotypes indicated a possible common origin for the variation in these areas. Results indicated that RAPD analysis could be successfully used for the estimation of genetic diversity among Ziziphus ecotypes and it can be useful for further investigations.

  19. Complete 1H NMR spectral analysis of ten chemical markers of Ginkgo biloba.

    Science.gov (United States)

    Napolitano, José G; Lankin, David C; Chen, Shao-Nong; Pauli, Guido F

    2012-08-01

    The complete and unambiguous (1)H NMR assignments of ten marker constituents of Ginkgo biloba are described. The comprehensive (1)H NMR profiles (fingerprints) of ginkgolide A, ginkgolide B, ginkgolide C, ginkgolide J, bilobalide, quercetin, kaempferol, isorhamnetin, isoquercetin, and rutin in DMSO-d(6) were obtained through the examination of 1D (1)H NMR and 2D (1)H,(1)H-COSY data, in combination with (1)H iterative full spin analysis (HiFSA). The computational analysis of discrete spin systems allowed a detailed characterization of all the (1)H NMR signals in terms of chemical shifts (δ(H)) and spin-spin coupling constants (J(HH)), regardless of signal overlap and higher order coupling effects. The capability of the HiFSA-generated (1)H fingerprints to reproduce experimental (1)H NMR spectra at different field strengths was also evaluated. As a result of this analysis, a revised set of (1)H NMR parameters for all ten phytoconstituents was assembled. Furthermore, precise (1)H NMR assignments of the sugar moieties of isoquercetin and rutin are reported for the first time. Copyright © 2012 John Wiley & Sons, Ltd.

  20. [Analysis of genetic diversity of Russian regional populations based on common STR markers used in DNA identification].

    Science.gov (United States)

    Pesik, V Yu; Fedunin, A A; Agdzhoyan, A T; Utevska, O M; Chukhraeva, M I; Evseeva, I V; Churnosov, M I; Lependina, I N; Bogunov, Yu V; Bogunova, A A; Ignashkin, M A; Yankovsky, N K; Balanovska, E V; Orekhov, V A; Balanovsky, O P

    2014-06-01

    We conducted the first genetic analysis of a wide a range of rural Russian populations in European Russia with a panel of common DNA markers commonly used in criminalistics genetic identification. We examined a total of 647 samples from indigenous ethnic Russian populations in Arkhangelsk, Belgorod, Voronezh, Kursk, Rostov, Ryazan, and Orel regions. We employed a multiplex genotyping kit, COrDIS Plus, to genotype Short Tandem Repeat (STR) loci, which included the genetic marker panel officially recommended for DNA identification in the Russian Federation, the United States, and the European Union. In the course of our study, we created a database of allelic frequencies, examined the distribution of alleles and genotypes in seven rural Russian populations, and defined the genetic relationships between these populations. We found that, although multidimensional analysis indicated a difference between the Northern gene pool and the rest of the Russian European populations, a pairwise comparison using 19 STR markers among all populations did not reveal significant differences. This is in concordance with previous studies, which examined up to 12 STR markers of urban Russian populations. Therefore, the database of allelic frequencies created in this study can be applied for forensic examinations and DNA identification among the ethnic Russian population over European Russia. We also noted a decrease in the levels of heterozygosity in the northern Russian population compared to ethnic populations in southern and central Russia, which is consistent with trends identified previously using classical gene markers and analysis of mitochondrial DNA.

  1. Transcriptome analysis and SSR/SNP markers information of the blunt snout bream (Megalobrama amblycephala.

    Directory of Open Access Journals (Sweden)

    Zexia Gao

    Full Text Available BACKGROUND: Blunt snout bream (Megalobrama amblycephala is an herbivorous freshwater fish species native to China and has been recognized as a main aquaculture species in the Chinese freshwater polyculture system with high economic value. Right now, only limited EST resources were available for M. amblycephala. Recent advances in large-scale RNA sequencing provide a fast, cost-effective, and reliable approach to generate large expression datasets for functional genomic analysis, which is especially suitable for non-model species with un-sequenced genomes. METHODOLOGY AND PRINCIPAL FINDINGS: Using 454 pyrosequencing, a total of 1,409,706 high quality reads (total length 577 Mbp were generated from the normalized cDNA of pooled M. amblycephala individuals. These sequences were assembled into 26,802 contigs and 73,675 singletons. After BLAST searches against the NCBI non-redundant (NR and UniProt databases with an arbitrary expectation value of E(-10, over 40,000 unigenes were functionally annotated and classified using the FunCat functional annotation scheme. A comparative genomics approach revealed a substantial proportion of genes expressed in M. amblycephala tanscriptome to be shared across the genomes of zebrafish, medaka, tetraodon, fugu, stickleback, human, mouse, and chicken, and identified a substantial number of potentially novel M. amblycephala genes. A total number of 4,952 SSRs were found and 116 polymorphic loci have been characterized. A significant number of SNPs (25,697 and indels (23,287 were identified based on specific filter criteria in the M. amblycephala. CONCLUSIONS: This study is the first comprehensive transcriptome analysis for a fish species belonging to the genus Megalobrama. These large EST resources are expected to be valuable for the development of molecular markers, construction of gene-based linkage map, and large-scale expression analysis of M. amblycephala, as well as comparative genome analysis for the genus

  2. Analysis of Separated Flow over Blocked Surface

    Directory of Open Access Journals (Sweden)

    Onur YEMENİCİ

    2013-04-01

    Full Text Available In this study, the separated flow over flat and blocked surfaces was investigated experimentally. Velocity and turbulence intensity measurements were carried out by a constanttemperature hot wire anemometer and static pressure measurements by a micro-manometer. The flow separations and reattachments were occurred before the first block, on the first block, between blocks and after the last block, and the presence of the blocks significantly increased the turbulent intensity

  3. Analysis of surface contaminants on beryllium windows

    International Nuclear Information System (INIS)

    Gmur, N.F.

    1986-12-01

    It is known that various crystalline and liquid compounds form on the downstream surfaces of beryllium windows exposed to air. It is also known that the integrity of such windows may be compromised resulting in leaks through the window. The purpose of this report is to document the occurrences described as they pertain to the NSLS and to analyze, where possible, the various substances formed

  4. Surface noise analysis using a single-ion sensor

    Science.gov (United States)

    Daniilidis, N.; Gerber, S.; Bolloten, G.; Ramm, M.; Ransford, A.; Ulin-Avila, E.; Talukdar, I.; Häffner, H.

    2014-06-01

    We use a single-ion electric-field noise sensor in combination with in situ surface treatment and analysis tools, to investigate the relationship between electric-field noise from metal surfaces in vacuum and the composition of the surface. These experiments are performed in a setup that integrates ion trapping capabilities with surface analysis tools. We find that treatment of an aluminum-copper surface with energetic argon ions significantly reduces the level of room-temperature electric-field noise, but the surface does not need to be atomically clean to show noise levels comparable to those of the best cryogenic traps. The noise levels after treatment are low enough to allow fault-tolerant trapped-ion quantum information processing on a microfabricated surface trap at room temperature.

  5. Teaching practice and experiences of verifying the three laws of genetics based on the SSLP marker analysis.

    Science.gov (United States)

    Huang, Xue-Ying; Fan, Kai; Ye, Yan-Fang; Wang, Bin; Wu, Wei-Ren; Lan, Tao

    2017-09-20

    We explored the practical effect of the genetic analysis of simple sequence length polymorphism (SSLP) molecular markers in rice in the genetics lab course. Two parents and their F 2 population were analyzed and detected with three SSLP molecular markers that located on two chromosomes of the rice genome. The markers' genotype data were used to verify the three laws of genetics, including segregation, independent assortment and linkage and crossing-over. Our practice has proved not only beneficial to deepen students' understandings about the three laws of genetics, but also conducive to cultivate students' interests in research and innovation and improve their skills and comprehensive analysis abilities. At the same time, the application scope of the experiment was discussed. This comprehensive experiment is also useful for the transformation of scientific research achievements into undergraduate experimental teaching.

  6. Use of Tumor Markers in Gastrointestinal Cancers: Surgeon Perceptions and Cost-Benefit Trade-Off Analysis.

    Science.gov (United States)

    Acharya, Amish; Markar, Sheraz R; Matar, Michael; Ni, Melody; Hanna, George B

    2017-05-01

    Gastrointestinal cancers constitute the third most common cancers worldwide. Tumor markers have long since been used in the postoperative surveillance of these malignancies; however, the true value in clinical practice remains undetermined. This study aimed to evaluate the clinical utility of three tumor markers in colorectal and esophagogastric cancer. A systematic review of the literature was undertaken to elicit the sensitivity, specificity, statistical heterogeneity and ability to predict recurrence and metastases for carcinoembryonic antigen (CEA), cancer antigen (CA) 19-9 and CA125. European surgeons were surveyed to assess their current practice and the characteristics of tumor markers they most valued. Data from the included studies and survey were combined in a cost-benefit trade-off analysis to assess which tumor markers are of most use in clinical practice. Diagnostic sensitivity and specificity were ranked the most desirable characteristics of a tumor marker by those surveyed. Overall, 156 studies were included to inform the cost-benefit trade-off. The cost-benefit trade-off showed that CEA outperformed both CA19-9 and CA125, with lower financial cost and a higher sensitivity, and diagnostic accuracy for metastases at presentation (area under the curve [AUC] 0.70 vs. 0.61 vs. 0.46), as well as similar diagnostic accuracy for recurrence (AUC 0.46 vs. 0.48). Cost-benefit trade-off analysis identified CEA to be the best performing tumor marker. Further studies should seek to evaluate new tumor markers, with investigation tailored to factors that meet the requirements of practicing clinicians.

  7. Visibility graph analysis of heart rate time series and bio-marker of congestive heart failure

    Science.gov (United States)

    Bhaduri, Anirban; Bhaduri, Susmita; Ghosh, Dipak

    2017-09-01

    Study of RR interval time series for Congestive Heart Failure had been an area of study with different methods including non-linear methods. In this article the cardiac dynamics of heart beat are explored in the light of complex network analysis, viz. visibility graph method. Heart beat (RR Interval) time series data taken from Physionet database [46, 47] belonging to two groups of subjects, diseased (congestive heart failure) (29 in number) and normal (54 in number) are analyzed with the technique. The overall results show that a quantitative parameter can significantly differentiate between the diseased subjects and the normal subjects as well as different stages of the disease. Further, the data when split into periods of around 1 hour each and analyzed separately, also shows the same consistent differences. This quantitative parameter obtained using the visibility graph analysis thereby can be used as a potential bio-marker as well as a subsequent alarm generation mechanism for predicting the onset of Congestive Heart Failure.

  8. Markers of atherosclerosis in patients with Cushing's syndrome: a meta-analysis of literature studies.

    Science.gov (United States)

    Lupoli, Roberta; Ambrosino, Pasquale; Tortora, Anna; Barba, Livia; Lupoli, Gelsy Arianna; Di Minno, Matteo Nicola Dario

    2017-05-01

    Several studies reported an increased cardiovascular (CV) risk in Cushing's syndrome (CS). We performed a meta-analysis on the impact of CS on major markers of atherosclerosis. Studies on intima-media thickness (IMT), carotid plaques prevalence, and flow-mediated dilation (FMD) in CS patients and controls were searched in the PubMed, Web of Science, Scopus, and EMBASE. Differences between cases and controls were expressed as mean difference (MD) with 95% confidence intervals (95%CI) for continuous variables, and as Odds Ratio (OR) with 95%CI for dichotomous variables. Fourteen studies (332 CS, 462 controls) were included. Compared with controls, CS patients showed higher IMT (MD: 0.20 mm; 95% CI: 0.12, 0.28; p atherosclerosis and CV risk. These findings could help establish more specific CV prevention strategies in this clinical setting. Key messages A series of studies reported an increased cardiovascular risk in patients with Cushing's syndrome (CS). In the present meta-analysis we demonstrated that CS is associated with an increased intima-media thickness, higher prevalence of carotid plaques, and lower flow-mediated dilation as compared with controls. These data consistently suggest the need for a strict monitoring of early signs of subclinical atherosclerosis in CS patients.

  9. Plasma diagnostics surface analysis and interactions

    CERN Document Server

    Auciello, Orlando

    2013-01-01

    Plasmas and their interaction with materials have become subjects of major interest because of their importance in modern forefront technologies such as microelectronics, fusion energy, and space. Plasmas are used in microelectronics to process semiconductors (etching of patterns for microcircuits, plasma-induced deposition of thin films, etc.); plasmas produce deleterious erosion effects on surfaces of materials used for fusion devices and spaceships exposed to the low earth environment.Diagnostics of plasmas and materials exposed to them are fundamental to the understanding of the physical a

  10. Analysis of surface with low energy ions

    International Nuclear Information System (INIS)

    Oliver, A.; Miranda, J.

    1989-01-01

    Nuclear techniques applied to element analysis presents different characteristics depending on projectile energy. It can seen observed than an energy (E ≅ 1 MeV) exists which separate two regions for which sensitivity, information analysis and resolution in detection are different. For this work, we describe for the energy region E ≤ 1 MeV, the advantage of the three most used techniques which are PIXE, RBS y RNR. (Author)

  11. Molecular marker analysis of heading date Hd1 locus in Egyptian ...

    African Journals Online (AJOL)

    Nine molecular markers derived from the heading date QTL Hd1 DNA sequence for cultivated rice were used to study the heading date allelic diversity of the cultivated Egyptian rice varieties. The results showed that among the nine simple sequence repeats (SSR) and sequence tagged-sites (STS) markers used, one SSR ...

  12. SNP marker analysis for validating the authenticity of Tunisian olive oil

    Indian Academy of Sciences (India)

    The other. SNP, called SOD, is an insertion/deletion polymorphism type localized in Cu–Zn superoxide dismutase gene which is involved in the oxidative stress, one of .... Authenticity of olive oil by SNP markers. Table 1. Characteristics of SNP markers used for DNA amplification. Size of. SNP amplicon. Gene name. SNPs.

  13. Development of simple sequence repeat markers and diversity analysis in alfalfa (Medicago sativa L.).

    Science.gov (United States)

    Wang, Zan; Yan, Hongwei; Fu, Xinnian; Li, Xuehui; Gao, Hongwen

    2013-04-01

    Efficient and robust molecular markers are essential for molecular breeding in plant. Compared to dominant and bi-allelic markers, multiple alleles of simple sequence repeat (SSR) markers are particularly informative and superior in genetic linkage map and QTL mapping in autotetraploid species like alfalfa. The objective of this study was to enrich SSR markers directly from alfalfa expressed sequence tags (ESTs). A total of 12,371 alfalfa ESTs were retrieved from the National Center for Biotechnology Information. Total 774 SSR-containing ESTs were identified from 716 ESTs. On average, one SSR was found per 7.7 kb of EST sequences. Tri-nucleotide repeats (48.8 %) was the most abundant motif type, followed by di-(26.1 %), tetra-(11.5 %), penta-(9.7 %), and hexanucleotide (3.9 %). One hundred EST-SSR primer pairs were successfully designed and 29 exhibited polymorphism among 28 alfalfa accessions. The allele number per marker ranged from two to 21 with an average of 6.8. The PIC values ranged from 0.195 to 0.896 with an average of 0.608, indicating a high level of polymorphism of the EST-SSR markers. Based on the 29 EST-SSR markers, assessment of genetic diversity was conducted and found that Medicago sativa ssp. sativa was clearly different from the other subspecies. The high transferability of those EST-SSR markers was also found for relative species.

  14. Determination of optimal fiducial marker across image-guided radiation therapy (IGRT) modalities: visibility and artifact analysis of gold, carbon, and polymer fiducial markers.

    Science.gov (United States)

    Handsfield, Lydia L; Yue, Ning J; Zhou, Jinghao; Chen, Ting; Goyal, Sharad

    2012-09-06

    The purpose of this study was to evaluate the visibility and artifact created by gold, carbon, and polymer fiducial markers in a simple phantom across computed tomography (CT), kilovoltage (kV), and megavoltage (MV) linear accelerator imaging and MV tomotherapy imaging. Three types of fiducial markers (gold, carbon, and polymer) were investigated for their visibility and artifacts in images acquired with various modalities and with different imaging parameters (kV, mAs, slice thickness). The imaging modalities include kV CT, 2D linac-based kilovoltage and megavoltage X-ray imaging systems, kV cone-beam CT, and normal and fine tomotherapy imaging. The images were acquired on a phantom constructed using Superflab bolus in which markers of each type were inserted into the center layer. The visibility and artifacts produced by each marker were assessed qualitatively and quantitatively. All tested markers could be identified clearly on the acquired CT and linac-based kV images; gold markers demonstrated the highest contrast. On the CT images, gold markers produced a significant artifact, while no artifacts were observed with polymer markers. Only gold markers were visible when using linac-based MV and tomotherapy imaging. For linac-based kV images, the contrast increased with kV and mAs values for all the markers, with the gold being the most pronounced. On CT images, the contrast increased with kV for the gold markers, while decreasing for the polymer and carbon marker. With the bolus phantom used, we found that when kV imaging-based treatment verification equipment is available, polymer and carbon markers may be the preferred choice for target localization and patient treatment positioning verification due to less image artifacts. If MV imaging will be the sole modality for positioning verification, it may be necessary to use gold markers despite the artifacts they create on the simulation CT images.

  15. Expression of surface markers on the human monocytic leukaemia cell line, THP-1, as indicators for the sensitizing potential of chemicals.

    Science.gov (United States)

    An, Susun; Kim, Seoyoung; Huh, Yong; Lee, Tae Ryong; Kim, Han-Kon; Park, Kui-Lea; Eun, Hee Chul

    2009-04-01

    Evaluation of skin sensitization potential is an important part of the safety assessment of cosmetic ingredients and topical drugs. Recently, evaluation of changes in surface marker expression induced in dendritic cells (DC) or DC surrogate cell lines following exposure to chemicals represents one approach for in vitro test methods. The study aimed to test the change of expression patterns of surface markers on THP-1 cells by chemicals as a predictive in vitro method for contact sensitization. We investigated the expression of CD54, CD86, CD83, CD80, and CD40 after a 1-day exposure to sensitizers (1-chloro-2,4-dinitrobenzene; 2,4-dinitrofluorobenzene; benzocaine; 5-chloro-2-methyl-4-isothiazolin-3-one; hexyl cinnamic aldehyde; eugenol; nickel sulfate hexahydrate; potassium dichromate; cobalt sulfate; 2-mercaptobenzothiazole; and ammonium tetrachloroplatinate) and non-sensitizers (sodium lauryl sulfate, benzalkonium chloride, lactic acid, salicylic acid, isopropanol, and dimethyl sulphoxide). The test concentrations were 0.1x, 0.5x, and 1x of the 50% inhibitory concentration, and the relative fluorescence intensity was used as an expression indicator. By evaluating the expression patterns of CD54, CD86, and CD40, we could classify the chemicals as sensitizers or non-sensitizers, but CD80 and CD83 showed non-specific patterns of expression. These data suggest that the THP-1 cells are good model for screening contact sensitizers and CD40 could be a useful marker complementary to CD54 and CD86.

  16. Modern sample preparation techniques for gas chromatography-mass spectrometry analysis of environmental markers of chemical warfare agents use

    NARCIS (Netherlands)

    Terzic, O.; de Voogt, P.; Banoub, J.

    2014-01-01

    The chapter introduces problematics of on-site chemical analysis in the investigations of past chemical warfare agents (CWA) events. An overview of primary environmental degradation pathways of CWA leading to formation of chemical markers of their use is given. Conventional and modern sample

  17. In situ surface-enhanced raman spectroelectrochemical analysis system with a hemin modified nanostructured gold surface

    NARCIS (Netherlands)

    Yuan, Tao; Le Thi Ngoc, Loan; van Nieuwkasteele, Jan William; Odijk, Mathieu; van den Berg, Albert; Permentier, Hjalmar; Bischoff, Rainer; Carlen, Edwin

    2015-01-01

    An integrated surface-enhanced Raman scattering (SERS) spectroelectrochemical (SEC) analysis system is presented that combines a small volume microfluidic sample chamber (<100 mu L) with a compact three-electrode configuration for in situ surface-enhanced Raman spectroelectrochemistry. The SEC

  18. In situ surface-enhanced Raman spectroelectrochemical analysis system with a hemin modified nanostructured gold surface

    NARCIS (Netherlands)

    Yuan, Tao; Le Thi Ngoc, Loan; van Nieuwkasteele, Jan; Odijk, Mathieu; van den Berg, Albert; Permentier, Hjalmar; Bischoff, Rainer; Carlen, Edwin T

    2015-01-01

    An integrated surface-enhanced Raman scattering (SERS) spectroelectrochemical (SEC) analysis system is presented that combines a small volume microfluidic sample chamber (<100 μL) with a compact three-electrode configuration for in situ surface-enhanced Raman spectroelectrochemistry. The SEC system

  19. Applied immuno-epidemiological research: an approach for integrating existing knowledge into the statistical analysis of multiple immune markers.

    Science.gov (United States)

    Genser, Bernd; Fischer, Joachim E; Figueiredo, Camila A; Alcântara-Neves, Neuza; Barreto, Mauricio L; Cooper, Philip J; Amorim, Leila D; Saemann, Marcus D; Weichhart, Thomas; Rodrigues, Laura C

    2016-05-20

    Immunologists often measure several correlated immunological markers, such as concentrations of different cytokines produced by different immune cells and/or measured under different conditions, to draw insights from complex immunological mechanisms. Although there have been recent methodological efforts to improve the statistical analysis of immunological data, a framework is still needed for the simultaneous analysis of multiple, often correlated, immune markers. This framework would allow the immunologists' hypotheses about the underlying biological mechanisms to be integrated. We present an analytical approach for statistical analysis of correlated immune markers, such as those commonly collected in modern immuno-epidemiological studies. We demonstrate i) how to deal with interdependencies among multiple measurements of the same immune marker, ii) how to analyse association patterns among different markers, iii) how to aggregate different measures and/or markers to immunological summary scores, iv) how to model the inter-relationships among these scores, and v) how to use these scores in epidemiological association analyses. We illustrate the application of our approach to multiple cytokine measurements from 818 children enrolled in a large immuno-epidemiological study (SCAALA Salvador), which aimed to quantify the major immunological mechanisms underlying atopic diseases or asthma. We demonstrate how to aggregate systematically the information captured in multiple cytokine measurements to immunological summary scores aimed at reflecting the presumed underlying immunological mechanisms (Th1/Th2 balance and immune regulatory network). We show how these aggregated immune scores can be used as predictors in regression models with outcomes of immunological studies (e.g. specific IgE) and compare the results to those obtained by a traditional multivariate regression approach. The proposed analytical approach may be especially useful to quantify complex immune

  20. Statistical analysis of the Martian surface

    Science.gov (United States)

    Landais, F.; Schmidt, F.; Lovejoy, S.

    2015-10-01

    We investigate the scaling properties of the topography of Mars [10]. Planetary topographic fields are well known to exhibit (mono)fractal behavior. Indeed, fractal formalism is efficient to reproduce the variability observed in topography. Still, a single fractal dimension is not enough to explain the huge variability and intermittency. Previous study have shown that fractal dimensions might be different from a region to another, excluding a general description at the planetary scale. In this project, we are analyzing the Martian topographic data with a multifractal formalism to study the scaling intermittency. In the multifractal paradigm, the local variation of the fractal dimension is interpreted as a statistical property of multifractal fields. The results suggest a multifractal behaviour from planetary scale down to 10 km. From 10 km to 600 m, the topography seems to be simple monofractal. This transition indicates a significant in the geological processes governing the Red Planet's surface.

  1. Image segmentation for uranium isotopic analysis by SIMS: Combined adaptive thresholding and marker controlled watershed approach

    Energy Technology Data Exchange (ETDEWEB)

    Willingham, David G.; Naes, Benjamin E.; Heasler, Patrick G.; Zimmer, Mindy M.; Barrett, Christopher A.; Addleman, Raymond S.

    2016-05-31

    A novel approach to particle identification and particle isotope ratio determination has been developed for nuclear safeguard applications. This particle search approach combines an adaptive thresholding algorithm and marker-controlled watershed segmentation (MCWS) transform, which improves the secondary ion mass spectrometry (SIMS) isotopic analysis of uranium containing particle populations for nuclear safeguards applications. The Niblack assisted MCWS approach (a.k.a. SEEKER) developed for this work has improved the identification of isotopically unique uranium particles under conditions that have historically presented significant challenges for SIMS image data processing techniques. Particles obtained from five NIST uranium certified reference materials (CRM U129A, U015, U150, U500 and U850) were successfully identified in regions of SIMS image data 1) where a high variability in image intensity existed, 2) where particles were touching or were in close proximity to one another and/or 3) where the magnitude of ion signal for a given region was count limited. Analysis of the isotopic distributions of uranium containing particles identified by SEEKER showed four distinct, accurately identified 235U enrichment distributions, corresponding to the NIST certified 235U/238U isotope ratios for CRM U129A/U015 (not statistically differentiated), U150, U500 and U850. Additionally, comparison of the minor uranium isotope (234U, 235U and 236U) atom percent values verified that, even in the absence of high precision isotope ratio measurements, SEEKER could be used to segment isotopically unique uranium particles from SIMS image data. Although demonstrated specifically for SIMS analysis of uranium containing particles for nuclear safeguards, SEEKER has application in addressing a broad set of image processing challenges.

  2. [Comparative genome analysis in pea Pisum sativum L. varieties and lines with chromosomal and molecular markers].

    Science.gov (United States)

    Samatadze, T E; Zelenina, D A; Shostak, N G; Volkov, A A; Popov, K V; Rachinskaia, O V; Borisov, A Iu; Tikhonovich, I A; Zelenin, A V; Muravenko, O V

    2008-12-01

    C banding, Ag-NOR staining, FISH with pTa71 (45S rDNA) and pTa794 (5S rDNA), and RAPD-PCR analysis were used to study the genome and chromosome polymorphism in four varieties (Frisson, Sparkle, Rondo, and Finale) and two genetic lines (Sprint-2 and SGE) of pea Pisum sativum L. A comparison of the C-banding patterns did not reveal any polymorphism within the varieties. The most significant between-variety differences were observed for the size of C bands on satellite chromosomes 4 and 7. All grain pea varieties (Frisson, Sparkle, and Rondo) had a large C band in the satellite of chromosome 4 and a medium C band in the region adjacent to the satellite thread on chromosome 7. C bands were almost of the same size in the genetic lines and vegetable variety Finale. In all accessions, 45S rDNA mapped to the secondary constriction regions of chromosomes 1, 3, and 5. The signal from chromosome 5 in the lines was more intense than in the varieties. Ag-NOR staining showed that the transcriptional activity of the 45S rRNA genes on chromosome 7 was higher than on chromosome 4 in all accessions. No more than four Ag-NOR-positive nucleoli were observed in interphase nuclei. Statistical analysis of the total area of Ag-NOR-stained nucleoli did not detect any significant difference between the accessions examined. RAPD-PCR analysis revealed high between-variety and low within-variety genomic polymorphism. Chromosomal and molecular markers proved to be promising for genome identification in pea varieties and lines.

  3. DNA Microarray Analysis Identifies CKS2 and LEPR as Potential Markers of Meningioma Recurrence

    Science.gov (United States)

    Menghi, Francesca; Orzan, Francesca N.; Eoli, Marica; Farinotti, Mariangela; Maderna, Emanuela; Pisati, Federica; Bianchessi, Donatella; Valletta, Lorella; Lodrini, Sandro; Galli, Giuseppe; Anghileri, Elena; Pellegatta, Serena; Pollo, Bianca

    2011-01-01

    Meningiomas are the most frequent intracranial tumors. Surgery can be curative, but recurrences are possible. We performed gene expression analyses and loss of heterozygosity (LOH) studies looking for new markers predicting the recurrence risk. We analyzed expression profiles of 23 meningiomas (10 grade I, 10 grade II, and 3 grade III) and validated the data using quantitative polymerase chain reaction (qPCR). We performed LOH analysis on 40 meningiomas, investigating chromosomal regions on 1p, 9p, 10q, 14q, and 22q. We found 233 and 268 probe sets to be significantly down- and upregulated, respectively, in grade II or III meningiomas. Genes downregulated in high-grade meningiomas were overrepresented on chromosomes 1, 6, 9, 10, and 14. Based on functional enrichment analysis, we selected LIM domain and actin binding 1 (LIMA1), tissue inhibitor of metalloproteinases 3 (TIMP3), cyclin-dependent kinases regulatory subunit 2 (CKS2), leptin receptor (LEPR), and baculoviral inhibitor of apoptosis repeat-containing 5 (BIRC5) for validation using qPCR and confirmed their differential expression in the two groups of tumors. We calculated ΔCt values of CKS2 and LEPR and found that their differential expression (C-L index) was significantly higher in grade I than in grade II or III meningiomas (p < .0001). Interestingly, the C-L index of nine grade I meningiomas from patients who relapsed in <5 years was significantly lower than in grade I meningiomas from patients who did not relapse. These findings indicate that the C-L index may be relevant to define the progression risk in meningioma patients, helping guide their clinical management. A prospective analysis on a larger number of cases is warranted. PMID:21948653

  4. The analysis of pigments on rock surfaces

    International Nuclear Information System (INIS)

    Fankhauser, B.; O'Connor, S.; Pittelkow, Y.

    1997-01-01

    A limestone slab of roof fall coated with a red pigment was recovered from a Rockshelter in the Napier Ranges of the Kimberley region, Western Australia. Next to the roof fall fragment in the same stratigraphic layer was a piece of ochre. Three questions were presented: (1) is the red substance an ochre? (2) is the piece of ochre identical to the red substance on the roof fall? and (3) are the layers of pigment on the top and bottom of the limestone slab the same? In addition, as an extension from these questions, a general method was developed for the in situ analysis of ochre pigments on substrates to determine likely compositions and ochre sources. The analysis of the red pigment presented an analytical problem because the substance was intimately associated with the rock slab and therefore the analysis had to be done in situ. Not only was the red layer thin, but on a micro level it was uneven. Energy dispersive x-ray analysis (EDXA) penetrated the red layer, simultaneously analysing this layer and the rock substrate to different degrees depending upon the thickness of the red layer. Determining if the substance was actually ochre involved a comparison of elemental analyses between the background (slab) and background with red coating. Coatings of other ochres with known elemental concentrations on the same limestone background gave a comparison of the effect of simultaneously analysing a thin layer and background with different compositions. Three graphical methods useful for insitu analysis are demeonstrated. The find dates (around 40,000 BP) add to a growing body of data in support of the widespread use of ochre accompanying the earliest documented use of widely separated and environmentally diverse regions of Australia by Aboriginal people

  5. Error analysis of aspheric surface with reference datum.

    Science.gov (United States)

    Peng, Yanglin; Dai, Yifan; Chen, Shanyong; Song, Ci; Shi, Feng

    2015-07-20

    Severe requirements of location tolerance provide new challenges for optical component measurement, evaluation, and manufacture. Form error, location error, and the relationship between form error and location error need to be analyzed together during error analysis of aspheric surface with reference datum. Based on the least-squares optimization method, we develop a least-squares local optimization method to evaluate form error of aspheric surface with reference datum, and then calculate the location error. According to the error analysis of a machined aspheric surface, the relationship between form error and location error is revealed, and the influence on the machining process is stated. In different radius and aperture of aspheric surface, the change laws are simulated by superimposing normally distributed random noise on an ideal surface. It establishes linkages between machining and error analysis, and provides an effective guideline for error correcting.

  6. Auto-correlation analysis of ocean surface wind vectors

    Indian Academy of Sciences (India)

    M. Senthilkumar (Newgen Imaging) 1461 1996 Oct 15 13:05:22

    In this work, an auto-correlation analysis of a time series data of surface winds measured in situ by a deep water buoy in the Indian Ocean has been carried out. Hourly time series data available for 240 hours in the month of May, 1999 were subjected to an auto-correlation analysis. The analysis indicates an exponential fall ...

  7. Transforming Growth Factor-β2 Downregulates Major Histocompatibility Complex (MHC) I and MHC II Surface Expression on Equine Bone Marrow-Derived Mesenchymal Stem Cells Without Altering Other Phenotypic Cell Surface Markers.

    Science.gov (United States)

    Berglund, Alix K; Fisher, Matthew B; Cameron, Kristin A; Poole, Emma J; Schnabel, Lauren V

    2017-01-01

    Allogeneic mesenchymal stem cells (MSCs) are a promising cell source for treating musculoskeletal injuries in horses. Effective and safe allogeneic therapy may be hindered, however, by recipient immune recognition and rejection of major histocompatibility complex (MHC)-mismatched MSCs. Development of strategies to prevent immune rejection of MHC-mismatched MSCs in vivo is necessary to enhance cell survival and potentially increase the efficacy and safety of allogeneic MSC therapy. The purposes of this study were to evaluate if transforming growth factor-β2 (TGF-β2) downregulated MHC expression on equine MSCs and to determine if TGF-β2 treatment altered the phenotype of MSCs. Equine bone marrow-derived MSCs from 12 horses were treated with 1, 5, or 10 ng/ml TGF-β2 from initial isolation until MHC expression analysis. TGF-β2-treated MSCs had reduced MHC I and MHC II surface expression compared to untreated controls. TGF-β2 treatment also partially blocked IFN-γ-induced upregulation of MHC I and MHC II. Constitutive and IFN-γ-induced MHC I and MHC II expression on equine MSCs was dynamic and highly variable, and the effect of TGF-β2 was significantly dependent on the donor animal and baseline MHC expression. TGF-β2 treatment did not appear to change morphology, surface marker expression, MSC viability, or secretion of TGF-β1, but did significantly increase the number of cells obtained from culture. These results indicate that TGF-β2 treatment has promise for regulating MHC expression on MSCs to facilitate allogeneic therapy, but further work is needed to maintain MHC stability when exposed to an inflammatory stimulus.

  8. Download - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available arch and download 1 README README_e.html - 2 Registered plant list pgdbj_dna_marker_linkage_map_plant_specie... of This Database Site Policy | Contact Us Download - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ... ...switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods

  9. Analysis of genetic diversity and differentiation of seven stocks of Litopenaeus vannamei using microsatellite markers

    Science.gov (United States)

    Zhang, Kai; Wang, Weiji; Li, Weiya; Zhang, Quanqi; Kong, Jie

    2014-08-01

    Seven microsatellite markers were used to evaluate the genetic diversity and differentiation of seven stocks of Litopenaeus vannamei, which were introduced from Central and South America to China. All seven microsatellite loci were polymorphic, with polymorphism information content ( PIC) values ranging from 0.593 to 0.952. Totally 92 alleles were identified, and the number of alleles ( Na) and effective alleles ( Ne) varied between 4 and 21 and 2.7 and 14.6, respectively. Observed heterozygosity ( H o) values were lower than the expected heterozygosity ( H e) values (0.526-0.754), which indicated that the seven stocks possessed a rich genetic diversity. Thirty-seven tests were detected for reasonable significant deviation from Hardy-Weinberg equilibrium. F is values were positive at five loci, suggesting that there was a relatively high degree of inbreeding within stocks. Pairwise F st values ranged from 0.0225 to 0.151, and most of the stock pairs were moderately differentiated. Genetic distance and cluster analysis using UPGMA revealed a close genetic relationship of L. vannamei between Pop2 and Pop3. AMOVA indicated that the genetic variation among stocks (11.3%) was much lower than that within stocks (88.7%). Although the seven stocks had a certain degree of genetic differentiation and a rich genetic diversity, there is an increasing risk of decreased performance due to inbreeding in subsequent generations.

  10. Molecular analysis of genetic diversity among vine accessions using DNA markers.

    Science.gov (United States)

    da Costa, A F; Teodoro, P E; Bhering, L L; Tardin, F D; Daher, R F; Campos, W F; Viana, A P; Pereira, M G

    2017-04-13

    Viticulture presents a number of economic and social advantages, such as increasing employment levels and fixing the labor force in rural areas. With the aim of initiating a program of genetic improvement in grapevine from the State University of the state of Rio de Janeiro North Darcy Ribeiro, genetic diversity between 40 genotypes (varieties, rootstock, and species of different subgenera) was evaluated using Random amplified polymorphic DNA (RAPD) molecular markers. We built a matrix of binary data, whereby the presence of a band was assigned as "1" and the absence of a band was assigned as "0." The genetic distance was calculated between pairs of genotypes based on the arithmetic complement from the Jaccard Index. The results revealed the presence of considerable variability in the collection. Analysis of the genetic dissimilarity matrix revealed that the most dissimilar genotypes were Rupestris du Lot and Vitis rotundifolia because they were the most genetically distant (0.5972). The most similar were genotypes 31 (unidentified) and Rupestris du lot, which showed zero distance, confirming the results of field observations. A duplicate was confirmed, consistent with field observations, and a short distance was found between the variety 'Italy' and its mutation, 'Ruby'. The grouping methods used were somewhat concordant.

  11. Development of Transcriptomic Markers for Population Analysis Using Restriction Site Associated RNA Sequencing (RARseq.

    Directory of Open Access Journals (Sweden)

    Magdy S Alabady

    Full Text Available We describe restriction site associated RNA sequencing (RARseq, an RNAseq-based genotype by sequencing (GBS method. It includes the construction of RNAseq libraries from double stranded cDNA digested with selected restriction enzymes. To test this, we constructed six single- and six-dual-digested RARseq libraries from six F2 pitcher plant individuals and sequenced them on a half of a Miseq run. On average, the de novo approach of population genome analysis detected 544 and 570 RNA SNPs, whereas the reference transcriptome-based approach revealed an average of 1907 and 1876 RNA SNPs per individual, from single- and dual-digested RARseq data, respectively. The average numbers of RNA SNPs and alleles per loci are 1.89 and 2.17, respectively. Our results suggest that the RARseq protocol allows good depth of coverage per loci for detecting RNA SNPs and polymorphic loci for population genomics and mapping analyses. In non-model systems where complete genomes sequences are not always available, RARseq data can be analyzed in reference to the transcriptome. In addition to enriching for functional markers, this method may prove particularly useful in organisms where the genomes are not favorable for DNA GBS.

  12. Sesame mutant induced space flight treatment and analysis of polymorphism by AFLP molecular marker

    International Nuclear Information System (INIS)

    Lu Haixia; Zhang Yanxin; Wang Linhai; Wei Wenliang; Li Donghua; Zhang Xiaoyan; Zhang Xiurong

    2011-01-01

    Seeds of two sesame varieties (Yuzhi 8 and H98) were carried by 'Shijian 8' satellite for space treatment. Variants is SP 2 and SP 1 were observed and the genetic diversity of mutation generation was analyzed using 30 pair of AFLP markers. The results showed that: (1) variants of leaf, plant height, plant characters, floral organs, capsule, fertility, pre-flowering date were observed in SP 2 and SP 3 of two varieties, variations frequency and variations type of two sesame varieties were significantly different, but only the small capsule variations and tall plant variations could be inherited from SP 2 to SP 3 generation; (2) AFLP analysis of primers randomly selected to analyze variant plants in SP 2 and SP 3 generation, showed that multiple sites in sesame genome were induced by space environment and mutation rate was high, while mutation rate was different in molecular level between varieties; (3) variation sites were diverse between different variations types, and mutation sites were also diverse between different plants of same mutation type, this result indicated that variation of sesame genome DNA could not been expressed totally; (4) The same mutant of botany characteristics and the same locus mutation of molecular level were both detected. (authors)

  13. Genetic Analysis of Pinus sylvestris L. and Pinus sylvestris forma turfosa L. Using RAPD Markers

    Directory of Open Access Journals (Sweden)

    Beáta ÁBRAHÁM

    2010-03-01

    Full Text Available The purpose of the present study was to determine the level of genetic diversity within and among Ciuc basin, Romania (populations from Mohos and Luci raised bogs in Harghita Mountain and Sumuleu in Ciuc Mountain Pinus sylvestris populations using molecular markers. Two of populations (Mohos and Luci seems to be the descendants that survived the continental glaciation. Genetic diversity was analyzed by RAPD (Random Amplified Polymorphic DNA. Nine primers were selected for analysis, which generated reproducible bands. On base of presence or absence of homologues bands Nei’s gene diversity, the percentage of polymorphic loci and Nei’s unbiased genetic distance were calculated. The level of genetic variation among populations was found to be low. For both populations the variation values among populations were higher than within populations. The fossil records and geological historical data explain the extremely low genetic diversity of this species. Pinus sylvestris experienced strong bottlenecks during its evolutionary history, which caused the loss of genetic variation. Genetic drift and breeding in post-bottlenecked small populations may be the major forces that contribute to low genetic diversity and genetic differentiation of populations. Human activities may have accelerated the loss of genetic diversity in Pinus sylvestris.

  14. Development of microsatellite markers for the genetic analysis of Magnaporthe grisea

    Directory of Open Access Journals (Sweden)

    Brondani Claudio

    2000-01-01

    Full Text Available An AG microsatellite-enriched genomic DNA library was constructed for Magnaporthe grisea (anamorph Pyricularia grisea, the causal agent of rice blast. Seventy-two DNA clones containing microsatellite repeats were isolated and sequenced in order to develop a series of new PCR-based molecular markers to be used in genetic studies of the fungus. Twenty-four of these clones were selected to design primer pairs for the PCR amplification of microsatellite alleles. Single spore cultures of M. grisea isolated from rice and wheat in Brazil, Colombia and China were genotyped at three microsatellite loci. Isolates from southern Brazil were predominantly monomorphic at the tested SSR loci, indicating a low level of genetic variability in these samples. However, seven alleles were observed at the MGM-1 locus in isolates from Central Brazil and at least nine alleles were detected at the same locus in a sample of Colombian isolates. Polymorphism analysis at SSR loci is a simple and direct approach for estimating the genetic diversity of M. grisea isolates and a powerful tool for studying M. grisea genetics.

  15. Analysis of the NMI01 marker for a population database of cannabis seeds.

    Science.gov (United States)

    Shirley, Nicholas; Allgeier, Lindsay; Lanier, Tommy; Coyle, Heather Miller

    2013-01-01

    We have analyzed the distribution of genotypes at a single hexanucleotide short tandem repeat (STR) locus in a Cannabis sativa seed database along with seed-packaging information. This STR locus is defined by the polymerase chain reaction amplification primers CS1F and CS1R and is referred to as NMI01 (for National Marijuana Initiative) in our study. The population database consists of seed seizures of two categories: seed samples from labeled and unlabeled packages regarding seed bank source. Of a population database of 93 processed seeds including 12 labeled Cannabis varieties, the observed genotypes generated from single seeds exhibited between one and three peaks (potentially six alleles if in homozygous state). The total number of observed genotypes was 54 making this marker highly specific and highly individualizing even among seeds of common lineage. Cluster analysis associated many but not all of the handwritten labeled seed varieties tested to date as well as the National Park seizure to our known reference database containing Mr. Nice Seedbank and Sensi Seeds commercially packaged reference samples. © 2012 American Academy of Forensic Sciences.

  16. [A new method of calibration and positioning in quantitative analysis of multicomponents by single marker].

    Science.gov (United States)

    He, Bing; Yang, Shi-Yan; Zhang, Yan

    2012-12-01

    This paper aims to establish a new method of calibration and positioning in quantitative analysis of multicomponents by single marker (QAMS), using Shuanghuanglian oral liquid as the research object. Establishing relative correction factors with reference chlorogenic acid to other 11 active components (neochlorogenic acid, cryptochlorogenic acid, cafferic acid, forsythoside A, scutellarin, isochlorogenic acid B, isochlorogenic acid A, isochlorogenic acid C, baicalin and phillyrin wogonoside) in Shuanghuanglian oral liquid by 3 correction methods (multipoint correction, slope correction and quantitative factor correction). At the same time chromatographic peak was positioned by linear regression method. Only one standard uas used to determine the content of 12 components in Shuanghuanglian oral liquid, in stead of needing too many reference substance in quality control. The results showed that within the linear ranges, no significant differences were found in the quantitative results of 12 active constituents in 3 batches of Shuanghuanglian oral liquid determined by 3 correction methods and external standard method (ESM) or standard curve method (SCM). And this method is simpler and quicker than literature methods. The results were accurate and reliable, and had good reproducibility. While the positioning chromatographic peaks by linear regression method was more accurate than relative retention time in literature. The slope and the quantitative factor correction controlling the quality of Chinese traditional medicine is feasible and accurate.

  17. Indian Ocean surface winds from NCMRWF analysis as compared to ...

    Indian Academy of Sciences (India)

    The quality of the surface wind analysis at the National Centre for Medium Range Weather Forecasts (NCMRWF), New Delhi over the tropical Indian Ocean and its improvement in 2001 are examined by comparing it with in situ buoy measurements and satellite derived surface winds from NASA QuikSCAT satellite (QSCT) ...

  18. Auto-correlation analysis of ocean surface wind vectors

    Indian Academy of Sciences (India)

    The nature of the inherent temporal variability of surface winds is analyzed by comparison of winds obtained through different measurement methods. In this work, an auto-correlation analysis of a time series data of surface winds measured in situ by a deep water buoy in the Indian Ocean has been carried out. Hourly time ...

  19. Assessing ground compaction via time lapse surface wave analysis

    Czech Academy of Sciences Publication Activity Database

    Dal Moro, Giancarlo; Al-Arifi, N.; Moustafa, S.S.R.

    2016-01-01

    Roč. 13, č. 3 (2016), s. 249-256 ISSN 1214-9705 Institutional support: RVO:67985891 Keywords : Full velocity spectrum (FVS) analysis * ground compaction * ground compaction * phase velocities * Rayleigh waves * seismic data inversion * surface wave dispersion * surface waves Subject RIV: DC - Siesmology, Volcanology, Earth Structure Impact factor: 0.699, year: 2016

  20. Applications of surface analysis in the wire industry

    Science.gov (United States)

    Stout, David A.

    The quality of wire is judged not only by its physical properties such as tensile strength and fatigue resistance, but also by its surface finish. The surface roughness, oxide formation, cleanliness, and plating homogeneity and porosity are just a few of the surface properties than can influence the performance of a wire product. Coupled to this is the large amount of surface area generated in drawing wire. For example, a ten pound spool holds nine miles of 0.006″ diameter stainless steel wire. For these reasons surface analysis has become important both to the manufacturer and consumer of wire products. When surface analysis equipment such as AES, ESCA, and SIMS was first becoming commercially available in the late sixties and early seventies, the wire industry was beginning to enter a phase of technological development for many of its products. Wire manufacturers and users began using surface analysis to investigate such topics as adhesion of brass plated automobile tire cord to rubber and diffusion of layered deposits. Examples of surface analysis used for process control, problem solving, and project development include discoloration problems on stainless steel wire, welding problems with composite wires, diffusion formed brass coatings, and diffusion problems with solder coated and Cu plated steel wire.

  1. Synthesis, Structure and Hirshfeld surface analysis, vibrational and ...

    Indian Academy of Sciences (India)

    3

    lead to the formation of a three-dimensional architecture. Hirshfeld surface analysis for visually analyzing intermolecular interactions in crystal structures employing molecular surface contours and 2D fingerprint plots have been used to scrutinize molecular shapes. The vibration properties of this structure were studied by IR ...

  2. Identification and Characterization of Microsatellite Markers Derived from the Whole Genome Analysis of Taenia solium.

    Directory of Open Access Journals (Sweden)

    Mónica J Pajuelo

    2015-12-01

    Full Text Available Infections with Taenia solium are the most common cause of adult acquired seizures worldwide, and are the leading cause of epilepsy in developing countries. A better understanding of the genetic diversity of T. solium will improve parasite diagnostics and transmission pathways in endemic areas thereby facilitating the design of future control measures and interventions. Microsatellite markers are useful genome features, which enable strain typing and identification in complex pathogen genomes. Here we describe microsatellite identification and characterization in T. solium, providing information that will assist in global efforts to control this important pathogen.For genome sequencing, T. solium cysts and proglottids were collected from Huancayo and Puno in Peru, respectively. Using next generation sequencing (NGS and de novo assembly, we assembled two draft genomes and one hybrid genome. Microsatellite sequences were identified and 36 of them were selected for further analysis. Twenty T. solium isolates were collected from Tumbes in the northern region, and twenty from Puno in the southern region of Peru. The size-polymorphism of the selected microsatellites was determined with multi-capillary electrophoresis. We analyzed the association between microsatellite polymorphism and the geographic origin of the samples.The predicted size of the hybrid (proglottid genome combined with cyst genome T. solium genome was 111 MB with a GC content of 42.54%. A total of 7,979 contigs (>1,000 nt were obtained. We identified 9,129 microsatellites in the Puno-proglottid genome and 9,936 in the Huancayo-cyst genome, with 5 or more repeats, ranging from mono- to hexa-nucleotide. Seven microsatellites were polymorphic and 29 were monomorphic within the analyzed isolates. T. solium tapeworms were classified into two genetic groups that correlated with the North/South geographic origin of the parasites.The availability of draft genomes for T. solium represents a

  3. NOAA High-Resolution Sea Surface Temperature (SST) Analysis Products

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This archive covers two high resolution sea surface temperature (SST) analysis products developed using an optimum interpolation (OI) technique. The analyses have a...

  4. Synthesis, structure and Hirshfeld surface analysis, vibrational and ...

    Indian Academy of Sciences (India)

    dimensional architecture. Hirshfeld surface analysis for visually analysing intermolecular interactions in crystal structures employing molecular sur- face contours and 2D fingerprint plots has been used to scrutinize molecular shapes. The vibration ...

  5. Microscopic Analysis and Modeling of Airport Surface Sequencing, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — Although a number of airportal surface models exist and have been successfully used for analysis of airportal operations, only recently has it become possible to...

  6. Microscopic Analysis and Modeling of Airport Surface Sequencing, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — The complexity and interdependence of operations on the airport surface motivate the need for a comprehensive and detailed, yet flexible and validated analysis and...

  7. Analysis of Terminal Metallic Armor Plate Free-Surface Bulging

    National Research Council Canada - National Science Library

    Rapacki, Jr, E. J

    2008-01-01

    An analysis of the bulge formed on the free-surface of the terminal metallic plate of an armor array is shown to lead to reasonable estimates of the armor array's remaining penetration/perforation resistance...

  8. Characterizing the marker-dye correction for Gafchromic(®) EBT2 film: a comparison of three analysis methods.

    Science.gov (United States)

    McCaw, Travis J; Micka, John A; Dewerd, Larry A

    2011-10-01

    Gafchromic(®) EBT2 film has a yellow marker dye incorporated into the active layer of the film that can be used to correct the film response for small variations in thickness. This work characterizes the effect of the marker-dye correction on the uniformity and uncertainty of dose measurements with EBT2 film. The effect of variations in time postexposure on the uniformity of EBT2 is also investigated. EBT2 films were used to measure the flatness of a (60)Co field to provide a high-spatial resolution evaluation of the film uniformity. As a reference, the flatness of the (60)Co field was also measured with Kodak EDR2 films. The EBT2 films were digitized with a flatbed document scanner 24, 48, and 72 h postexposure, and the images were analyzed using three methods: (1) the manufacturer-recommended marker-dye correction, (2) an in-house marker-dye correction, and (3) a net optical density (OD) measurement in the red color channel. The field flatness was calculated from orthogonal profiles through the center of the field using each analysis method, and the results were compared with the EDR2 measurements. Uncertainty was propagated through a dose calculation for each analysis method. The change in the measured field flatness for increasing times postexposure was also determined. Both marker-dye correction methods improved the field flatness measured with EBT2 film relative to the net OD method, with a maximum improvement of 1% using the manufacturer-recommended correction. However, the manufacturer-recommended correction also resulted in a dose uncertainty an order of magnitude greater than the other two methods. The in-house marker-dye correction lowered the dose uncertainty relative to the net OD method. The measured field flatness did not exhibit any unidirectional change with increasing time postexposure and showed a maximum change of 0.3%. The marker dye in EBT2 can be used to improve the response uniformity of the film. Depending on the film analysis method used

  9. Oxidative and Anti-Oxidative Stress Markers in Chronic Glaucoma: A Systematic Review and Meta-Analysis

    Science.gov (United States)

    Benoist d’Azy, Cédric; Pereira, Bruno; Chiambaretta, Frédéric

    2016-01-01

    Chronic glaucoma is a multifactorial disease among which oxidative stress may play a major pathophysiological role. We conducted a systematic review and meta-analysis to evaluate the levels of oxidative and antioxidative stress markers in chronic glaucoma compared with a control group. The PubMed, Cochrane Library, Embase and Science Direct databases were searched for studies reporting oxidative and antioxidative stress markers in chronic glaucoma and in healthy controls using the following keywords: “oxidative stress” or “oxidant stress” or “nitrative stress” or “oxidative damage” or “nitrative damage” or “antioxidative stress” or “antioxidant stress” or “antinitrative stress” and “glaucoma”. We stratified our meta-analysis on the type of biomarkers, the type of glaucoma, and the origin of the sample (serum or aqueous humor). We included 22 case-control studies with a total of 2913 patients: 1614 with glaucoma and 1319 healthy controls. We included 12 studies in the meta-analysis on oxidative stress markers and 19 on antioxidative stress markers. We demonstrated an overall increase in oxidative stress markers in glaucoma (effect size = 1.64; 95%CI 1.20–2.09), ranging from an effect size of 1.29 in serum (95%CI 0.84–1.74) to 2.62 in aqueous humor (95%CI 1.60–3.65). Despite a decrease in antioxidative stress marker in serum (effect size = –0.41; 95%CI –0.72 to –0.11), some increased in aqueous humor (superoxide dismutase, effect size = 3.53; 95%CI 1.20–5.85 and glutathione peroxidase, effect size = 6.60; 95%CI 3.88–9.31). The differences in the serum levels of oxidative stress markers between glaucoma patients and controls were significantly higher in primary open angle glaucoma vs primary angle closed glaucoma (effect size = 12.7; 95%CI 8.78–16.6, P stress increased in glaucoma, both in serum and aqueous humor. Malonyldialdehyde seemed the best biomarkers of oxidative stress in serum. The increase of some

  10. De novo transcriptome assembly of Zanthoxylum bungeanum using Illumina sequencing for evolutionary analysis and simple sequence repeat marker development

    OpenAIRE

    Feng, Shijing; Zhao, Lili; Liu, Zhenshan; Liu, Yulin; Yang, Tuxi; Wei, Anzhi

    2017-01-01

    Zanthoxylum, an ancient economic crop in Asia, has a satisfying aromatic taste and immense medicinal values. A lack of genomic information and genetic markers has limited the evolutionary analysis and genetic improvement of Zanthoxylum species and their close relatives. To better understand the evolution, domestication, and divergence of Zanthoxylum, we present a de novo transcriptome analysis of an elite cultivar of Z. bungeanum using Illumina sequencing; we then developed simple sequence re...

  11. Genome analysis methods - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available tabase Description Download License Update History of This Database Site Policy | Contact Us Genome analysis methods - PGDBj Regis...switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods

  12. Quantitation of Surface Coating on Nanoparticles Using Thermogravimetric Analysis.

    Science.gov (United States)

    Dongargaonkar, Alpana A; Clogston, Jeffrey D

    2018-01-01

    Nanoparticles are critical components in nanomedicine and nanotherapeutic applications. Some nanoparticles, such as metallic nanoparticles, consist of a surface coating or surface modification to aid in its dispersion and stability. This surface coating may affect the behavior of nanoparticles in a biological environment, thus it is important to measure. Thermogravimetric analysis (TGA) can be used to determine the amount of coating on the surface of the nanoparticle. TGA experiments run under inert atmosphere can also be used to determine residual metal content present in the sample. In this chapter, the TGA technique and experimental method are described.

  13. A SUBLOCUS OF THE MULTICOPY MICROSATELLITE MARKER CMS1 MAPS PROXIMAL TO SPINAL MUSCULAR-ATROPHY (SMA) AS SHOWN BY RECOMBINANT ANALYSIS

    NARCIS (Netherlands)

    VANDERSTEEGE, G; COBBEN, JM; OSINGA, J; SCHEFFER, H; VANOMMEN, GJB; BUYS, CHCM

    1995-01-01

    The critical region containing the spinal muscular atrophy (SMA) gene is flanked by the 5q11-q13 markers, D5S435 and D5S557, as determined by linkage analysis. Here we present the results of an analysis of a Dutch SMA family with the multicopy microsatellite marker CMS1. A crossover is revealed in

  14. Plant DB link - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available e Site Policy | Contact Us Plant DB link - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ... ...switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods

  15. QTL list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available Policy | Contact Us QTL list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ... ...switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods

  16. Potential genetic markers for nonsyndromic oral clefts in the Brazilian population: A systematic review and meta-analysis.

    Science.gov (United States)

    Assis Machado, Renato; de Toledo, Isabela Porto; Martelli-Júnior, Hercilio; Reis, Silvia Regina; Neves Silva Guerra, Eliete; Coletta, Ricardo D

    2018-02-15

    Although various genes and genomic regions were described as of susceptibility for nonsyndromic oral clefts (NOC), recent reports have demonstrated significant interethnic variations in the genetic predisposition, a situation that affects the Brazilian population, one of the most admixed populations in the world. Therefore, the purpose of this review was to describe the available information on genetic risk markers for NOC in the Brazilian population. A systematic search of the literature was performed using LILACS, LIVIVO, PubMed, Scopus, and Web of Science databases, and studies that investigated genetic susceptibility markers for NOC in the Brazilian population were retrieved. Markers with enough statistical data were subjected to meta-analysis using random- or fixed-effects model with odds ratio (OR) and 95% confidence intervals (95% CI) as effect measures. Forty-nine studies conducted since 1999 were found, and in these 114 markers were evaluated throughout case-control or family-based approaches. Most of the studies were conducted with patients affected by nonsyndromic cleft lip with or without cleft palate (NSCL ± P), and 79 markers (69.3%) were evaluated by a single study only. Meta-analysis was performed with nine markers, and the most promising results were obtained for IRF6 (rs642961), 8q24 (rs987525 and rs1530300) and MTHFR (rs1801133), which were associated with increased risk for NSCL ± P, and for BMP4 (rs17563) that showed a protective effect for NSCL ± P. A large number of genetic markers distributed in several genes/loci was associated with NOC in the Brazilian population, but in general the original studies included limited number of samples and unsatisfactory protocols. The classical risk markers located in IRF6 and 8q24 showed promising results as well as rs1801133 in MTHFR and rs17563 in BMP4, and they should be validated in larger and multicenter studies taking in consideration the variations in the miscegenation of Brazilian

  17. Aberration analysis for freeform surface terms overlay on general decentered and tilted optical surfaces.

    Science.gov (United States)

    Yang, Tong; Cheng, Dewen; Wang, Yongtian

    2018-03-19

    Aberration theory helps designers to better understand the nature of imaging systems. However, the existing aberration theory of freeform surfaces has many limitations. For example, it only works in the special case when the central area of the freeform surface is used. In addition, the light footprint is limited to a circle, which does not match the case of an elliptical footprint for general systems. In this paper, aberrations generated by freeform surface term overlay on general decentered and tilted optical surfaces are analyzed. For the case when the off-axis section of a freeform surface is used, the aberration equation for using stop and nonstop surfaces is discussed, and the aberrations generated by Zernike terms up to Z 17/18 are analyzed in detail. To solve the problem of the elliptical light footprint for tilted freeform surfaces, the scaled pupil vector is used in the aberration analysis. The mechanism of aberration transformation is discovered, and the aberrations generated by different Zernike terms in this case are calculated. Finally we proposed aberration equations for freeform terms on general decentered and tilted freeform surfaces. The research result given in this paper offers an important reference for optical designers and engineers, and it is of great importance in developing analytical methods for general freeform system design, tolerance analysis, and system assembly.

  18. Multiscale analysis of surface morphologies by curvelet and contourlet transforms

    International Nuclear Information System (INIS)

    Li, Linfu; Zhang, Xiangchao; Zhang, Hao; He, Xiaoying; Xu, Min

    2015-01-01

    The surface topographies of precision components are critical to their functionalities. However, it is challenging to characterize the topographies of complex surfaces, especially for structured surfaces. The wavelet families are promising for the multiscale geometry analysis of nonstochastic surfaces. The second-generation curvelet transform provides a sparse representation and good multiscale decomposition for curve singularities. However, the contourlet expansion, composed of bases oriented along various directions in multiple scales with smaller redundancy rates, has a remarkable capability of representing borderlines. In this paper they are both adopted for the characterization of surface topographies. Different components can be extracted according to their scales and morphological characteristics; as a result, the corresponding manufacturing processes and functionalities can be analyzed specifically. Numerical experiments are given to demonstrate the capabilities of these methods in sparse representation and effective extraction of geometry features of different nonstochastic surfaces. (paper)

  19. ISSR marker-assisted genetic diversity analysis of Dioscorea hispida and selection of the best variety for sustainable production.

    Science.gov (United States)

    Nudin, Nur Fatihah Hasan; Ali, Abdul Manaf; Ngah, Norhayati; Mazlan, Nor Zuhailah; Mat, Nashriyah; Ghani, Mohd Noor Abd; Alias, Nadiawati; Zakaria, Abd Jamil; Jahan, Md Sarwar

    2017-08-01

    Plant breeding is a way of selection of a particular individual for the production of the progeny by separating or combining desired characteristics. The objective of this study was to justify different characteristics of Dioscorea hispida (Ubi gadong) varieties using molecular techniques to select the best variety for sustainable production at the farmer's level. A total of 160 germplasms of Ubi gadong were collected from different locations at the Terengganu and Kelantan states of Malaysia. Forty eight (48) out of 160 germplasms were selected as "primary" selection based on yield and other qualitative characters. Selected collections were then grown and maintained for ISSR marker-assisted genetic diversity analysis. Overall plant growth and yield of tubers were also determined. A total of 12 ISSR markers were tested to justify the characteristics of Ubi gadong varieties among which three markers showed polymorphic bands and on average 57.3% polymorphism were observed representing the highest variation among germplasms. The ISSR marker based on UPGMA cluster analysis grouped all 48 D. hispida into 10 vital groups that proved a vast genetic variation among germplasm collections. Therefore, hybridization should be made between two distant populations. The D. hispida is already proved as the highest starch content tuber crops and very rich in vitamins with both micro and macro minerals. Considering all these criteria and results from marker-assisted diversity analysis, accessions that are far apart based on their genetic coefficient (like DH27 and DH71; DH30 and DH70; DH43 and DH62; DH45 and DH61; DH77 and DH61; DH78 and DH57) could be selected as parents for further breeding programs. This will bring about greater diversity, which will lead to high productive index in terms of increase in yield and overall quality and for the ultimate target of sustainable Ubi gadong production. Copyright © 2017 Académie des sciences. Published by Elsevier Masson SAS. All rights

  20. Ion induced optical emission for surface and depth profile analysis

    International Nuclear Information System (INIS)

    White, C.W.

    1977-01-01

    Low-energy ion bombardment of solid surfaces results in the emission of infrared, visible, and ultraviolet radiation produced by inelastic ion-solid collision processes. The emitted optical radiation provides important insight into low-energy particle-solid interactions and provides the basis for an analysis technique which can be used for surface and depth profile analysis with high sensitivity. The different kinds of collision induced optical radiation emitted as a result of low-energy particle-solid collisions are reviewed. Line radiation arising from excited states of sputtered atoms or molecules is shown to provide the basis for surface and depth profile analysis. The spectral characteristics of this type of radiation are discussed and applications of the ion induced optical emission technique are presented. These applications include measurements of ion implant profiles, detection sensitivities for submonolayer quantities of impurities on elemental surfaces, and the detection of elemental impurities on complex organic substrates

  1. Recurrent parent genome recovery analysis in a marker-assisted backcrossing program of rice (Oryza sativa L.).

    Science.gov (United States)

    Miah, Gous; Rafii, Mohd Y; Ismail, Mohd R; Puteh, Adam B; Rahim, Harun A; Latif, Mohammad A

    2015-02-01

    Backcross breeding is the most commonly used method for incorporating a blast resistance gene into a rice cultivar. Linkage between the resistance gene and undesirable units can persist for many generations of backcrossing. Marker-assisted backcrossing (MABC) along with marker-assisted selection (MAS) contributes immensely to overcome the main limitation of the conventional breeding and accelerates recurrent parent genome (RPG) recovery. The MABC approach was employed to incorporate (a) blast resistance gene(s) from the donor parent Pongsu Seribu 1, the blast-resistant local variety in Malaysia, into the genetic background of MR219, a popular high-yielding rice variety that is blast susceptible, to develop a blast-resistant MR219 improved variety. In this perspective, the recurrent parent genome recovery was analyzed in early generations of backcrossing using simple sequence repeat (SSR) markers. Out of 375 SSR markers, 70 markers were found polymorphic between the parents, and these markers were used to evaluate the plants in subsequent generations. Background analysis revealed that the extent of RPG recovery ranged from 75.40% to 91.3% and from 80.40% to 96.70% in BC1F1 and BC2F1 generations, respectively. In this study, the recurrent parent genome content in the selected BC2F2 lines ranged from 92.7% to 97.7%. The average proportion of the recurrent parent in the selected improved line was 95.98%. MAS allowed identification of the plants that are more similar to the recurrent parent for the loci evaluated in backcross generations. The application of MAS with the MABC breeding program accelerated the recovery of the RP genome, reducing the number of generations and the time for incorporating resistance against rice blast. Copyright © 2014 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  2. Genetic diversity analysis of tropical sugar beet (Beta vulgaris L. varieties in Bangladesh using RAPD markers

    Directory of Open Access Journals (Sweden)

    Saclain Saidin

    2016-01-01

    Full Text Available Knowledge on intra-specific genetic variation of an organism is important for its genetic improvement and conservation. In order to estimate genetic variation and relatedness in eleven tropical Sugar beet varieties we used randomly amplified polymorphic DNA (RAPD markers. The RAPD analysis was performed using six decamer random primers, which amplified a total of 63 DNA fragments of which 43 (68.25% were found polymorphic. The average polymorphic bands per primer was 7.17 and the overall gene diversity was 0.24. Among the 43 polymorphic loci studied, 2 were specific for 2K 310, 1 for Shubraha, 1 for Natura and 1 for HI-0473 varieties. Pair wise genetic distance and similarity indices were ranged from 0.12-0.51 and 66.73-92.91, respectively. Cauvery and 2K 310 were found to be the most distantly related with a higher genetic distance value (GD = 0.51 and lower similarity index (SI = 66.73, while Aranka and Serenada were the most closely related with their lower GD (0.12 and higher SI(92.91 values. In an unweighted pair group method of arithmetic mean dendrogram constructed on the basis of genetic distances, the eleven varieties grouped into two main clusters: 2K 310 alone was in one cluster whereas 10 other varieties grouped into a major cluster. This indicates that 2K 310 was distantly related with each of the other varieties. Distantly related varieties based on estimated genetic variation could be selected for future breeding program that could result in improvement of this crop.

  3. Near surface stress analysis strategies for axisymmetric fretting

    Indian Academy of Sciences (India)

    In this paper, we develop design tools for Near Surface Analysis (NSA) for understanding axisymmetric fretting. Axisymmetric Fretting Analysis (AFA) becomes formidable owing to localised tractions that call for Fourier transform techniques. We develop two different NSA strategies based on two-dimensional plane strain ...

  4. Construction of a genetic map using EST-SSR markers and QTL analysis of major agronomic characters in hexaploid sweet potato (Ipomoea batatas (L.) Lam).

    Science.gov (United States)

    Kim, Jin-Hee; Chung, Il Kyung; Kim, Kyung-Min

    2017-01-01

    The Sweet potato, Ipomoea batatas (L.) Lam, is difficult to study in genetics and genomics because it is a hexaploid. The sweet potato study not have been performed domestically or internationally. In this study was performed to construct genetic map and quantitative trait loci (QTL) analysis. A total of 245 EST-SSR markers were developed, and the map was constructed by using 210 of those markers. The total map length was 1508.1 cM, and the mean distance between markers was 7.2 cM. Fifteen characteristics were investigated for QTLs analysis. According to those, the Four QTLs were identified, and The LOD score was 3.0. Further studies need to develop molecular markers in terms of EST-SSR markers for doing to be capable of efficient breeding. The genetic map created here using EST-SSR markers will facilitate planned breeding of sweet potato cultivars with various desirable traits.

  5. Construction of a genetic map using EST-SSR markers and QTL analysis of major agronomic characters in hexaploid sweet potato (Ipomoea batatas (L.) Lam)

    Science.gov (United States)

    Kim, Jin-Hee; Chung, Il Kyung

    2017-01-01

    The Sweet potato, Ipomoea batatas (L.) Lam, is difficult to study in genetics and genomics because it is a hexaploid. The sweet potato study not have been performed domestically or internationally. In this study was performed to construct genetic map and quantitative trait loci (QTL) analysis. A total of 245 EST-SSR markers were developed, and the map was constructed by using 210 of those markers. The total map length was 1508.1 cM, and the mean distance between markers was 7.2 cM. Fifteen characteristics were investigated for QTLs analysis. According to those, the Four QTLs were identified, and The LOD score was 3.0. Further studies need to develop molecular markers in terms of EST-SSR markers for doing to be capable of efficient breeding. The genetic map created here using EST-SSR markers will facilitate planned breeding of sweet potato cultivars with various desirable traits. PMID:29020092

  6. Marker-trait association analysis for agronomic and compositional traits in sainfoin (Onobrychis viciifolia).

    Science.gov (United States)

    Kempf, K; Malisch, C S; Grieder, C; Widmer, F; Kölliker, R

    2017-01-23

    Sainfoin (Onobrychis viciifolia) is a perennial forage legume with great potential for use in sustainable agriculture due to its low input requirements, good drought tolerance, and production of forage rich in polyphenolic compounds, which are beneficial for animal health. However, its distribution and cultivation are limited due to its moderate agronomic performance and a general lack of well adapted, highly yielding cultivars. Faster progress in breeding is imperative, but is often hampered by the complex inheritance of traits and limited knowledge on the genetic composition of this tetraploid, outbreeding species. Molecular genetic tools might aid phenotypic selection; however, to date no information on marker-trait associations is available for sainfoin. Hence, the goal of the present study was to detect marker-trait associations in a biparental F 1 population. Single plants were screened for recently developed genetic markers and phenotyped for important agronomic traits and concentrations of different polyphenolic compounds. Significant trait-associated markers (TAM) were detected for plant height (11), plant vigor (1), and seed yield (7). These three traits were positively correlated with each other and shared some TAMs. Correlations among markers suggested that two independent loci control these three vigor-related traits. One additional, independent TAM was detected for the share of prodelphinidins in total condensed tannins. Our results provide insight into the genetic control of important traits of sainfoin, and the TAMs reported here could assist selection in combination with phenotypic assessment.

  7. Analysis of Anomaly in Land Surface Temperature Using MODIS Products

    Science.gov (United States)

    Yorozu, K.; Kodama, T.; Kim, S.; Tachikawa, Y.; Shiiba, M.

    2011-12-01

    Atmosphere-land surface interaction plays a dominant role on the hydrologic cycle. Atmospheric phenomena cause variation of land surface state and land surface state can affect on atmosphereic conditions. Widely-known article related in atmospheric-land interaction was published by Koster et al. in 2004. The context of this article is that seasonal anomaly in soil moisture or soil surface temperature can affect summer precipitation generation and other atmospheric processes especially in middle North America, Sahel and south Asia. From not only above example but other previous research works, it is assumed that anomaly of surface state has a key factor. To investigate atmospheric-land surface interaction, it is necessary to analyze anomaly field in land surface state. In this study, soil surface temperature should be focused because it can be globally and continuously observed by satellite launched sensor. To land surface temperature product, MOD11C1 and MYD11C1 products which are kinds of MODIS products are applied. Both of them have 0.05 degree spatial resolution and daily temporal resolution. The difference of them is launched satellite, MOD11C1 is Terra and MYD11C1 is Aqua. MOD11C1 covers the latter of 2000 to present and MYD11C1 covers the early 2002 to present. There are unrealistic values on provided products even if daily product was already calibrated or corrected. For pre-analyzing, daily data is aggregated into 8-days data to remove irregular values for stable analysis. It was found that there are spatial and temporal distribution of 10-years average and standard deviation for each 8-days term. In order to point out extreme anomaly in land surface temperature, standard score for each 8-days term is applied. From the analysis of standard score, it is found there are large anomaly in land surface temperature around north China plain in early April 2005 and around Bangladesh in early May 2009.

  8. Polymorphism of the FABP2 gene: a population frequency analysis and an association study with cardiovascular risk markers in Argentina

    Directory of Open Access Journals (Sweden)

    Mayorga Luis S

    2007-06-01

    Full Text Available Abstract Background The FABP2 gene encodes for the intestinal FABP (IFABP protein, which is expressed only in intestinal enterocytes. A polymorphism at codon 54 in exon 2 of the FABP2 gene exchanges an Alanine (Ala, in the small helical region of the protein, for Threonine (Thr. Given the potential physiological role of the Ala54Thr FABP2 polymorphism, we assess in this study the local population frequency and analyze possible associations with five selected markers, i.e. glycemia, total cholesterol, body mass index (BMI, hypertension, and high Cardiovascular Risk Index (CVR index. Methods We studied 86 men and 116 women. DNA was extracted from a blood drop for genotype analysis. Allele frequencies were calculated by direct counting. Hardy Weinberg Equilibrium was evaluated using a Chi-square goodness of fit test. For the polymorphism association analysis, five markers were selected, i.e. blood pressure, Framingham Risk Index, total cholesterol, BMI, and glycemia. For each marker, the Odds Ratio (OR was calculated by an online statistic tool. Results Our results reveal a similar population polymorphism frequency as in previous European studies, with q = 0.277 (95% confidence limits 0.234–0.323. No significant association was found with any of the tested markers in the context of our Argentine nutritional and cultural habits. We did, however, observe a tendency for increased Cholesterol and high BMI in Thr54 carriers. Conclusion This is the first study to look at the population frequency of the Thr54 allele in Argentina. The obtained result does not differ from previously reported frequencies in European populations. Moreover, we found no association between the Thr54 allele and any of the five selected markers. The observed tendency to increased total cholesterol and elevated BMI in Thr54 carriers, even though not significant for p

  9. A comparative phylogenetic analysis of medicinal plant Tribulus terrestris in Northwest India revealed by RAPD and ISSR markers

    Directory of Open Access Journals (Sweden)

    ASHWANI KUMAR

    2012-07-01

    Full Text Available Kumar A, Verma N. 2012. A comparative phylogenetic analysis of medicinal plant Tribulus terrestris in Northwest India revealed by RAPD and ISSR markers. Biodiversitas 13: 107-113. Several DNA marker systems and associated techniques are available today for fingerprinting of plant varieties. A total of 5 RAPD and 8 ISSR primers were used. Amplification of genomic DNA of the 6 genotypes, using RAPD analysis, yielded 164 fragments that could be scored, of which 47 were polymorphic, with an average of 9.4 polymorphic fragments per primer. Number of amplified fragments with random primers ranged from 6 (AKR-1 to 10 (AKR-4 and varied in size from 200 bp to 2,500 bp. Percentage polymorphism ranged from 16% (AKR-4 to a maximum of 41% (AKR-4, with an average of 29.6%. The 8 ISSR primers used in the study produced 327 bands across 6 genotypes, of which 114 were polymorphic. The number of amplified bands varied from 7 (ISSR 7 to 12 (ISSR 1&3, with a size range of 250-2,800 bp. The average numbers of bands per primer and polymorphic bands per primer were 40.87 and 14.25, respectively. Percentage polymorphism ranged from 24% (ISSR 4 to 53.84% (ISSR 2, with an average percentage polymorphism of 35.59% across all the genotypes. The 3′-anchored primers based on poly (AC and poly (AT motifs produced high average polymorphisms of 53.84% and 40.81%, respectively. ISSR markers were more efficient than the RAPD assay, as they detected 35.59% polymorphic DNA markers in Tribulus terrestris as compared to 29.6% for RAPD markers. Clustering of genotypes within groups was not similar when RAPD and ISSR derived dendrogram were compared, whereas the pattern of clustering of the genotypes remained more or less the same in ISSR and combined data of RAPD and ISSR.

  10. Field Performance of Five Soybean Mutants Under Drought Stress Conditions and Molecular Analysis Using SSR Markers

    Directory of Open Access Journals (Sweden)

    Y Yuliasti

    2017-08-01

    Full Text Available The objectives of this research wereto evaluate (1 the performance of soybean mutant lines under drought stress conditions, and(2 the genetic diversity and relationship among the mutant lines using SSR markers.The field evaluation was conducted during the dry season of 2011 and 2012 at the experimental Farm of Mataram University, West Nusa Tenggara, Indonesia. The field experiment was set up in a randomized block design. Ten mutant lines and two control varieties were evaluated in four replications. Genetic distance among evaluated lines were determined based on allelic diversity analysis using 40 simple sequence repeat (SSR loci. Under drought stress conditions, two mutant lines, Kdl3 and Kdl8,showed a better performance compared to the other ones. The high yielding mutant lines were Kdl3and Kdl8, which yielded 1.75 t ha-1and 1.69 t ha-1, respectively, compared to the parent and national control, Panderman 1.43 t ha-1 and Muria 1.32 t ha-1. These mutant linesrequired 30.75 to 32days to flower and 79.75 to 83.75 day to harvest with relatively short plant height 28.25 and 23.35 cmrespectively. Those mutant characters were better than those of the other three mutants, the original parents, and the control soybean species. Since the evaluated soybean mutant lines yielded more under drought stress conditions than the standard varieties, they can be used and registered as drought-tolerant soybean mutants. Moreover, the evaluated soybean accessions showed a wide genetic distance. The accessions were clustered into two groups according to their genetic background, namelygroup I (the Panderman with three mutant lines and group II (the Muria with two mutant lines. Twenty-three out of 40 evaluated SSR loci, including AW31, BE806, CMAC7L, S080, S126, S57, S171, S224, S285, S294, S393, S294, S383, S511, S511, S520, S540, S547, S551, S571, S577, and S578, provided polymorphic alleles between the parents and their mutants and could be used to differentiate

  11. Microsatellite markers for identification and parentage analysis in the European wild boar (Sus scrofa

    Directory of Open Access Journals (Sweden)

    Costa Vânia

    2012-09-01

    Full Text Available Abstract Background The wild boar (Sus scrofa is among the most widespread mammal species throughout the old world. Presently, studies concerning microsatellites in domestic pigs and wild boars have been carried out in order to investigate domestication, social behavior and general diversity patterns among either populations or breeds. The purpose of the current study is to develop a robust set of microsatellites markers for parentage analyses and individual identification. Findings A set of 14 previously reported microsatellites markers have been optimized and tested in three populations from Hungary, Portugal and Spain, in a total of 167 samples. The results indicate high probabilities of exclusion (0.99999, low probability of identity (2.0E-13 – 2.5E-9 and a parentage assignment of 100%. Conclusions Our results demonstrate that this set of markers is a useful and efficient tool for the individual identification and parentage assignment in wild boars.

  12. Preliminary Comparative Analysis of Phenological Varieties of Quercus robur by ISSR-Markers

    Directory of Open Access Journals (Sweden)

    Vasiliy Chokheli

    2016-01-01

    Full Text Available Quercus robur L. is a valuable wood species having long ontogeny and promising to create long-living artificial plantings of recreational and ameliorative purposes in the steppes zone of Russia and other countries. In this work we have performed the genotyping of varieties of Quercus robur L. obtained from collection of Botanical Garden of Southern Federal University using intersimple sequence repeat (ISSR molecular markers. The most polymorphic ISSR-marker (GA 8YC was found in the collection. The polymorphic DNA markers identified in the present study can be used for the future breeding works to obtain valuable genotypes of Quercus genus. In addition we have performed DNA fingerprinting of the prospective sample of the variety Q. robur var. tardiflora Czern.

  13. Analysis of Bone Mineral Density According to the Biochemical Variable Markers in Adults

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sun Geun [Dept. of Radiology, Woosuk University Hospital, Chonju (Korea, Republic of); Kweon, Dae Cheol; Song, Woon Heung [Shinheung College University, Uijungbu (Korea, Republic of)

    2009-12-15

    To evaluate the bone mineral density (BMD) and biochemical markers. We evaluated the BMD of femoral neck and lumbar spines of 998(male 568, female 430) persons who took a regular health screening in Woosuk University Hospital from September 2007 to March 2008 by dual energy bone mineral densitometry. Results of BMD are different in terms of biochemical markers. Especially aged people showed osteoporotic change progressively. Degree of osteoporosis increases with age. A steep decrease of BMD can be found in postmenopausal women who have low level of female hormone. More persistent effort is needed to find out the factors that can reduce BMD values for prevention of problems by osteoporosis. In essence, research on factors related to other biochemical markers must be studied continuously.

  14. Integrative miRNA and mRNA analysis in penile carcinomas reveals markers and pathways with potential clinical impact

    DEFF Research Database (Denmark)

    Kuasne, Hellen; Barros-Filho, Mateus Camargo; Busso-Lopes, Ariane F

    2017-01-01

    Penile carcinoma (PeCa) is an important public health issue in poor and developing countries, and has only recently been explored in terms of genetic and epigenetic studies. Integrative data analysis is a powerful method for the identification of molecular drivers involved in cancer development a......, an integrative analysis using mRNA and miRNA profiles revealed markers related with tumor development and progression. Furthermore, MMP1 expression level was a predictive marker for lymph node metastasis in patients with PeCa....... and PPARG and hsa-miR-31-5p, hsa-miR-224-5p, and hsa-miR-223-3p were able to distinguish tumors from NPT with high sensitivity and specificity. Higher MMP1 expression was detected as a better predictor of lymph node metastasis than the clinical-pathological data. In addition, PPARG and EGFR were highlighted...

  15. Genomic-assisted haplotype analysis and the development of high-throughput SNP markers for salinity tolerance in soybean

    Science.gov (United States)

    Patil, Gunvant; Do, Tuyen; Vuong, Tri D.; Valliyodan, Babu; Lee, Jeong-Dong; Chaudhary, Juhi; Shannon, J. Grover; Nguyen, Henry T.

    2016-01-01

    Soil salinity is a limiting factor of crop yield. The soybean is sensitive to soil salinity, and a dominant gene, Glyma03g32900 is primarily responsible for salt-tolerance. The identification of high throughput and robust markers as well as the deployment of salt-tolerant cultivars are effective approaches to minimize yield loss under saline conditions. We utilized high quality (15x) whole-genome resequencing (WGRS) on 106 diverse soybean lines and identified three major structural variants and allelic variation in the promoter and genic regions of the GmCHX1 gene. The discovery of single nucleotide polymorphisms (SNPs) associated with structural variants facilitated the design of six KASPar assays. Additionally, haplotype analysis and pedigree tracking of 93 U.S. ancestral lines were performed using publically available WGRS datasets. Identified SNP markers were validated, and a strong correlation was observed between the genotype and salt treatment phenotype (leaf scorch, chlorophyll content and Na+ accumulation) using a panel of 104 soybean lines and, an interspecific bi-parental population (F8) from PI483463 x Hutcheson. These markers precisely identified salt-tolerant/sensitive genotypes (>91%), and different structural-variants (>98%). These SNP assays, supported by accurate phenotyping, haplotype analyses and pedigree tracking information, will accelerate marker-assisted selection programs to enhance the development of salt-tolerant soybean cultivars. PMID:26781337

  16. Subclassification and Detection of New Markers for the Discrimination of Primary Liver Tumors by Gene Expression Analysis Using Oligonucleotide Arrays.

    Science.gov (United States)

    Hass, Holger G; Vogel, Ulrich; Scheurlen, Michael; Jobst, Jürgen

    2017-12-26

    The failure to correctly differentiate between intrahepatic cholangiocarcinoma [CC] and hepatocellular carcinoma [HCC] is a significant clinical problem, particularly in terms of the different treatment goals for both cancers. In this study a specific gene expression profile to discriminate these two subgroups of liver cancer was established and potential diagnostic markers for clinical use were analyzed. To evaluate the gene expression profiles of HCC and intrahepatic CC, Oligonucleotide arrays ( Affymetrix U133A) were used. Overexpressed genes were checked for their potential use as new markers for discrimination and their expression values were validated by reverse transcription polymerase chain reaction and immunohistochemistry analyses. 695 genes/expressed sequence tags (ESTs) in HCC (245 up-/450 down-regulated) and 552 genes/ESTs in CC (221 up-/331 down-regulated) were significantly dysregulated (p〈0.05, fold change >2, ≥70%). Using a supervised learning method, and one-way analysis of variance a specific 270-gene expression profile that enabled rapid, reproducible differentiation between both tumors and non-malignant liver tissues was established. A panel of 12 genes (e.g. HSP90β, ERG1, GPC3, TKT, ACLY, and NME1 for HCC; SPT2, T4S3, CNX43, TTD1, HBD01 for CC) were detected and partly described for the first time as potential discrimination markers. A specific gene expression profile for discrimination of primary liver cancer was identified and potential marker genes with feasible clinical impact were described.

  17. Enterococci in river Ganga surface waters: Propensity of species distribution, dissemination of antimicrobial-resistance and virulence-markers among species along landscape

    Directory of Open Access Journals (Sweden)

    Shanker Rishi

    2009-07-01

    Full Text Available Abstract Background Surface waters quality has declined in developing countries due to rapid industrialization and population growth. The microbiological quality of river Ganga, a life-sustaining surface water resource for large population of northern India, is adversely affected by several point and non-point sources of pollution. Further, untreated surface waters are consumed for drinking and various household tasks in India making the public vulnerable to water-borne diseases and outbreaks. Enterococci, the 'indicator' of water quality, correlates best with the incidence of gastrointestinal diseases as well as prevalence of other pathogenic microorganisms. Therefore, this study aims to determine the distribution of species diversity, dissemination of antimicrobial-resistance and virulence-markers in enterococci with respect to rural-urban landscape along river Ganga in northern India. Results Enterococci density (χ2: 1900, df: 1; p 2: 100.4, df: 20; p E. faecalis, E. faecium, E. durans and E. hirae down the gradient. Statistically discernible (p: 0.0156 – Enterococcus spp. recovered from five sites in the up-to-down gradient landscape. A significant correlation was observed in the distribution of multiple-antimicrobial-resistance (viz., erythromycin-rifampicin-gentamicin-methicillin and vancomycin-gentamicin-streptomycin; rs: 0.9747; p: 0.0083 and multiple-virulence-markers (viz., gelE+esp+; rs: 0.9747; p: 0.0083; gelE+efaA+; rs: 0.8944; p: 0.0417 among different Enterococcus spp. Conclusion Our observations show prevalence of multiple-antimicrobial-resistance as well as multiple-virulence traits among different Enterococcus spp. The observed high background pool of resistance and virulence in enterococci in river waters of populous countries has the potential to disseminate more alarming antimicrobial-resistant pathogenic bacteria of same or other lineage in the environment. Therefore, the presence of elevated levels of virulent

  18. MCM - 2 and Ki - 67 as proliferation markers in renal cell carcinoma: A quantitative and semi - quantitative analysis.

    Science.gov (United States)

    Mehdi, Muhammad Zain; Nagi, Abdul Hanan; Naseem, Nadia

    2016-01-01

    Fuhrman nuclear grade is the most important histological parameter to predict prognosis in a patient of renal cell carcinoma (RCC). However, it suffers from inter-observer and intra-observer variation giving rise to need of a parameter that not only correlates with nuclear grade but is also objective and reproducible. Proliferation is the measure of aggressiveness of a tumour and it is strongly correlated with Fuhrman nuclear grade, clinical survival and recurrence in RCC. Ki-67 is conventionally used to assess proliferation. Mini-chromosome maintenance 2 (MCM-2) is a lesser known marker of proliferation and identifies a greater proliferation faction. This study was designed to assess the prognostic significance of MCM-2 by comparing it with Fuhrman nuclear grade and Ki-67. n=50 cases of various ages, stages, histological subtypes and grades of RCC were selected for this study. Immunohistochemical staining using Ki-67(MIB-1, Mouse monoclonal antibody, Dako) and MCM-2 (Mouse monoclonal antibody, Thermo) was performed on the paraffin embedded blocks in the department of Morbid anatomy and Histopathology, University of Health Sciences, Lahore. Labeling indices (LI) were determined by two pathologists independently using quantitative and semi-quantitative analysis. Statistical analysis was carried out using SPSS 20.0. Kruskall-Wallis test was used to determine a correlation of proliferation markers with grade, and Pearson's correlate was used to determine correlation between the two proliferation markers. Labeling index of MCM-2 (median=24.29%) was found to be much higher than Ki-67(median=13.05%). Both markers were significantly related with grade (p=0.00; Kruskall-Wallis test). LI of MCM-2 was found to correlate significantly with LI of Ki-67(r=0.0934;p=0.01 with Pearson's correlate). Results of semi-quantitative analysis correlated well with quantitative analysis. Both Ki-67 and MCM-2 are markers of proliferation which are closely linked to grade. Therefore, they

  19. Sequential analysis of biochemical markers of bone resorption and bone densitometry in multiple myeloma

    DEFF Research Database (Denmark)

    Abildgaard, Niels; Brixen, Kim; Eriksen, Erik Fink

    2004-01-01

    BACKGROUND AND OBJECTIVES: Bone lesions often occur in multiple myeloma (MM), but no tests have proven useful in identifying patients with increased risk. Bone marker assays and bone densitometry are non-invasive methods that can be used repeatedly at low cost. This study was performed to evaluate...... 6 weeks, DEXA-scans performed every 3 months, and skeletal radiographs were done every 6 months as well as when indicated. RESULTS: Serum ICTP and urinary NTx were predictive of progressive bone events. Markers of bone formation, bone mineral density assessments, and M component measurements were...

  20. Toolbox Approaches Using Molecular Markers and 16S rRNA Gene Amplicon Data Sets for Identification of Fecal Pollution in Surface Water.

    Science.gov (United States)

    Ahmed, W; Staley, C; Sadowsky, M J; Gyawali, P; Sidhu, J P S; Palmer, A; Beale, D J; Toze, S

    2015-10-01

    In this study, host-associated molecular markers and bacterial 16S rRNA gene community analysis using high-throughput sequencing were used to identify the sources of fecal pollution in environmental waters in Brisbane, Australia. A total of 92 fecal and composite wastewater samples were collected from different host groups (cat, cattle, dog, horse, human, and kangaroo), and 18 water samples were collected from six sites (BR1 to BR6) along the Brisbane River in Queensland, Australia. Bacterial communities in the fecal, wastewater, and river water samples were sequenced. Water samples were also tested for the presence of bird-associated (GFD), cattle-associated (CowM3), horse-associated, and human-associated (HF183) molecular markers, to provide multiple lines of evidence regarding the possible presence of fecal pollution associated with specific hosts. Among the 18 water samples tested, 83%, 33%, 17%, and 17% were real-time PCR positive for the GFD, HF183, CowM3, and horse markers, respectively. Among the potential sources of fecal pollution in water samples from the river, DNA sequencing tended to show relatively small contributions from wastewater treatment plants (up to 13% of sequence reads). Contributions from other animal sources were rarely detected and were very small (pollution in an urban river. This study is a proof of concept, and based on the results, we recommend using bacterial community analysis (where possible) along with PCR detection or quantification of host-associated molecular markers to provide information on the sources of fecal pollution in waterways. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  1. Genetic analysis of Apuleia leiocarpa as revealed by random amplified polymorphic DNA markers: prospects for population genetic studies.

    Science.gov (United States)

    Lencina, K H; Konzen, E R; Tsai, S M; Bisognin, D A

    2016-12-19

    Apuleia leiocarpa (Vogel) J.F. MacBride is a hardwood species native to South America, which is at serious risk of extinction. Therefore, it is of prime importance to examine the genetic diversity of this species, information required for developing conservation, sustainable management, and breeding strategies. Although scarcely used in recent years, random amplified polymorphic DNA markers are useful resources for the analysis of genetic diversity and structure of tree species. This study represents the first genetic analysis based on DNA markers in A. leiocarpa that aimed to investigate the levels of polymorphism and to select markers for the precise characterization of its genetic structure. We adapted the original DNA extraction protocol based on cetyltrimethyl ammonium bromide, and describe a simple procedure that can be used to obtain high-quality samples from leaf tissues of this tree. Eighteen primers were selected, revealing 92 bands, from which 75 were polymorphic and 61 were sufficient to represent the overall genetic structure of the population without compromising the precision of the analysis. Some fragments were conserved among individuals, which can be sequenced and used to analyze nucleotide diversity parameters through a wider set of A. leiocarpa individuals and populations. The individuals were separated into 11 distinct groups with variable levels of genetic diversity, which is important for selecting desirable genotypes and for the development of a conservation and sustainable management program. Our results are of prime importance for further investigations concerning the genetic characterization of this important, but vulnerable species.

  2. Contribution of surface analysis spectroscopic methods to the lubrication field

    International Nuclear Information System (INIS)

    Blanc, C.

    1979-01-01

    The analytical surface technics such as ESCA, AES and SIMS are tested to be applied to a particular lubrication field. One deals with a 100 C 6 steel surface innumered in tricresylphosphate at 110 0 C for 15 days. The nature of the first layers is studied after relevant solvant cleaning. An iron oxide layer is produced on the bearing surface, namely αFe 2 -O 3 . ESCA, AES and SIMS studies show an overlayer of iron phosphate. The exact nature of iron phosphate is not clearly established but the formation of a ferrous phosphate coating can be assumed from ESCA analysis [fr

  3. Autonomous Aerobraking: Thermal Analysis and Response Surface Development

    Science.gov (United States)

    Dec, John A.; Thornblom, Mark N.

    2011-01-01

    A high-fidelity thermal model of the Mars Reconnaissance Orbiter was developed for use in an autonomous aerobraking simulation study. Response surface equations were derived from the high-fidelity thermal model and integrated into the autonomous aerobraking simulation software. The high-fidelity thermal model was developed using the Thermal Desktop software and used in all phases of the analysis. The use of Thermal Desktop exclusively, represented a change from previously developed aerobraking thermal analysis methodologies. Comparisons were made between the Thermal Desktop solutions and those developed for the previous aerobraking thermal analyses performed on the Mars Reconnaissance Orbiter during aerobraking operations. A variable sensitivity screening study was performed to reduce the number of variables carried in the response surface equations. Thermal analysis and response surface equation development were performed for autonomous aerobraking missions at Mars and Venus.

  4. Markers of Autolysis in Acute ST Elevation Myocardial Infarction – A Comparative Analysis

    Directory of Open Access Journals (Sweden)

    Prabindra Maharjan

    2015-06-01

    Conclusions: MVP, Lp (a, TC, and CK-MB levels and myocardial wall motion at the presentation may play the role of markers for IRA patency status that will help in early identification of patients with IRA, for whom repeat thrombolysis or rescue PCI may not be required. Keywords: acute coronary syndrome; infarct related artery; myocardial infarction.

  5. Sequential analysis of biochemical markers of bone resorption and bone densitometry in multiple myeloma

    DEFF Research Database (Denmark)

    Abildgaard, Niels; Brixen, Kim; Eriksen, Erik Fink

    2004-01-01

    BACKGROUND AND OBJECTIVES: Bone lesions often occur in multiple myeloma (MM), but no tests have proven useful in identifying patients with increased risk. Bone marker assays and bone densitometry are non-invasive methods that can be used repeatedly at low cost. This study was performed to evaluate...

  6. Semi-quantitative analysis of endometrial receptivity marker mRNA ...

    African Journals Online (AJOL)

    In fertile women, expression of molecular marker of endometrial receptivity, HOXA11, leukemia inhibitory factor (LIF) and basic transcriptional element binding protein 1 (BTEB1), rises during the luteal phase with the peak occurring during the implantation window. We evaluated the transcript levels of HOXA-11, LIF and ...

  7. Characterization of the 17p amplicon in human sarcomas: microsatellite marker analysis

    NARCIS (Netherlands)

    Wolf, M.; Tarkkanen, M.; Hulsebos, T.; Larramendy, M. L.; Forus, A.; Myklebost, O.; Aaltonen, L. A.; Elomaa, I.; Knuutila, S.

    1999-01-01

    The structure of the 17p amplicon from 9 human sarcoma specimens evaluated by comparative genomic hybridization (CGH) has been studied by analyzing 28 microsatellite markers by PCR. Eleven sarcoma specimens showing no DNA copy number increases at 17p by CGH were analyzed as control samples. Five

  8. Oral cancer risk and molecular markers.

    Science.gov (United States)

    Chimenos-Küstner, Eduardo; Font-Costa, Imma; López-López, José

    2004-01-01

    The clinical appearance and, especially, the degree of dysplasia that may be shown by pre-cancerous lesions in the oral cavity suggest a potential for malignisation. An increasing number of studies are seeking new, more specific markers that would help to determine the degree of cell alteration and enable a better understanding of the degree of malignant degeneration of these cells. The present review considers the most recent findings for these markers, grouping them into families: tumour growth markers; markers of tumour suppression and anti-tumour response; angiogenesis markers; markers of tumour invasion and metastatic potential; cell surface markers; intracellular markers; markers derived from arachidonic acid; and enzymatic markers.

  9. Glass fibres reinforced polyester composites degradation monitoring by surface analysis

    Energy Technology Data Exchange (ETDEWEB)

    Croitoru, Catalin [“Transilvania” University of Brasov, Materials Engineering and Welding Department, Eroilor 29 Str., 500036 Brasov (Romania); Patachia, Silvia, E-mail: st.patachia@unitbv.ro [“Transilvania” University of Brasov, Product Design Environment and Mechatronics Department, Eroilor 29 Str., 500036 Brasov (Romania); Papancea, Adina [“Transilvania” University of Brasov, Product Design Environment and Mechatronics Department, Eroilor 29 Str., 500036 Brasov (Romania); Baltes, Liana; Tierean, Mircea [“Transilvania” University of Brasov, Materials Engineering and Welding Department, Eroilor 29 Str., 500036 Brasov (Romania)

    2015-12-15

    Highlights: • Glass fibre-reinforced polyester composites surface analysis by photographic method. • The composites are submitted to accelerated ageing by UV irradiation at 254 nm. • The UV irradiation promotes differences in the surface chemistry of the composites. • MB dye is differently adsorbed on surfaces with different degradation degrees. • Good correlation between the colouring degree and surface chemistry. - Abstract: The paper presents a novel method for quantification of the modifications that occur on the surface of different types of gel-coated glass fibre-reinforced polyester composites under artificial UV-ageing at 254 nm. The method implies the adsorption of an ionic dye, namely methylene blue, on the UV-aged composite, and computing the CIELab colour space parameters from the photographic image of the coloured composite's surface. The method significantly enhances the colour differences between the irradiated composites and the reference, in contrast with the non-coloured ones. The colour modifications that occur represent a good indicative of the surface degradation, alteration of surface hydrophily and roughness of the composite and are in good correlation with the ATR-FTIR spectroscopy and optical microscopy results. The proposed method is easier, faster and cheaper than the traditional ones.

  10. Ion beam analysis of metal ion implanted surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Evans, P.J.; Chu, J.W.; Johnson, E.P.; Noorman, J.T. [Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW (Australia); Sood, D.K. [Royal Melbourne Inst. of Tech., VIC (Australia)

    1993-12-31

    Ion implantation is an established method for altering the surface properties of many materials. While a variety of analytical techniques are available for the characterisation of implanted surfaces, those based on particle accelerators such as Rutherford backscattering (RBS) and nuclear reaction analysis (NRA) provide some of the most useful and powerful for this purpose. Application of the latter techniques to metal ion implantation research at ANSTO will be described with particular reference to specific examples from recent studies. Where possible, the information obtained from ion beam analysis will be compared with that derived from other techniques such as Energy Dispersive X-ray (EDX) and Auger spectroscopies. 4 refs., 5 figs.

  11. The ROCK inhibitor Y-27632 improves recovery of human embryonic stem cells after fluorescence-activated cell sorting with multiple cell surface markers.

    Directory of Open Access Journals (Sweden)

    Nil Emre

    Full Text Available BACKGROUND: Due to the inherent sensitivity of human embryonic stem cells (hESCs to manipulations, the recovery and survival of hESCs after fluorescence-activated cell sorting (FACS can be low. Additionally, a well characterized and robust methodology for performing FACS on hESCs using multiple-cell surface markers has not been described. The p160-Rho-associated coiled kinase (ROCK inhibitor, Y-27632, previously has been identified as enhancing survival of hESCs upon single-cell dissociation, as well as enhancing recovery from cryopreservation. Here we examined the application of Y-27632 to hESCs after FACS to improve survival in both feeder-dependent and feeder-independent growth conditions. METHODOLOGY/PRINCIPAL FINDINGS: HESCs were sorted using markers for SSEA-3, TRA-1-81, and SSEA-1. Cells were plated after sorting for 24 hours in either the presence or the absence of Y-27632. In both feeder-dependent and feeder-independent conditions, cell survival was greater when Y-27632 was applied to the hESCs after sort. Specifically, treatment of cells with Y-27632 improved post-sort recovery up to four fold. To determine the long-term effects of sorting with and without the application of Y-27632, hESCs were further analyzed. Specifically, hESCs sorted with and without the addition of Y-27632 retained normal morphology, expressed hESC-specific markers as measured by immunocytochemistry and flow cytometry, and maintained a stable karyotype. In addition, the hESCs could differentiate into three germ layers in vitro and in vivo in both feeder-dependent and feeder-independent growth conditions. CONCLUSIONS/SIGNIFICANCE: The application of Y-27632 to hESCs after cell sorting improves cell recovery with no observed effect on pluripotency, and enables the consistent recovery of hESCs by FACS using multiple surface markers. This improved methodology for cell sorting of hESCs will aid many applications such as removal of hESCs from secondary cell types

  12. Analysis of passive surface-wave noise in surface microseismic data and its implications

    Science.gov (United States)

    Forghani-Arani, F.; Willis, M.; Haines, S.; Batzle, M.; Davidson, M.

    2011-01-01

    Tight gas reservoirs are projected to be a major portion of future energy resources. Because of their low permeability, hydraulic fracturing of these reservoirs is required to improve the permeability and reservoir productivity. Passive seismic monitoring is one of the few tools that can be used to characterize the changes in the reservoir due to hydraulic fracturing. Although the majority of the studies monitoring hydraulic fracturing exploit down hole microseismic data, surface microseismic monitoring is receiving increased attention because it is potentially much less expensive to acquire. Due to a broader receiver aperture and spatial coverage, surface microseismic data may be more advantageous than down hole microseismic data. The effectiveness of this monitoring technique, however, is strongly dependent on the signal-to-noise ratio of the data. Cultural and ambient noise can mask parts of the waveform that carry information about the subsurface, thereby decreasing the effectiveness of surface microseismic analysis in identifying and locating the microseismic events. Hence, time and spatially varying suppression of the surface-wave noise ground roll is a critical step in surface microseismic monitoring. Here, we study a surface passive dataset that was acquired over a Barnett Shale Formation reservoir during two weeks of hydraulic fracturing, in order to characterize and suppress the surface noise in this data. We apply techniques to identify the characteristics of the passive ground roll. Exploiting those characteristics, we can apply effective noise suppression techniques to the passive data. ?? 2011 Society of Exploration Geophysicists.

  13. Use of Simple Sequence Repeat (SSR) markers for DNA fingerprinting and diversity analysis of sugarcane (Saccharum spp.) cultivars resistant and susceptible to red rot

    Science.gov (United States)

    In recent years SSR markers have been used widely for the genetic analysis. The objective of present research was to use SSR markers to develop DNA-based genetic identification and analyze genetic relationship of sugarcane cultivars grown in Pakistan either resistant or susceptible to red rot. Twent...

  14. Marker-less reconstruction of dense 4-D surface motion fields using active laser triangulation for respiratory motion management.

    Science.gov (United States)

    Bauer, Sebastian; Berkels, Benjamin; Ettl, Svenja; Arold, Oliver; Hornegger, Joachim; Rumpf, Martin

    2012-01-01

    To manage respiratory motion in image-guided interventions a novel sparse-to-dense registration approach is presented. We apply an emerging laser-based active triangulation (AT) sensor that delivers sparse but highly accurate 3-D measurements in real-time. These sparse position measurements are registered with a dense reference surface extracted from planning data. Thereby a dense displacement field is reconstructed which describes the 4-D deformation of the complete patient body surface and recovers a multi-dimensional respiratory signal for application in respiratory motion management. The method is validated on real data from an AT prototype and synthetic data sampled from dense surface scans acquired with a structured light scanner. In a study on 16 subjects, the proposed algorithm achieved a mean reconstruction accuracy of +/- 0.22 mm w.r.t. ground truth data.

  15. [Genotyping of Vaginal Candida glabrata Isolates Using Microsatellite Marker Analysis and DNA Sequencing to Identify Mutations Associated with Antifungal Resistance].

    Science.gov (United States)

    Döğen, Aylin; Durukan, Hüseyin; Güzel, Ahmet Barış; Oksüz, Zehra; Kaplan, Engin; Serin, Mehmet Sami; Serin, Ayşe; Emekdaş, Gürol; Aslan, Gönül; Tezcan, Seda; Kalkancı, Ayşe; Ilkit, Macit

    2013-01-01

    Vulvovaginal candidosis is the second most common cause of vaginitis (17-39%) after bacterial vaginosis (22-50%). Since the diagnosis of vulvovaginal candidosis mainly depends on clinical findings without mycologic confirmatory tests and treated empirically, the actual incidence rate of vulvovaginal candidosis is unknown. Approximately 70-90% of vulvovaginal candidosis cases are caused by Candida albicans, however the increasing incidence of C.glabrata infections and its reduced susceptibility to azole drug therapy have generated increasing attention. The epidemiology and population structure of vulvovaginal candidosis due to C.glabrata are poorly characterized. This study was aimed to genotype the C.glabrata strains isolated from vaginal samples in Cukurova region, Turkey by microsatellite markers, to investigate the antifungal susceptibility profiles of the strains and to determine the molecular mechanisms leading to phenotypical azole resistance. A total of 34 unrelated vaginal C.glabrata strains isolated from patients with acute (n= 11) and recurrent (n= 14) vulvovaginal candidosis, control group (n= 9) without vaginitis symptoms, and a reference strain of C.glabrata CBS 138 (ATCC 2001) were included in the study. These isolates were genotyped using multiple-locus variable number tandem repeat analysis of three microsatellite markers (RPM2, MTI, and Cg6). Analysis of microsatellite markers was performed by fragment size determination of RPM2, MTI, and Cg6 PCR products through capillary electrophoresis. For each of the evaluated strains, DNA sequence analysis was performed for one gene (CgERG11) and four loci (CgPDR1, NTM1, TRP1, and URA3) to detect mutations possibly associated with antifungal resistance in each strain. In vitro susceptibility profiles of the strains to 13 antifungals and boric acid were determined according to CLSI document M27-A3 to investigate possible relationships between detected mutations and phenotypic resistance. C.glabrata CBS 138

  16. Generalized surface momentum balances for the analysis of surface dilatational data

    NARCIS (Netherlands)

    Sagis, L.M.C.

    2013-01-01

    Dilatational rheological properties of interfaces are often determined using drop tensiometers, in which the interface of the droplet is subjected to oscillatory area changes. A dynamic surface tension is determined either by image analysis of the droplet profile or by measuring the capillary

  17. An Integrated Transcriptome-Wide Analysis of Cave and Surface Dwelling Astyanax mexicanus

    Science.gov (United States)

    Gross, Joshua B.; Furterer, Allison; Carlson, Brian M.; Stahl, Bethany A.

    2013-01-01

    Numerous organisms around the globe have successfully adapted to subterranean environments. A powerful system in which to study cave adaptation is the freshwater characin fish, Astyanax mexicanus. Prior studies in this system have established a genetic basis for the evolution of numerous regressive traits, most notably vision and pigmentation reduction. However, identification of the precise genetic alterations that underlie these morphological changes has been delayed by limited genetic and genomic resources. To address this, we performed a transcriptome analysis of cave and surface dwelling Astyanax morphs using Roche/454 pyrosequencing technology. Through this approach, we obtained 576,197 Pachón cavefish-specific reads and 438,978 surface fish-specific reads. Using this dataset, we assembled transcriptomes of cave and surface fish separately, as well as an integrated transcriptome that combined 1,499,568 reads from both morphotypes. The integrated assembly was the most successful approach, yielding 22,596 high quality contiguous sequences comprising a total transcriptome length of 21,363,556 bp. Sequence identities were obtained through exhaustive blast searches, revealing an adult transcriptome represented by highly diverse Gene Ontology (GO) terms. Our dataset facilitated rapid identification of sequence polymorphisms between morphotypes. These data, along with positional information collected from the Danio rerio genome, revealed several syntenic regions between Astyanax and Danio. We demonstrated the utility of this positional information through a QTL analysis of albinism in a surface x Pachón cave F2 pedigree, using 65 polymorphic markers identified from our integrated assembly. We also adapted our dataset for an RNA-seq study, revealing many genes responsible for visual system maintenance in surface fish, whose expression was not detected in adult Pachón cavefish. Conversely, several metabolism-related genes expressed in cavefish were not detected in

  18. Metabolomics of prematurity: analysis of patterns of amino acids, enzymes, and endocrine markers by categories of gestational age.

    Science.gov (United States)

    Wilson, Kumanan; Hawken, Steven; Ducharme, Robin; Potter, Beth K; Little, Julian; Thébaud, Bernard; Chakraborty, Pranesh

    2014-02-01

    Prematurity may influence the levels of amino acids, enzymes, and endocrine markers obtained through newborn screening. Identifying which analytes are the most affected by degree of prematurity could provide insight into how prematurity impacts metabolism. Analytes from blood spots assayed by Newborn Screening Ontario between March 2006 and April 2009 were used in this analysis. We examined the associations between the degree of prematurity and the levels of amino acids, enzymes, and endocrine markers in all newborns with and without adjustment for birth weight, feeding status, sample timing, transfusion, and sex. Our analysis included the following cohorts: 373,819 children born at term (>36 wk gestation), 26,483 near-term children (33-36 wk gestation), 4,354 very premature children (28-32 wk gestation), and 1,146 extremely premature children (prematurity, the levels of three amino acids (arginine, leucine, and valine) were at least 50% different between the cohorts of extremely premature and term children. The levels of 17-hydroxyprogesterone increased with increasing prematurity, while thyrotropin-stimulating hormone values consistently decreased with increasing prematurity. None of the three enzyme markers we examined showed a trend in levels across categories of prematurity. This study demonstrates that children at different stages of prematurity are metabolically distinct. Future research should focus on the mechanism by which specific analytes are influenced by prematurity.

  19. Genetic diversity and population structure analysis between Indian red jungle fowl and domestic chicken using microsatellite markers.

    Science.gov (United States)

    Kumar, Vinay; Shukla, Sanjeev K; Mathew, Jose; Sharma, Deepak

    2015-01-01

    The present study was conducted to assess the genetic diversity, population structure, and relatedness in Indian red jungle fowl (RJF, Gallus gallus murgi) from northern India and three domestic chicken populations (gallus gallus domesticus), maintained at the institute farms, namely White Leghorn (WL), Aseel (AS) and Red Cornish (RC) using 25 microsatellite markers. All the markers were polymorphic, the number of alleles at each locus ranged from five (MCW0111) to forty-three (LEI0212) with an average number of 19 alleles per locus. Across all loci, the mean expected heterozygosity and polymorphic information content were 0.883 and 0.872, respectively. Population-specific alleles were found in each population. A UPGMA dendrogram based on shared allele distances clearly revealed two major clusters among the four populations; cluster I had genotypes from RJF and WL whereas cluster II had AS and RC genotypes. Furthermore, the estimation of population structure was performed to understand how genetic variation is partitioned within and among populations. The maximum ▵K value was observed for K = 4 with four identified clusters. Furthermore, factorial analysis clearly showed four clustering; each cluster represented the four types of population used in the study. These results clearly, demonstrate the potential of microsatellite markers in elucidating the genetic diversity, relationships, and population structure analysis in RJF and domestic chicken populations.

  20. Application of Microsatellite Markers in Conservation Genetics and Fisheries Management: Recent Advances in Population Structure Analysis and Conservation Strategies

    Science.gov (United States)

    Abdul-Muneer, P. M.

    2014-01-01

    Microsatellites are the most popular and versatile genetic marker with myriads of applications in population genetics, conservation biology, and evolutionary biology. These are the arrays of DNA sequences, consisting of tandemly repeating mono-, di-, tri-, and tetranucleotide units, which are distributed throughout the genomes of most eukaryotic species. Microsatellites are codominant in nature, highly polymorphic, easily typed, and Mendelian inherited, all properties which make them very suitable for the study of population structure and pedigree analysis and capable of detecting differences among closely related species. PCR for microsatellites can be automated for identifying simple sequence repeat polymorphism. Small amount of blood samples or alcohol preserved tissue is adequate for analyzing them. Most of the microsatellites are noncoding, and therefore variations are independent of natural selection. These properties make microsatellites ideal genetic markers for conservation genetics and fisheries management. This review addresses the applications of microsatellite markers in conservation genetics and recent advances in population structure analysis in the context of fisheries management. PMID:24808959

  1. Genetic diversity and population structure of pea (Pisum sativum L.) varieties derived from combined retrotransposon, microsatellite and morphological marker analysis.

    Science.gov (United States)

    Smýkal, Petr; Hýbl, Miroslav; Corander, Jukka; Jarkovský, Jirí; Flavell, Andrew J; Griga, Miroslav

    2008-08-01

    One hundred and sixty-four accessions representing Czech and Slovak pea (Pisum sativum L.) varieties bred over the last 50 years were evaluated for genetic diversity using morphological, simple sequence repeat (SSR) and retrotransposon-based insertion polymorphism (RBIP) markers. Polymorphic information content (PIC) values of 10 SSR loci and 31 RBIP markers were on average high at 0.89 and 0.73, respectively. The silhouette method after the Ward clustering produced the most probable cluster estimate, identifying nine clusters from molecular data and five to seven clusters from morphological characters. Principal component analysis of nine qualitative and eight quantitative morphological parameters explain over 90 and 93% of total variability, respectively, in the first three axes. Multidimensional scaling of molecular data revealed a continuous structure for the set. To enable integration and evaluation of all data types, a Bayesian method for clustering was applied. Three clusters identified using morphology data, with clear separation of fodder, dry seed and afila types, were resolved by DNA data into 17, 12 and five sub-clusters, respectively. A core collection of 34 samples was derived from the complete collection by BAPS Bayesian analysis. Values for average gene diversity and allelic richness for molecular marker loci and diversity indexes of phenotypic data were found to be similar between the two collections, showing that this is a useful approach for representative core selection.

  2. Update History of This Database - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available L of The original website information 2014/10/10 PGDBj Registered plant list, Marker list, QTL list, Plant D...B link & Genome analysis methods English archive site is opened. 2012/08/08 PGDBj Regis...ate History of This Database - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ... ...switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods

  3. Surface composition of biomedical components by ion beam analysis

    International Nuclear Information System (INIS)

    Kenny, M.J.; Wielunski, L.S.; Baxter, G.R.

    1991-01-01

    Materials used for replacement body parts must satisfy a number of requirements such as biocompatibility and mechanical ability to handle the task with regard to strength, wear and durability. When using a CVD coated carbon fibre reinforced carbon ball, the surface must be ion implanted with uniform dose of nitrogen ions in order to make it wear resistant. The mechanism by which the wear resistance is improved is one of radiation damage and the required dose of about 10 16 cm -2 can have a tolerance of about 20%. To implant a spherical surface requires manipulation of the sample within the beam and control system (either computer or manually operated) to enable uniform dose all the way from polar to equatorial regions on the surface. A manipulator has been designed and built for this purpose. In order to establish whether the dose is uniform, nuclear reaction analysis using the reaction 14 N(d,α) 12 C is an ideal method of profiling. By taking measurements at a number of points on the surface, the uniformity of nitrogen dose can be ascertained. It is concluded that both Rutherford Backscattering and Nuclear Reaction Analysis can be used for rapid analysis of surface composition of carbon based materials used for replacement body components. 2 refs., 2 figs

  4. Joint surface reconstruction and 4D deformation estimation from sparse data and prior knowledge for marker-less Respiratory motion tracking.

    Science.gov (United States)

    Berkels, Benjamin; Bauer, Sebastian; Ettl, Svenja; Arold, Oliver; Hornegger, Joachim; Rumpf, Martin

    2013-09-01

    The intraprocedural tracking of respiratory motion has the potential to substantially improve image-guided diagnosis and interventions. The authors have developed a sparse-to-dense registration approach that is capable of recovering the patient's external 3D body surface and estimating a 4D (3D + time) surface motion field from sparse sampling data and patient-specific prior shape knowledge. The system utilizes an emerging marker-less and laser-based active triangulation (AT) sensor that delivers sparse but highly accurate 3D measurements in real-time. These sparse position measurements are registered with a dense reference surface extracted from planning data. Thereby a dense displacement field is recovered, which describes the spatio-temporal 4D deformation of the complete patient body surface, depending on the type and state of respiration. It yields both a reconstruction of the instantaneous patient shape and a high-dimensional respiratory surrogate for respiratory motion tracking. The method is validated on a 4D CT respiration phantom and evaluated on both real data from an AT prototype and synthetic data sampled from dense surface scans acquired with a structured-light scanner. In the experiments, the authors estimated surface motion fields with the proposed algorithm on 256 datasets from 16 subjects and in different respiration states, achieving a mean surface reconstruction accuracy of ± 0.23 mm with respect to ground truth data-down from a mean initial surface mismatch of 5.66 mm. The 95th percentile of the local residual mesh-to-mesh distance after registration did not exceed 1.17 mm for any subject. On average, the total runtime of our proof of concept CPU implementation is 2.3 s per frame, outperforming related work substantially. In external beam radiation therapy, the approach holds potential for patient monitoring during treatment using the reconstructed surface, and for motion-compensated dose delivery using the estimated 4D surface motion field in

  5. Development of SSR Markers Based on Transcriptome Sequencing and Association Analysis with Drought Tolerance in Perennial Grass Miscanthus from China

    Directory of Open Access Journals (Sweden)

    Gang Nie

    2017-05-01

    Full Text Available Drought has become a critical environmental stress affecting on plant in temperate area. As one of the promising bio-energy crops to sustainable biomass production, the genus Miscanthus has been widely studied around the world. However, the most widely used hybrid cultivar among this genus, Miscanthus × giganteus is proved poor drought tolerance compared to some parental species. Here we mainly focused on Miscanthus sinensis, which is one of the progenitors of M. × giganteus providing a comparable yield and well abiotic stress tolerance in some places. The main objectives were to characterize the physiological and photosynthetic respond to drought stress and to develop simple sequence repeats (SSRs markers associated with drought tolerance by transcriptome sequencing within an originally collection of 44 Miscanthus genotypes from southwest China. Significant phenotypic differences were observed among genotypes, and the average of leaf relative water content (RWC were severely affected by drought stress decreasing from 88.27 to 43.21%, which could well contribute to separating the drought resistant and drought sensitive genotype of Miscanthus. Furthermore, a total of 16,566 gene-associated SSRs markers were identified based on Illumina RNA sequencing under drought conditions, and 93 of them were randomly selected to validate. In total, 70 (75.3% SSRs were successfully amplified and the generated loci from 30 polymorphic SSRs were used to estimate the genetic differentiation and population structure. Finally, two optimum subgroups of the population were determined by structure analysis and based on association analysis, seven significant associations were identified including two markers with leaf RWC and five markers with photosynthetic traits. With the rich sequencing resources annotation, such associations would serve an efficient tool for Miscanthus drought response mechanism study and facilitate genetic improvement of drought resistant for

  6. Surface analysis of graphite fiber reinforced polyimide composites

    Science.gov (United States)

    Messick, D. L.; Progar, D. J.; Wightman, J. P.

    1983-01-01

    Several techniques have been used to establish the effect of different surface pretreatments on graphite-polyimide composites. Composites were prepared from Celion 6000 graphite fibers and the polyimide LARC-160. Pretreatments included mechanical abrasion, chemical etching and light irradiation. Scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS) were used in the analysis. Contact angle of five different liquids of varying surface tensions were measured on the composites. SEM results showed polymer-rich peaks and polymer-poor valleys conforming to the pattern of the release cloth used durng fabrication. Mechanically treated and light irradiated samples showed varying degrees of polymer peak removal, with some degradation down to the graphite fibers. Minimal changes in surface topography were observed on concentrations of surface fluorine even after pretreatment. The light irradiation pretreatment was most effective at reducing surface fluorine concentrations whereas chemical pretreatment was the least effective. Critical surface tensions correlated directly with the surface fluorine to carbon ratios as calculated from XPS.

  7. Genetic diversity analysis in the section Caulorrhizae (genus Arachis) using microsatellite markers.

    Science.gov (United States)

    Palmieri, Darío A; Bechara, Marcelo D; Curi, Rogério A; Monteiro, Jomar P; Valente, Sérgio E S; Gimenes, Marcos A; Lopes, Catalina R

    2010-01-01

    Diversity in 26 microsatellite loci from section Caulorrhizae germplasm was evaluated by using 33 accessions of A. pintoi Krapov. & W.C. Gregory and ten accessions of Arachis repens Handro. Twenty loci proved to be polymorphic and a total of 196 alleles were detected with an average of 9.8 alleles per locus. The variability found in those loci was greater than the variability found using morphological characters, seed storage proteins and RAPD markers previously used in this germplasm. The high potential of these markers to detect species-specific alleles and discriminate among accessions was demonstrated. The set of microsatellite primer pairs developed by our group for A. pintoi are useful molecular tools for evaluating Section Caulorrhizae germplasm, as well as that of species belonging to other Arachis sections.

  8. Genetic diversity analysis in the section Caulorrhizae (genus Arachis using microsatellite markers

    Directory of Open Access Journals (Sweden)

    Darío A. Palmieri

    2010-01-01

    Full Text Available Diversity in 26 microsatellite loci from section Caulorrhizae germplasm was evaluated by using 33 accessions of A. pintoi Krapov. & W.C. Gregory and ten accessions of Arachis repens Handro. Twenty loci proved to be polymorphic and a total of 196 alleles were detected with an average of 9.8 alleles per locus. The variability found in those loci was greater than the variability found using morphological characters, seed storage proteins and RAPD markers previously used in this germplasm. The high potential of these markers to detect species-specific alleles and discriminate among accessions was demonstrated. The set of microsatellite primer pairs developed by our group for A. pintoi are useful molecular tools for evaluating Section Caulorrhizae germplasm, as well as that of species belonging to other Arachis sections.

  9. Left Ventricular Hypertrophy: An allometric comparative analysis of different ECG markers

    Science.gov (United States)

    Bonomini, M. P.; Ingallina, F.; Barone, V.; Valentinuzzi, M. E.; Arini, P. D.

    2011-12-01

    Allometry, in general biology, measures the relative growth of a part in relation to the whole living organism. Left ventricular hypertrophy (LVH) is the heart adaptation to excessive load (systolic or diastolic). The increase in left ventricular mass leads to an increase in the electrocardiographic voltages. Based on clinical data, we compared the allometric behavior of three different ECG markers of LVH. To do this, the allometric fit AECG = δ + β (VM) relating left ventricular mass (estimated from ecocardiographic data) and ECG amplitudes (expressed as the Cornell-Voltage, Sokolow and the ECG overall voltage indexes) were compared. Besides, sensitivity and specifity for each index were analyzed. The more sensitive the ECG criteria, the better the allometric fit. In conclusion: The allometric paradigm should be regarded as the way to design new and more sensitive ECG-based LVH markers.

  10. Left Ventricular Hypertrophy: An allometric comparative analysis of different ECG markers

    International Nuclear Information System (INIS)

    Bonomini, MP; Valentinuzzi, M E; Arini, P D; Ingallina, F; Barone, V

    2011-01-01

    Allometry, in general biology, measures the relative growth of a part in relation to the whole living organism. Left ventricular hypertrophy (LVH) is the heart adaptation to excessive load (systolic or diastolic). The increase in left ventricular mass leads to an increase in the electrocardiographic voltages. Based on clinical data, we compared the allometric behavior of three different ECG markers of LVH. To do this, the allometric fit AECG δ + β (VM) relating left ventricular mass (estimated from ecocardiographic data) and ECG amplitudes (expressed as the Cornell-Voltage, Sokolow and the ECG overall voltage indexes) were compared. Besides, sensitivity and specificity for each index were analyzed. The more sensitive the ECG criteria, the better the allometric fit. In conclusion: The allometric paradigm should be regarded as the way to design new and more sensitive ECG-based LVH markers.

  11. Analysis of surface degradation of high density polyethylene (HDPE ...

    Indian Academy of Sciences (India)

    Unknown

    Analysis of surface degradation of high density polyethylene (HDPE) insulation ... ammonium chloride as the contaminant, in high density polyethylene ..... liquid in the material. When diffusion is driven by the concentration gradient and if there is no chemical change between liquid and material, this would result in mass.

  12. Synthesis, structure and Hirshfeld surface analysis, vibrational and ...

    Indian Academy of Sciences (India)

    Hirshfeld surface analysis for visually analysing intermolecular interactions in crystal structures employing molecular surfacecontours and 2D fingerprint plots has been used to scrutinize molecular shapes. The vibration properties of this structure were studied by IR spectroscopy and Raman scattering. Vibration spectra ...

  13. Indian Ocean surface winds from NCMRWF analysis as compared to ...

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    Indian Ocean surface winds from NCMRWF analysis as compared to QuikSCAT and moored buoy winds. B N Goswami1 and E N Rajagopal2. 1Centre for Atmospheric and Oceanic Sciences, Indian Institute of Science, Bangalore 560 012, India. 2National Centre for Medium Range Weather Forecasting, Department of ...

  14. Difraction analysis of iron materials after surface machining

    Czech Academy of Sciences Publication Activity Database

    Čerňanský, Marian; Ganev, N.; Barcal, J.; Drahokoupil, Jan; Kolařík, K.

    2006-01-01

    Roč. 2006, suppl. 23 (2006), s. 369-374 ISSN 0044-2968 Institutional research plan: CEZ:AV0Z10100520 Keywords : iron materials * surface treatment * size-strain * residual stress * phase analysis Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.897, year: 2006

  15. Boundary surface and microstructure analysis of ceramic materials

    International Nuclear Information System (INIS)

    Woltersdorf, J.; Pippel, E.

    1992-01-01

    The article introduces the many possibilities of high voltage (HVEM) and high resolution electron microscopy (HREM) for boundary surface and microstructure analysis of ceramic materials. The investigations are limited to ceramic long fibre composites and a ceramic fibre/glass matrix system. (DG) [de

  16. Hirschfeld surface analysis of two new phosporothioic triamides structures

    Czech Academy of Sciences Publication Activity Database

    Alamdar, A.H.; Pourayoubi, M.; Saneei, A.; Dušek, Michal; Kučeráková, Monika; Henriques, Margarida Isabel Sousa

    2015-01-01

    Roč. 71, č. 9 (2015), s. 824-833 ISSN 2053-2296 R&D Projects: GA ČR(CZ) GA14-03276S Institutional support: RVO:68378271 Keywords : phosphorothioic triamide * Hirshfeld surface analysis * two-dimensional fingerprint plot * crystal structure * hydrogen-bonding pattern. Subject RIV: CC - Organic Chemistry Impact factor: 0.479, year: 2015

  17. Surface analysis of DLC coating on cam-tappet system

    OpenAIRE

    FOUVRY, Siegfried; PAGNOUX, Geoffrey; PEIGNEY, Michael; DELATTRE, Benoit; MERMAT-ROLLET, Guillaume

    2013-01-01

    Tribomechanical properties of diamond-like carbon (DLC) coatings make them particularly interesting for numerous applications, like automotive ones. But although DLC coatings show a generally high wear resistance, they sometimes can exhibit severe multiple wear. In this study, a surface analysis of worn coated tappets is performed, leading to a complete coupled wear scenario.

  18. Surface water quality assessment using factor analysis | Boyacioglu ...

    African Journals Online (AJOL)

    In this study, the factor analysis technique is applied to surface water quality data sets obtained from the Buyuk Menderes River Basin, Turkey, during two different hydrological periods. Results show that the indices which changed the quality of water in two seasons and locations differed. During low-flow conditions, water ...

  19. Transcriptome Analysis of Orange Head Chinese Cabbage (Brassica rapa L. ssp. pekinensis and Molecular Marker Development

    Directory of Open Access Journals (Sweden)

    Jingjuan Li

    2017-01-01

    Full Text Available Due to the visual appearance and high carotenoid content, orange inner leaves are a desirable trait for the Chinese cabbage. To understand the molecular mechanism underlying the formation of orange inner leaves, the BrCRTISO (Bra031539 gene, as the Br-or candidate gene, was analyzed among the white and orange varieties, and 7 single nucleotide polymorphisms (SNPs were identified. However, only one SNP (C952 to T952 altered the amino acid sequence, resulting in a mutation from Leu318 to Phe318 in the orange varieties. Additionally, we analyzed differentially expressed genes (DEGs between the orange and white F2 individuals (14-401 × 14-490 and found four downregulated genes were involved in the carotenoid biosynthesis pathway, which may lead to the accumulation of prolycopene and other carotenoid pigments in the orange inner leaves. In addition, we developed a novel InDel marker in the first intron, which cosegregates with the phenotypes of orange color inner leaves. In conclusion, these findings enhance our understanding of the underlying mechanism of pigment accumulation in the inner leaves of the Chinese cabbage. Additionally, the SNP (C952 to T952 and the InDel marker will facilitate the marker-assisted selection during Chinese cabbage breeding.

  20. Doppler-based fetal heart rate analysis markers for the detection of early intrauterine growth restriction.

    Science.gov (United States)

    Stroux, Lisa; Redman, Christopher W; Georgieva, Antoniya; Payne, Stephen J; Clifford, Gari D

    2017-11-01

    One indicator for fetal risk of mortality is intrauterine growth restriction (IUGR). Whether markers reflecting the impact of growth restriction on the cardiovascular system, computed from a Doppler-derived heart rate signal, would be suitable for its detection antenatally was studied. We used a cardiotocography archive of 1163 IUGR cases and 1163 healthy controls, matched for gestation and gender. We assessed the discriminative power of short-term variability and long-term variability of the fetal heart rate, computed over episodes of high and low variation aiming to separate growth-restricted fetuses from controls. Metrics characterizing the sleep state distribution within a trace were also considered for inclusion into an IUGR detection model. Significant differences in the risk markers comparing growth-restricted with healthy fetuses were found. When used in a logistic regression classifier, their performance for identifying IUGR was considerably superior before 34 weeks of gestation. Long-term variability in active sleep was superior to short-term variability [area under the receiver operator curve (AUC) of 72% compared with 71%]. Most predictive was the number of minutes in high variation per hour (AUC of 75%). A multivariate IUGR prediction model improved the AUC to 76%. We suggest that heart rate variability markers together with surrogate information on sleep states can contribute to the detection of early-onset IUGR. © 2017 Nordic Federation of Societies of Obstetrics and Gynecology.

  1. Analysis of genetic diversity of Hyptis pectinata (L.) Poit. plants using ISSR markers.

    Science.gov (United States)

    Feitosa-Alcantara, R B; Silva, A V C; Blank, A F; Almeida, C S; Alvares-Carvalho, S V; Arrigoni-Blank, M F

    2017-08-17

    Hyptis pectinata, popularly known as 'sambacaitá' or 'canudinho', is a medicinal and aromatic species widely used in the Brazilian Northeast. In Sergipe, the excessive extraction of natural resources may reduce the genetic variability of native plants. Thus, molecular markers have frequently been applied to the characterization of genetic diversity as the basis for germplasm conservation and breeding programs. The objective of the present study was to evaluate the genetic diversity of H. pectinata plants collected in different municipalities of the State of Sergipe using ISSR molecular markers. Thirty-four primers were tested, nine of which were selected for providing reproducible and analyzable amplification products, resulting in 67 polymorphic bands. The expected heterozygosity ranged from 0.32 to 0.45, with a mean of 0.39. Polymorphism information content was of 0.49, which classifies the markers as moderately informative. A dendrogram was constructed using unweighted pair group method with arithmetic mean, forming three clusters: Cluster I (79 plants); Cluster II (4 plants); and Cluster III (2 plants). Jaccard's similarity coefficients ranged from 0.06 to 0.98. The plants SAM-117 and SAM-119 presented greater similarity. Conversely, SAM-107 and SAM-171 were the most genetically distant. In general, H. pectinata plants collected in the State of Sergipe presented low to moderate genetic diversity.

  2. The Analysis of the Discourse Markers in the Narratives Elicited from Persian-speaking Children

    Directory of Open Access Journals (Sweden)

    Iran Mehrabi Sari

    2013-05-01

    Full Text Available Discourse markers (DMs are linguistic elements that index different relations and coherence between units of talk. Most research on the development of these forms has focused on conversations rather than narratives. This article examines age and medium effects on use of various discourse markers in pre-school children. Fifteen normal Iranian monolingual children, male and female, participated in this study. They were divided into three age groups (4-5, 5-6, 6-7. Two tests, story production and story re-production (retelling, based on two different story books were used to elicit the children's narratives.  This study shows that the functions of DMs within the oral narrative context follow neither from their usual meanings nor from their usual discourse functions in other contexts. These markers just help to continue the narrative procedure. Narrative experts illustrate how DMs initiate and conclude narrative action, how they guide listeners to follow their interruption and sequence of narrative elements. The results showed no specific difference on the kind of DM being used regarding the age of the participants; furthermore, in terms of the number of utterances and also DMs, children overall behaved differently when they were asked to retell a story, comparing to the time when they were asked to produce a story.

  3. Cell surface marker profiling of human tracheal basal cells reveals distinct subpopulations, identifies MST1/MSP as a mitogenic signal, and identifies new biomarkers for lung squamous cell carcinomas.

    Science.gov (United States)

    Van de Laar, Emily; Clifford, Monica; Hasenoeder, Stefan; Kim, Bo Ram; Wang, Dennis; Lee, Sharon; Paterson, Josh; Vu, Nancy M; Waddell, Thomas K; Keshavjee, Shaf; Tsao, Ming-Sound; Ailles, Laurie; Moghal, Nadeem

    2014-12-31

    The large airways of the lungs (trachea and bronchi) are lined with a pseudostratified mucociliary epithelium, which is maintained by stem cells/progenitors within the basal cell compartment. Alterations in basal cell behavior can contribute to large airway diseases including squamous cell carcinomas (SQCCs). Basal cells have traditionally been thought of as a uniform population defined by basolateral position, cuboidal cell shape, and expression of pan-basal cell lineage markers like KRT5 and TP63. While some evidence suggests that basal cells are not all functionally equivalent, few heterogeneously expressed markers have been identified to purify and study subpopulations. In addition, few signaling pathways have been identified that regulate their cell behavior. The goals of this work were to investigate tracheal basal cell diversity and to identify new signaling pathways that regulate basal cell behavior. We used flow cytometry (FACS) to profile cell surface marker expression at a single cell level in primary human tracheal basal cell cultures that maintain stem cell/progenitor activity. FACS results were validated with tissue staining, in silico comparisons with normal basal cell and lung cancer datasets, and an in vitro proliferation assay. We identified 105 surface markers, with 47 markers identifying potential subpopulations. These subpopulations generally fell into more (~ > 13%) or less abundant (~ < 6%) groups. Microarray gene expression profiling supported the heterogeneous expression of these markers in the total population, and immunostaining of large airway tissue suggested that some of these markers are relevant in vivo. 24 markers were enriched in lung SQCCs relative to adenocarcinomas, with four markers having prognostic significance in SQCCs. We also identified 33 signaling receptors, including the MST1R/RON growth factor receptor, whose ligand MST1/MSP was mitogenic for basal cells. This work provides the largest description to date of

  4. Expressed sequence tag analysis of adult human optic nerve for NEIBank: Identification of cell type and tissue markers

    Directory of Open Access Journals (Sweden)

    Peterson Katherine

    2009-09-01

    Full Text Available Abstract Background The optic nerve is a pure white matter central nervous system (CNS tract with an isolated blood supply, and is widely used in physiological studies of white matter response to various insults. We examined the gene expression profile of human optic nerve (ON and, through the NEIBANK online resource, to provide a resource of sequenced verified cDNA clones. An un-normalized cDNA library was constructed from pooled human ON tissues and was used in expressed sequence tag (EST analysis. Location of an abundant oligodendrocyte marker was examined by immunofluorescence. Quantitative real time polymerase chain reaction (qRT-PCR and Western analysis were used to compare levels of expression for key calcium channel protein genes and protein product in primate and rodent ON. Results Our analyses revealed a profile similar in many respects to other white matter related tissues, but significantly different from previously available ON cDNA libraries. The previous libraries were found to include specific markers for other eye tissues, suggesting contamination. Immune/inflammatory markers were abundant in the new ON library. The oligodendrocyte marker QKI was abundant at the EST level. Immunofluorescence revealed that this protein is a useful oligodendrocyte cell-type marker in rodent and primate ONs. L-type calcium channel EST abundance was found to be particularly low. A qRT-PCR-based comparative mammalian species analysis reveals that L-type calcium channel expression levels are significantly lower in primate than in rodent ON, which may help account for the class-specific difference in responsiveness to calcium channel blocking agents. Several known eye disease genes are abundantly expressed in ON. Many genes associated with normal axonal function, mRNAs associated with axonal transport, inflammation and neuroprotection are observed. Conclusion We conclude that the new cDNA library is a faithful representation of human ON and EST data

  5. High-Throughput Analysis of Plasma Hybrid Markers for Early Detection of Cancers

    Directory of Open Access Journals (Sweden)

    Jung-hyun Rho

    2014-01-01

    Full Text Available Biomarkers for the early detection of cancer in the general population have to perform with high sensitivity and specificity in order to prevent the costs associated with over-diagnosis. There are only a few current tissue or blood markers that are recommended for generalized cancer screening. Despite the recognition that combinations of multiple biomarkers will likely improve their utility, biomarker panels are usually limited to a single class of molecules. Tissues and body fluids including plasma and serum contain not only proteins, DNA and microRNAs that are differentially expressed in cancers but further cancer specific information might be gleaned by comparing different classes of biomolecules. For example, the level of a certain microRNA might be related to the level of a particular protein in a cancer specific manner. Proteins might have cancer-specific post-translational modifications (e.g., phosphorylation or glycosylation or lead to the generation of autoantibodies. Most currently approved biomarkers are glycoproteins. Autoantibodies can be produced as a host’s early surveillance response to cancer-specific proteins in pre-symptomatic and pre-diagnostic stages of cancer. Thus, measurement of the level of a protein, the level of its glycosylation or phosphorylation and whether autoantibodies are produced to it can yield multi-dimensional information on each protein. We consider specific proteins that show consistent cancer-specific changes in two or three of these measurements to be “hybrid markers”. We hypothesize these markers will suffer less variation between different individuals since one component can act to “standardize” the other measurement. As a proof of principle, a 180 plasma sample set consisting of 120 cases (60 colon cancers and 60 adenomas and 60 controls were analyzed using our high-density antibody array for changes in their protein, IgG-complex and sialyl-Lewis A (SLeA modified proteins. At p < 0

  6. Corrected Debye-Hückel analysis of surface complexation. II. A theory of surface charging.

    Science.gov (United States)

    Gunnarsson, Magnus; Abbas, Zareen; Ahlberg, Elisabet; Gobom, Sylvia; Nordholm, Sture

    2002-05-01

    A theory of surface charging of colloidal particles suspended in an electrolyte solution is presented. The charging at the particle surface is assumed to originate from the adsorption and desorption of protons and is therefore strongly dependent on the acidity of the solution. The surface binding of protons occurs locally at sites of occupancy zero or one that are described by a binding energy u(0) and a three-dimensional vibration of frequency nu. The diffuse screening of ions at the surface is described by the corrected Debye-Hückel analysis assuming linear response. The model contains a capacitor layer close to the charged surface and the finite size of the electrolyte ions is taken into account. The theory has been applied to titrated surface charge data on goethite (alpha-FeOOH) at NaClO(4) background concentrations ranging from 0.01 to 1.0 M. The protonation mechanism used in the modeling of these data corresponds to the 1-pK approach. A very good description of the experimental data was obtained at the highest ionic strength. Close to the pH(pzc) the theory also gave a good description at lower ionic strengths. However, at low salt concentrations and pH values far away from the pH(pzc) the electrostatic potential outside the capacitor layer becomes so high that nonlinear electrostatic effects become important and the theory therefore underestimates the surface charge. These results were compared with model calculations obtained using existing surface complexation models.

  7. An analysis of endothelial microparticles as a function of cell surface antibodies and centrifugation techniques.

    Science.gov (United States)

    Venable, Adam S; Williams, Randall R; Haviland, David L; McFarlin, Brian K

    2014-04-01

    Chronic vascular disease is partially characterized by the presence of lesions along the vascular endothelial wall. Current FDA-approved clinical techniques lack the ability to measure very early changes in endothelial cell health. When endothelial cells are damaged, they release endothelial microparticles (EMPs) into circulation. Thus, blood EMP concentration may represent a useful cardiovascular disease biomarker. Despite the potential value of EMPs, current flow cytometry techniques may not consistently distinguish EMPs from other small cell particles. The purpose of this study was to use imaging flow cytometry to modify existing methods of identifying EMPs based on cell-surface receptor expression and visual morphology. Platelet poor plasma (PPP) was isolated using four different techniques, each utilizing a two-step serial centrifugation process. The cell-surface markers used in this study were selected based on those that are commonly reported in the literature. PPP (100μL) was labeled with CD31, CD42a, CD45, CD51, CD66b, and CD144 for 30-min in dark on ice. Based on replicated experiments, EMPs were best identified by cell-surface CD144 expression relative to other commonly reported EMP markers (CD31 & CD51). It is important to note that contaminating LMPs, GMPs, and PMPs were thought to be removed in the preparation of PPP. However, upon analysis of prepared samples staining CD31 against CD51 revealed a double-positive population that was less than 1% EMPs. In contrast, when using CD144 to identify EMPs, ~87% of observed particles were free of contaminating microparticles. Using a counterstain of CD42a, this purity can be improved to over 99%. More research is needed to understand how our improved EMP measurement method can be used in experimental models measuring acute vascular responses or chronic vascular diseases. Copyright © 2014 Elsevier B.V. All rights reserved.

  8. Assessing of organic content in surface sediments of Suez Gulf, Egypt depending on normal alkanes, terpanes and steranes biological markers indicators

    Directory of Open Access Journals (Sweden)

    Abedel Aziz Elfadly

    2017-12-01

    Full Text Available The Semi-enclosed Suez Gulf records various signals of high anthropic pressures from surrounding regions and the industrialized Suez countries. The sedimentary hydrocarbons have been studied in 6 coastal stations located in the Gulf of Suez. Non-aromatic hydrocarbons were analyzed by GC/FID and GC/MS to assess organic content in surface sediments of Suez Gulf, Egypt depending on alkanes, terpanes and steranes biological markers indicators. The results showed that the hydrocarbons are originated from multiple terrestrial inputs, biogenic, pyrolytic. Several ratios of hydrocarbons indicated the predominance of petrogenic in combination with biogenic hydrocarbons. Al-Attaqa harbor, Suez oil processing company, Al-Nasr Oil Company, AL-Kabanon and EL-Sukhna of Loloha Beach are the main sources of petroleum contamination.

  9. Cortisol, heart rate, and blood pressure as early markers of PTSD risk: A systematic review and meta-analysis.

    Science.gov (United States)

    Morris, Matthew C; Hellman, Natalie; Abelson, James L; Rao, Uma

    2016-11-01

    Individuals with posttraumatic stress disorder (PTSD) typically exhibit altered hypothalamic-pituitary-adrenal (HPA) function and sympathetic nervous system (SNS) activity. The goals of this study were to determine whether HPA and SNS alterations in the immediate aftermath of trauma predict subsequent PTSD symptom development and whether inconsistencies observed between studies can be explained by key demographic and methodological factors. This work informs secondary prevention of PTSD by identifying subgroups of trauma survivors at risk for PTSD. This meta-analysis (26 studies, N=5186 individuals) revealed that higher heart rate measured soon after trauma exposure was associated with higher PTSD symptoms subsequently (r=0.13). Neither cortisol (r=-0.07) nor blood pressure (diastolic: r=-0.01; systolic: r=0.02) were associated with PTSD symptoms which may be influenced by methodological limitations. Associations between risk markers (heart rate, cortisol, systolic blood pressure) and PTSD symptoms were in the positive direction for younger samples and negative direction for older samples. These findings extend developmental traumatology models of PTSD by revealing an age-related shift in the presentation of early risk markers. More work will be needed to identify risk markers and pathways to PTSD while addressing methodological limitations in order to shape and target preventive interventions. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. A Genome-Wide Association Study for Agronomic Traits in Soybean Using SNP Markers and SNP-Based Haplotype Analysis.

    Directory of Open Access Journals (Sweden)

    Rodrigo Iván Contreras-Soto

    Full Text Available Mapping quantitative trait loci through the use of linkage disequilibrium (LD in populations of unrelated individuals provides a valuable approach for dissecting the genetic basis of complex traits in soybean (Glycine max. The haplotype-based genome-wide association study (GWAS has now been proposed as a complementary approach to intensify benefits from LD, which enable to assess the genetic determinants of agronomic traits. In this study a GWAS was undertaken to identify genomic regions that control 100-seed weight (SW, plant height (PH and seed yield (SY in a soybean association mapping panel using single nucleotide polymorphism (SNP markers and haplotype information. The soybean cultivars (N = 169 were field-evaluated across four locations of southern Brazil. The genome-wide haplotype association analysis (941 haplotypes identified eleven, seventeen and fifty-nine SNP-based haplotypes significantly associated with SY, SW and PH, respectively. Although most marker-trait associations were environment and trait specific, stable haplotype associations were identified for SY and SW across environments (i.e., haplotypes Gm12_Hap12. The haplotype block 42 on Chr19 (Gm19_Hap42 was confirmed to be associated with PH in two environments. These findings enable us to refine the breeding strategy for tropical soybean, which confirm that haplotype-based GWAS can provide new insights on the genetic determinants that are not captured by the single-marker approach.

  11. Transferability of cucumber microsatellite markers used for phylogenetic analysis and population structure study in bottle gourd (Lagenaria siceraria (Mol.) Standl.).

    Science.gov (United States)

    Bhawna; Abdin, M Z; Arya, L; Verma, M

    2015-02-01

    Improved breeding for developing fruit quality in bottle gourd (Lagenaria siceraria (Mol.) Standl.) necessitates knowledge regarding its genetic diversity. To achieve this, a set of 108 locus-specific SSR markers has been developed in bottle gourd by cross-species transferability from 995 mapped Cucumis sativus SSR markers. During screening, 280 primer pairs amplified in the bottle gourd germplasm, which were further evaluated in a diverse set of 42 lines, resulting in 19 polymorphic, 89 monomorphic, 15 with multiple bands, and the rest 157 showed no or very non-specific amplification. The 19 polymorphic primer pairs produced a total of 54 alleles. Gene diversity, Shannon's information index, and Nei's coefficient of differentiation were calculated suggesting a moderate genetic variation at the species level. A model-based population structure analysis divided these germplasm into two subpopulations. This marker set will be applicable for evaluating the genetic structure for association mapping, DNA fingerprinting, and mounting linkage maps and will be a practical tool set for further genetics. This study provides one of the first quantitative views of population genetic variation in bottle gourd.

  12. SURFACE ELECTROMYOGRAPHY IN BIOMECHANICS: APPLICATIONS AND SIGNAL ANALYSIS ASPECTS

    Directory of Open Access Journals (Sweden)

    DEAK GRAłIELA-FLAVIA

    2009-12-01

    Full Text Available Surface electromyography (SEMG is a technique for detecting and recording the electrical activity of the muscles using surface electrodes. The EMG signal is used in biomechanics mainly as an indicator of the initiation of muscle activation, as an indicator of the force produced by a contracting muscle, and as an index ofthe fatigue occurring within a muscle. EMG, used as a method of investigation, can tell us if the muscle is active or not, if the muscle is more or less active, when it is on or off, how much active is it, and finally, if it fatigues.The purpose of this article is to discuss some specific EMG signal analysis aspects with emphasis on comparison type analysis and frequency fatigue analysis.

  13. Extending GelJ for interoperability: Filling the gap in the bioinformatics resources for population genetics analysis with dominant markers.

    Science.gov (United States)

    Domínguez, César; Heras, Jónathan; Mata, Eloy; Pascual, Vico; Vázquez-Garcidueñas, Maria Soledad; Vázquez-Marrufo, Gerardo

    2017-03-01

    The manual transformation of DNA fingerprints of dominant markers into the input of tools for population genetics analysis is a time-consuming and error-prone task; especially when the researcher deals with a large number of samples. In addition, when the researcher needs to use several tools for population genetics analysis, the situation worsens due to the incompatibility of data-formats across tools. The goal of this work consists in automating, from banding patterns of gel images, the input-generation for the great diversity of tools devoted to population genetics analysis. After a thorough analysis of tools for population genetics analysis with dominant markers, and tools for working with phylogenetic trees; we have detected the input requirements of those systems. In the case of programs devoted to phylogenetic trees, the Newick and Nexus formats are widely employed; whereas, each population genetics analysis tool uses its own specific format. In order to handle such a diversity of formats in the latter case, we have developed a new XML format, called PopXML, that takes into account the variety of information required by each population genetics analysis tool. Moreover, the acquired knowledge has been incorporated into the pipeline of the GelJ system - a tool for analysing DNA fingerprint gel images - to reach our automatisation goal. We have implemented, in the GelJ system, a pipeline that automatically generates, from gel banding patterns, the input of tools for population genetics analysis and phylogenetic trees. Such a pipeline has been employed to successfully generate, from thousands of banding patterns, the input of 29 population genetics analysis tools and 32 tools for managing phylogenetic trees. GelJ has become the first tool that fills the gap between gel image processing software and population genetics analysis with dominant markers, phylogenetic reconstruction, and tree editing software. This has been achieved by automating the process of

  14. De novo transcriptome assembly of Zanthoxylum bungeanum using Illumina sequencing for evolutionary analysis and simple sequence repeat marker development.

    Science.gov (United States)

    Feng, Shijing; Zhao, Lili; Liu, Zhenshan; Liu, Yulin; Yang, Tuxi; Wei, Anzhi

    2017-12-01

    Zanthoxylum, an ancient economic crop in Asia, has a satisfying aromatic taste and immense medicinal values. A lack of genomic information and genetic markers has limited the evolutionary analysis and genetic improvement of Zanthoxylum species and their close relatives. To better understand the evolution, domestication, and divergence of Zanthoxylum, we present a de novo transcriptome analysis of an elite cultivar of Z. bungeanum using Illumina sequencing; we then developed simple sequence repeat markers for identification of Zanthoxylum. In total, we predicted 45,057 unigenes and 22,212 protein coding sequences, approximately 90% of which showed significant similarities to known proteins in databases. Phylogenetic analysis indicated that Zanthoxylum is relatively recent and estimated to have diverged from Citrus ca. 36.5-37.7 million years ago. We also detected a whole-genome duplication event in Zanthoxylum that occurred 14 million years ago. We found no protein coding sequences that were significantly under positive selection by Ka/Ks. Simple sequence repeat analysis divided 31 Zanthoxylum cultivars and landraces into three major groups. This Zanthoxylum reference transcriptome provides crucial information for the evolutionary study of the Zanthoxylum genus and the Rutaceae family, and facilitates the establishment of more effective Zanthoxylum breeding programs.

  15. Cluster and principal component analysis based on SSR markers of Amomum tsao-ko in Jinping County of Yunnan Province

    Science.gov (United States)

    Ma, Mengli; Lei, En; Meng, Hengling; Wang, Tiantao; Xie, Linyan; Shen, Dong; Xianwang, Zhou; Lu, Bingyue

    2017-08-01

    Amomum tsao-ko is a commercial plant that used for various purposes in medicinal and food industries. For the present investigation, 44 germplasm samples were collected from Jinping County of Yunnan Province. Clusters analysis and 2-dimensional principal component analysis (PCA) was used to represent the genetic relations among Amomum tsao-ko by using simple sequence repeat (SSR) markers. Clustering analysis clearly distinguished the samples groups. Two major clusters were formed; first (Cluster I) consisted of 34 individuals, the second (Cluster II) consisted of 10 individuals, Cluster I as the main group contained multiple sub-clusters. PCA also showed 2 groups: PCA Group 1 included 29 individuals, PCA Group 2 included 12 individuals, consistent with the results of cluster analysis. The purpose of the present investigation was to provide information on genetic relationship of Amomum tsao-ko germplasm resources in main producing areas, also provide a theoretical basis for the protection and utilization of Amomum tsao-ko resources.

  16. A Probabilistic Analysis of Surface Water Flood Risk in London.

    Science.gov (United States)

    Jenkins, Katie; Hall, Jim; Glenis, Vassilis; Kilsby, Chris

    2017-10-30

    Flooding in urban areas during heavy rainfall, often characterized by short duration and high-intensity events, is known as "surface water flooding." Analyzing surface water flood risk is complex as it requires understanding of biophysical and human factors, such as the localized scale and nature of heavy precipitation events, characteristics of the urban area affected (including detailed topography and drainage networks), and the spatial distribution of economic and social vulnerability. Climate change is recognized as having the potential to enhance the intensity and frequency of heavy rainfall events. This study develops a methodology to link high spatial resolution probabilistic projections of hourly precipitation with detailed surface water flood depth maps and characterization of urban vulnerability to estimate surface water flood risk. It incorporates probabilistic information on the range of uncertainties in future precipitation in a changing climate. The method is applied to a case study of Greater London and highlights that both the frequency and spatial extent of surface water flood events are set to increase under future climate change. The expected annual damage from surface water flooding is estimated to be to be £171 million, £343 million, and £390 million/year under the baseline, 2030 high, and 2050 high climate change scenarios, respectively. © 2017 Society for Risk Analysis.

  17. Effect of aerobic and resistance training on inflammatory markers in heart failure patients: systematic review and meta-analysis.

    Science.gov (United States)

    Pearson, M J; Mungovan, S F; Smart, N A

    2018-02-02

    Elevated levels of pro-inflammatory markers are evident in patients with heart failure and are associated with disease severity and prognosis. Exercise training has been shown to reduce circulating levels of pro-inflammatory cytokines and other pro-inflammatory markers in healthy and clinical populations. The aim of the systematic review and meta-analysis was to investigate the effect of aerobic (AT) and resistance training (RT) interventions on circulating concentrations of inflammatory markers; tumour necrosis factor-alpha (TNF-α), interleukin 6 (IL-6), C-reactive protein (CRP), fibrinogen, soluble intercellular adhesion molecule (sICAM) and soluble vascular adhesion molecule (sVCAM) in heart failure patients. We conducted database searches (PubMed, EMBASE and Cochrane Trials Register to 30 June 2017) for exercise-based trials in heart failure, using the following search terms: exercise training, inflammation, tumour necrosis factor-alpha, interleukin 6, C-reactive protein, fibrinogen, soluble intercellular adhesions molecule-1, soluble vascular adhesion molecule-1. Twenty studies, representing 18 independent trials, were included in the review. Pooled data of six studies indicated a minimally favourable effect of exercise training on circulating TNF-α [SMD 0.42 (95% CI 0.15, 0.68), p = 0.002)]. However, together the pooled and descriptive analyses failed to provide strong evidence for a reduction in other pro-inflammatory markers. However, given the complexity of heart failure and the pathways involved in the immune and inflammatory process, large prospective trials considering aetiology, comorbidities and local skeletal muscle inflammation are required to elucidate on the anti-inflammatory effect of exercise in this population.

  18. Comparative genomic analysis reveals species-dependent complexities that explain difficulties with microsatellite marker development in molluscs.

    Science.gov (United States)

    McInerney, C E; Allcock, A L; Johnson, M P; Bailie, D A; Prodöhl, P A

    2011-01-01

    Reliable population DNA molecular markers are difficult to develop for molluscs, the reasons for which are largely unknown. Identical protocols for microsatellite marker development were implemented in three gastropods. Success rates were lower for Gibbula cineraria compared to Littorina littorea and L. saxatilis. Comparative genomic analysis of 47.2 kb of microsatellite containing sequences (MCS) revealed a high incidence of cryptic repetitive DNA in their flanking regions. The majority of these were novel, and could be grouped into DNA families based upon sequence similarities. Significant inter-specific variation in abundance of cryptic repetitive DNA and DNA families was observed. Repbase scans show that a large proportion of cryptic repetitive DNA was identified as transposable elements (TEs). We argue that a large number of TEs and their transpositional activity may be linked to differential rates of DNA multiplication and recombination. This is likely to be an important factor explaining inter-specific variation in genome stability and hence microsatellite marker development success rates. Gastropods also differed significantly in the type of TEs classes (autonomous vs non-autonomous) observed. We propose that dissimilar transpositional mechanisms differentiate the TE classes in terms of their propensity for transposition, fixation and/or silencing. Consequently, the phylogenetic conservation of non-autonomous TEs, such as CvA, suggests that dispersal of these elements may have behaved as microsatellite-inducing elements. Results seem to indicate that, compared to autonomous, non-autonomous TEs maybe have a more active role in genome rearrangement processes. The implications of the findings for genomic rearrangement, stability and marker development are discussed.

  19. Data Analysis Techniques for a Lunar Surface Navigation System Testbed

    Science.gov (United States)

    Chelmins, David; Sands, O. Scott; Swank, Aaron

    2011-01-01

    NASA is interested in finding new methods of surface navigation to allow astronauts to navigate on the lunar surface. In support of the Vision for Space Exploration, the NASA Glenn Research Center developed the Lunar Extra-Vehicular Activity Crewmember Location Determination System and performed testing at the Desert Research and Technology Studies event in 2009. A significant amount of sensor data was recorded during nine tests performed with six test subjects. This paper provides the procedure, formulas, and techniques for data analysis, as well as commentary on applications.

  20. Application of dissociation curve analysis to radiation hybrid panel marker scoring: generation of a map of river buffalo (B. bubalis chromosome 20

    Directory of Open Access Journals (Sweden)

    Schäffer Alejandro A

    2008-11-01

    Full Text Available Abstract Background Fluorescence of dyes bound to double-stranded PCR products has been utilized extensively in various real-time quantitative PCR applications, including post-amplification dissociation curve analysis, or differentiation of amplicon length or sequence composition. Despite the current era of whole-genome sequencing, mapping tools such as radiation hybrid DNA panels remain useful aids for sequence assembly, focused resequencing efforts, and for building physical maps of species that have not yet been sequenced. For placement of specific, individual genes or markers on a map, low-throughput methods remain commonplace. Typically, PCR amplification of DNA from each panel cell line is followed by gel electrophoresis and scoring of each clone for the presence or absence of PCR product. To improve sensitivity and efficiency of radiation hybrid panel analysis in comparison to gel-based methods, we adapted fluorescence-based real-time PCR and dissociation curve analysis for use as a novel scoring method. Results As proof of principle for this dissociation curve method, we generated new maps of river buffalo (Bubalus bubalis chromosome 20 by both dissociation curve analysis and conventional marker scoring. We also obtained sequence data to augment dissociation curve results. Few genes have been previously mapped to buffalo chromosome 20, and sequence detail is limited, so 65 markers were screened from the orthologous chromosome of domestic cattle. Thirty bovine markers (46% were suitable as cross-species markers for dissociation curve analysis in the buffalo radiation hybrid panel under a standard protocol, compared to 25 markers suitable for conventional typing. Computational analysis placed 27 markers on a chromosome map generated by the new method, while the gel-based approach produced only 20 mapped markers. Among 19 markers common to both maps, the marker order on the map was maintained perfectly. Conclusion Dissociation curve

  1. Analysis of leaf surfaces using scanning ion conductance microscopy.

    Science.gov (United States)

    Walker, Shaun C; Allen, Stephanie; Bell, Gordon; Roberts, Clive J

    2015-05-01

    Leaf surfaces are highly complex functional systems with well defined chemistry and structure dictating the barrier and transport properties of the leaf cuticle. It is a significant imaging challenge to analyse the very thin and often complex wax-like leaf cuticle morphology in their natural state. Scanning electron microscopy (SEM) and to a lesser extent Atomic force microscopy are techniques that have been used to study the leaf surface but their remains information that is difficult to obtain via these approaches. SEM is able to produce highly detailed and high-resolution images needed to study leaf structures at the submicron level. It typically operates in a vacuum or low pressure environment and as a consequence is generally unable to deal with the in situ analysis of dynamic surface events at submicron scales. Atomic force microscopy also possess the high-resolution imaging required and can follow dynamic events in ambient and liquid environments, but can over exaggerate small features and cannot image most leaf surfaces due to their inherent roughness at the micron scale. Scanning ion conductance microscopy (SICM), which operates in a liquid environment, provides a potential complementary analytical approach able to address these issues and which is yet to be explored for studying leaf surfaces. Here we illustrate the potential of SICM on various leaf surfaces and compare the data to SEM and atomic force microscopy images on the same samples. In achieving successful imaging we also show that SICM can be used to study the wetting of hydrophobic surfaces in situ. This has potentially wider implications than the study of leaves alone as surface wetting phenomena are important in a range of fundamental and applied studies. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

  2. Registered plant list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods Regis...tered plant list Data detail Data name Registered plant list DOI 10.18908/lsdba.nbdc01194-01-001 Descri...base Site Policy | Contact Us Registered plant list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ... ...switchLanguage; BLAST Search Image Search Home About Archive Update History Data

  3. License - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available f you use data from this database, please be sure attribute this database as follows: ... PGDBj Registered plan... Policy | Contact Us License - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ... ...switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods

  4. De novo transcriptome analysis and molecular marker development of two Hemarthria species

    Directory of Open Access Journals (Sweden)

    Xiu eHuang

    2016-04-01

    Full Text Available Hemarthria R. Br. is an important genus of perennial forage grasses that is widely used in subtropical and tropical regions. Hemarthria grasses have made remarkable contributions to the development of animal husbandry and agro-ecosystem maintenance; however, there is currently a lack of comprehensive genomic data available for these species. In this study, we used Illumina high-throughput deep sequencing to characterize of two agriculturally important Hemarthria materials, H. compressa ‘Yaan’ and H. altissima ‘1110.’ Sequencing runs that used each of four normalized RNA samples from the leaves or roots of the two materials yielded more than 24 million high-quality reads. After de novo assembly, 137,142 and 77,150 unigenes were obtained for ‘Yaan’ and ‘1110’, respectively. In addition, a total of 86,731 ‘Yaan’ and 48,645 ‘1110’ unigenes were successfully annotated. After consolidating the unigenes for both materials, 42,646 high-quality SNPs were identified in 10,880 unigenes and 10,888 SSRs were identified in 8,330 unigenes. To validate the identified markers, high quality PCR primers were designed for both SNPs and SSRs. We randomly tested 16 of the SNP primers and 54 of the SSR primers and found that the majority of these primers successfully amplified the desired PCR product. In addition, high cross-species transferability (61.11%-87.04% of SSR markers was achieved for four other Poaceae species. The amount of RNA sequencing data that was generated for these two Hemarthria species greatly increases the amount of genomic information available for Hemarthria and the SSR and SNP markers identified in this study will facilitate further advancements in genetic and molecular studies of the Hemarthria genus.

  5. Polymorphic microsatellite markers for population analysis of a tephritid pest species, Bactrocera tryoni.

    Science.gov (United States)

    Kinnear, M W; Bariana, H S; Sved, J A; Frommer, M

    1998-11-01

    To obtain a set of microsatellite markers for the Queensland fruit fly Bactrocera tryoni, a genomic library was screened with a number of simple repeat oligonucleotide probes. Sequencing recovered 22 repeat loci. The microsatellite sequences were short, with repeat numbers ranging from five to 11. Of these, 16 polymerase chain reaction (PCR) primer sets yielded amplifiable products, which were tested on 53 flies from five widely separated sites. All loci showed polymorphism in the population sample, with the number of alleles ranging from two to 16. Several dinucleotide repeats showed alleles separated by single-base differences and multiple steps, suggesting a mutation process more complex than the stepwise mutation model.

  6. Is voice a marker for autism spectrum disorder? A systematic review and meta-analysis

    DEFF Research Database (Denmark)

    Fusaroli, Riccardo; Lambrechts, Anna; Bang, Dan

    2017-01-01

    Individuals with Autism Spectrum Disorder (ASD) tend to show distinctive, atypical acoustic patterns of speech. These behaviours affect social interactions and social development and could represent a non-invasive marker for ASD. We systematically reviewed the literature quantifying acoustic......, with a sample size > 2, and the inclusion of a neurotypical comparison group and/or correlations between acoustic measures and severity of clinical features. We identified 34 articles, including 30 univariate studies and 15 multivariate machine-learning studies. We performed meta-analyses of the univariate...

  7. A description of the BNL active surface analysis facility

    International Nuclear Information System (INIS)

    Tyler, J.W.

    1989-11-01

    Berkeley Nuclear Laboratories has a responsibility for the assessment of radioactive specimens arising both from post irradiation examination of power reactor components and structures and experimental programmes concerned with fission and activation product transport. Existing analytical facilities have been extended with the commissioning of an active surface analysis instrument (XSAM 800pci, Kratos Analytical). Surface analysis involves the characterisation of the outer few atomic layers of a solid surface/interface whose chemical composition and electronic structure will probably be different from the bulk. The new instrument consists three interconnected chambers positioned in series; comprising of a high vacuum sample introduction chamber, an ultra-high vacuum sample treatment/fracture chamber and an ultra-high vacuum sample analysis chamber. The sample analysis chamber contains the electron, X-ray and ion-guns and the electron and ion detectors necessary for performing X-ray photoelectron spectroscopy, scanning Auger microscopy and secondary-ion mass spectroscopy. The chamber also contains a high stability manipulator to enable sub-micron imaging of specimens to be achieved and provide sample heating and cooling between - 180 and 600 0 C. (author)

  8. Examination of X chromosome markers in Rett syndrome: Exclusion mapping with a novel variation on multilocus linkage analysis

    Energy Technology Data Exchange (ETDEWEB)

    Ellison, K.A.; Fill, C.P. (Baylor College of Medicine, Houston, TX (United States)); Terwililger, J.; Percy, A.K.; Zobhbi, H. (Columbia University, NY (United States)); DeGennaro, L.J.; Ott, J. (University of Massachusetts Medical School, Worcester (United States)); Anvret, M.; Martin-Gallardo, A. (National Institutes of Health, Bethesda, MD (United States))

    1992-02-01

    Rett syndrome is a neurologic disorder characterized by early normal development followed by regression, acquired deceleration of head growth, autism, ataxia, and sterotypic hand movements. The exclusive occurrence of the syndrome in females and the occurrence of a few familial cases with inheritance through maternal lines suggest that this disorder is most likely secondary to a mutation on the X chromosome. To address this hypothesis and to identify candidate regions for the Rett syndrome gene locus, genotypic analysis was performed in two families with maternally related affected half-sisters by using 63 DNA markers from the X chromosome. Nineteen of the loci studied were chosen for multipoint linkage analysis because they have been previously genetically mapped using a large number of meioses from reference families. Using the exclusion criterion of a lod score less than [minus]2, the authors were able to exclude the region between the Duchenne muscular dystrophy locus and the DXS456 locus. This region extends from Xp21.2 to Xq21-q23. The use of the multipoint linkage analysis approach outlined in this study should allow the exclusion of additional regions of the X chromosome as new markers are analyzed.

  9. Detection of molecular markers by comparative sequence analysis of enzymes from mycobacteria species

    International Nuclear Information System (INIS)

    Asad, S.; Hussain, M.; Siddiqua, A.; Ain, Q.U.

    2014-01-01

    Mycobacterial species are one of the most important pathogens and among these members of non-tuberculous mycobacteria (NTM) and mycobacterial tuberculousis complex (MTC) are the causative agent of a relatively milder form of Tuberculosis. Traditional methods for identification of these groups of pathogens are time consuming, lack specificity and sensitivity and furthermore lead to the misidentification due to high similarity index. Therefore, more rapid, specific and cost-effective methods are required for the accurate identification of Mycobacterium species in routine diagnostics. In our study, we identified molecular markers in order to differentiate closely related cousin species of genus Mycobacterium including M. bovis, M. avium, M. leprae and M. tuberculosis. The nucleotide sequences of selected unique markers, i.e., enzymes (used previously in various biochemical tests for the identification of M. species) were selected and their ORFs were retrieved and selected functional proteins of respective biosynthetic pathways were compared in-silico. Result suggested that the variations in nucleotide sequences of the selected enzymes can be directly used for M. species discrimination in one step PCR test. We believe that the in-silico identification and storage of these distinctive characteristics of individual M. species will help in more precise recognition of pathogenic strains and hence specie specific targeted therapy. (author)

  10. DNA fingerprinting and diversity analysis in Aus genotypes using microsatellite markers

    Directory of Open Access Journals (Sweden)

    MD. MONIRUL ISLAM

    2015-08-01

    Full Text Available DNA fingerprinting and genetic diversity of 94 Aus (6 BRRI released Aus variety and 88 local Aus landraces genotypes were carried out to protect the Aus landraces from biopiracy. A total of 91 microsatellite markers were tested for screening the genotypes. Among 91 amplified products, 56% have polymorphic bands giving 195 alleles. The number of alleles per locus ranged from four (RM25 and RM147 to twenty seven (RM519, where average allele number was 9.76. The Polymorphism Information Contents (PIC lied between 0.455 (RM5 to 0.934 (RM519. Most robust marker was found RM519 since it provided the highest PIC value (0.934. Pair-wise genetic dissimilarity co-efficient showed the lowest genetic dissimilarity was found BRRI dhan42 and BRRI dhan43 and the highest genetic dissimilarity was found local landraces each other. Here it is shown that most Aus landraces is recognized to have broad genetic base. Thus it is recommended to use these landraces for future breeding program or include new and untouched local landraces to incorporate new genes and broaden genetic base.

  11. Genetic diversity analysis of chewing sugarcane (Saccharum officinarum L. varieties by using RAPD markers

    Directory of Open Access Journals (Sweden)

    S. M. Sarid Ullah

    2013-01-01

    Full Text Available In the present study an efficient and easy method was followed for the isolation of DNA from meristem cylinder in five chewing sugarcane varieties, namely Amrita, Bomaby, Babulal (Co.527, Q83 and Misrimala. The quality and quantity of DNA were assured by visual estimation using agarose gel electrophoresis and UV spectrophotometry. The highest amount of DNA was retrieved from the Amrita (3250 ng/ml and the lowest amount was attained from the variety Q83 (1450 ng/ml. The amount of recovered DNA was enough for PCR amplification and marker studies such as random amplified polymorphic DNA (RAPD. Using RAPD markers, bands obtained from fingerprinting (190 bp to 1200 bp showed 73.5% polymorphism. The dendrogram, based on linkage distance using unweighted pair group method of arithmetic means (UPGMA, indicated segregation of the five chewing varieties of sugarcane into two main clusters. Amrita, Bombay and Misrimala were grouped in cluster 1 (C1 followed by sub-clusters. Babulal and Q83 were grouped in cluster 2 (C2. The results of the present investigation also revealed that the twenty RAPD primers were able to identify and classify the chewing sugarcane varieties based on their genetic relationship.

  12. Microsatellite marker analysis of peach-potato aphids (Myzus persicae, Homoptera: Aphididae) from Scottish suction traps.

    Science.gov (United States)

    Malloch, G; Highet, F; Kasprowicz, L; Pickup, J; Neilson, R; Fenton, B

    2006-12-01

    The peach-potato aphid Myzus persicae (Sulzer) is an important vector of plant viruses. A network of suction traps collects aerial samples of this aphid in order to monitor and help predict its spatial distribution and likely impact on virus transmission in crops. A suction trap catch is thought to be a good representation of the total aphid pool. Sensitive molecular markers have been developed that determine the genetic composition of the M. persicae population. In Scotland, UK, these were applied to field collections revealing a limited number of clones. Molecular markers are less successful when applied to specimens that have been preserved in an ethanol-based trap fluid designed to preserve morphology. An assessment of different DNA extraction and PCR techniques is presented and the most efficient are used to analyse M. persicae specimens caught in the Dundee suction trap in 2001, a year when exceptionally high numbers were caught. The results reveal that the majority of the M. persicae caught belonged to two highly insecticide resistant clones. In addition, it was possible to compare the relative frequencies of genotypes caught in the trap with those collected at insecticide treated and untreated field sites in the vicinity. These results indicate that, in addition to suction trap data, the ability to sample field sites provides valuable early warning data which have implications for pest control and virus management strategies.

  13. A specific indel marker for the Philippines Schistosoma japonicum revealed by analysis of mitochondrial genome sequences.

    Science.gov (United States)

    Li, Juan; Chen, Fen; Sugiyama, Hiromu; Blair, David; Lin, Rui-Qing; Zhu, Xing-Quan

    2015-07-01

    In the present study, near-complete mitochondrial (mt) genome sequences for Schistosoma japonicum from different regions in the Philippines and Japan were amplified and sequenced. Comparisons among S. japonicum from the Philippines, Japan, and China revealed a geographically based length difference in mt genomes, but the mt genomic organization and gene arrangement were the same. Sequence differences among samples from the Philippines and all samples from the three endemic areas were 0.57-2.12 and 0.76-3.85 %, respectively. The most variable part of the mt genome was the non-coding region. In the coding portion of the genome, protein-coding genes varied more than rRNA genes and tRNAs. The near-complete mt genome sequences for Philippine specimens were identical in length (14,091 bp) which was 4 bp longer than those of S. japonicum samples from Japan and China. This indel provides a unique genetic marker for S. japonicum samples from the Philippines. Phylogenetic analyses based on the concatenated amino acids of 12 protein-coding genes showed that samples of S. japonicum clustered according to their geographical origins. The identified mitochondrial indel marker will be useful for tracing the source of S. japonicum infection in humans and animals in Southeast Asia.

  14. Bladder Carcinoma Data with Clinical Risk Factors and Molecular Markers: A Cluster Analysis

    Directory of Open Access Journals (Sweden)

    Enrique Redondo-Gonzalez

    2015-01-01

    Full Text Available Bladder cancer occurs in the epithelial lining of the urinary bladder and is amongst the most common types of cancer in humans, killing thousands of people a year. This paper is based on the hypothesis that the use of clinical and histopathological data together with information about the concentration of various molecular markers in patients is useful for the prediction of outcomes and the design of treatments of nonmuscle invasive bladder carcinoma (NMIBC. A population of 45 patients with a new diagnosis of NMIBC was selected. Patients with benign prostatic hyperplasia (BPH, muscle invasive bladder carcinoma (MIBC, carcinoma in situ (CIS, and NMIBC recurrent tumors were not included due to their different clinical behavior. Clinical history was obtained by means of anamnesis and physical examination, and preoperative imaging and urine cytology were carried out for all patients. Then, patients underwent conventional transurethral resection (TURBT and some proteomic analyses quantified the biomarkers (p53, neu, and EGFR. A postoperative follow-up was performed to detect relapse and progression. Clusterings were performed to find groups with clinical, molecular markers, histopathological prognostic factors, and statistics about recurrence, progression, and overall survival of patients with NMIBC. Four groups were found according to tumor sizes, risk of relapse or progression, and biological behavior. Outlier patients were also detected and categorized according to their clinical characters and biological behavior.

  15. Genetic Diversity Analysis of Tagetes Species Using PCR Based Molecular Markers

    International Nuclear Information System (INIS)

    Shahzadi, I.; Ahmad, R.; Waheed, U.; Shah, M. F.

    2016-01-01

    Tagetes is a genus of medicinally important wild and cultivated plants containing several chemical compounds. Lack of information on variation at molecular level present in Tagetes species is paramount to understand the genetic basis of medicinally important compounds. Current study aims at finding genetic variability in Tagetes species using random and specific molecular markers. Two primer systems including 25 RAPD and 3 STS (limonene gene) were used to ascertain genetic diversity of 15 Tagetes genotypes belonging to different species. We found that 20 of the 25 tested RAPD primers generated stable band patterns with 167 loci of amplification products. The proportion of polymorphic bands was 95.21 percent for RAPD primers. Three STS primers generated a total of 29 amplification products, of which 96.55 percent were polymorphic. Homology of genotypes was 53.18 percent and 51.11 percent with RAPD and STS primers respectively. The dendrogram obtained revealed that the range of overall genetic distances estimated was 22 percent to 100 percent through RAPD and 9 percent to 100 percent through STS markers. The findings help to establish that PCR-based assay such as RAPD and STS could be used successfully for estimation of genetic diversity of different genotypes of Tagetes that can be used for selection of parents for improvement of the species. (author)

  16. Multiphase chemical kinetics of OH radical uptake by molecular organic markers of biomass burning aerosols: humidity and temperature dependence, surface reaction, and bulk diffusion.

    Science.gov (United States)

    Arangio, Andrea M; Slade, Jonathan H; Berkemeier, Thomas; Pöschl, Ulrich; Knopf, Daniel A; Shiraiwa, Manabu

    2015-05-14

    Multiphase reactions of OH radicals are among the most important pathways of chemical aging of organic aerosols in the atmosphere. Reactive uptake of OH by organic compounds has been observed in a number of studies, but the kinetics of mass transport and chemical reaction are still not fully understood. Here we apply the kinetic multilayer model of gas-particle interactions (KM-GAP) to experimental data from OH exposure studies of levoglucosan and abietic acid, which serve as surrogates and molecular markers of biomass burning aerosol (BBA). The model accounts for gas-phase diffusion within a cylindrical coated-wall flow tube, reversible adsorption of OH, surface-bulk exchange, bulk diffusion, and chemical reactions at the surface and in the bulk of the condensed phase. The nonlinear dependence of OH uptake coefficients on reactant concentrations and time can be reproduced by KM-GAP. We find that the bulk diffusion coefficient of the organic molecules is approximately 10(-16) cm(2) s(-1), reflecting an amorphous semisolid state of the organic substrates. The OH uptake is governed by reaction at or near the surface and can be kinetically limited by surface-bulk exchange or bulk diffusion of the organic reactants. Estimates of the chemical half-life of levoglucosan in 200 nm particles in a biomass burning plume increase from 1 day at high relative humidity to 1 week under dry conditions. In BBA particles transported to the free troposphere, the chemical half-life of levoglucosan can exceed 1 month due to slow bulk diffusion in a glassy matrix at low temperature.

  17. Two Domains of Vimentin Are Expressed on the Surface of Lymph Node, Bone and Brain Metastatic Prostate Cancer Lines along with the Putative Stem Cell Marker Proteins CD44 and CD133

    Energy Technology Data Exchange (ETDEWEB)

    Steinmetz, Nicole F. [Case Western Reserve University, Department of Biomedical Engineering, 10900 Euclid Ave, Cleveland, OH 44106 (United States); Maurer, Jochen [Sanford-Burnham, Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037 (United States); Sheng, Huiming [Torrey Pines Institute for Molecular Studies, Division of Immune Regulation, 3550 General Atomics Court, San Diego, CA 92121 (United States); Bensussan, Armand [INSERM U976, Hôpital Saint Louis, F-75475 Paris (France); Department of Immunology, Dermatology and Oncology, Univ Paris Diderot, Sorbonne Paris Cité, UMRS976 F-75475 Paris (France); Maricic, Igor; Kumar, Vipin [Torrey Pines Institute for Molecular Studies, Laboratory of Autoimmunity, 3550 General Atomics Court, San Diego, CA 92121 (United States); Braciak, Todd A., E-mail: tbraciak@tpims.org [Torrey Pines Institute for Molecular Studies, Division of Immune Regulation, 3550 General Atomics Court, San Diego, CA 92121 (United States)

    2011-07-13

    Vimentin was originally identified as an intermediate filament protein present only as an intracellular component in many cell types. However, this protein has now been detected on the surface of a number of different cancer cell types in a punctate distribution pattern. Increased vimentin expression has been indicated as an important step in epithelial-mesenchymal transition (EMT) required for the metastasis of prostate cancer. Here, using two vimentin-specific monoclonal antibodies (SC5 and V9 directed against the coil one rod domain and the C-terminus of the vimentin protein, respectively), we examined whether either of these domains would be displayed on the surface of three commonly studied prostate cancer cell lines isolated from different sites of metastases. Confocal analysis of LNCaP, PC3 and DU145 prostate cancer cell lines (derived from lymph node, bone or brain prostate metastases, respectively) demonstrated that both domains of vimentin are present on the surface of these metastatic cancer cell types. In addition, flow cytometric analysis revealed that vimentin expression was readily detected along with CD44 expression but only a small subpopulation of prostate cancer cells expressed vimentin and the putative stem cell marker CD133 along with CD44. Finally, Cowpea mosaic virus (CPMV) nanoparticles that target vimentin could bind and internalize into tested prostate cancer cell lines. These results demonstrate that at least two domains of vimentin are present on the surface of metastatic prostate cancer cells and suggest that vimentin could provide a useful target for nanoparticle- or antibody- cancer therapeutic agents directed against highly invasive cancer and/or stem cells.

  18. Identification of Potential Transcriptomic Markers in Developing Ankylosing Spondylitis: A Meta-Analysis of Gene Expression Profiles

    Science.gov (United States)

    Fang, Fang; Pan, Jian; Xu, Lixiao; Li, Gang; Wang, Jian

    2015-01-01

    The goal of this study was to identify potential transcriptomic markers in developing ankylosing spondylitis by a meta-analysis of multiple public microarray datasets. Using the INMEX (integrative meta-analysis of expression data) program, we performed the meta-analysis to identify consistently differentially expressed (DE) genes in ankylosing spondylitis and further performed functional interpretation (gene ontology analysis and pathway analysis) of the DE genes identified in the meta-analysis. Three microarray datasets (26 cases and 29 controls in total) were collected for meta-analysis. 905 consistently DE genes were identified in ankylosing spondylitis, among which 482 genes were upregulated and 423 genes were downregulated. The upregulated gene with the smallest combined rank product (RP) was GNG11 (combined RP = 299.64). The downregulated gene with the smallest combined RP was S100P (combined RP = 335.94). In the gene ontology (GO) analysis, the most significantly enriched GO term was “immune system process” (P = 3.46 × 10−26). The most significant pathway identified in the pathway analysis was antigen processing and presentation (P = 8.40 × 10−5). The consistently DE genes in ankylosing spondylitis and biological pathways associated with those DE genes identified provide valuable information for studying the pathophysiology of ankylosing spondylitis. PMID:25688367

  19. Identification of Potential Transcriptomic Markers in Developing Ankylosing Spondylitis: A Meta-Analysis of Gene Expression Profiles

    Directory of Open Access Journals (Sweden)

    Fang Fang

    2015-01-01

    Full Text Available The goal of this study was to identify potential transcriptomic markers in developing ankylosing spondylitis by a meta-analysis of multiple public microarray datasets. Using the INMEX (integrative meta-analysis of expression data program, we performed the meta-analysis to identify consistently differentially expressed (DE genes in ankylosing spondylitis and further performed functional interpretation (gene ontology analysis and pathway analysis of the DE genes identified in the meta-analysis. Three microarray datasets (26 cases and 29 controls in total were collected for meta-analysis. 905 consistently DE genes were identified in ankylosing spondylitis, among which 482 genes were upregulated and 423 genes were downregulated. The upregulated gene with the smallest combined rank product (RP was GNG11 (combined RP=299.64. The downregulated gene with the smallest combined RP was S100P (combined RP=335.94. In the gene ontology (GO analysis, the most significantly enriched GO term was “immune system process” (P=3.46×10-26. The most significant pathway identified in the pathway analysis was antigen processing and presentation (P=8.40×10-5. The consistently DE genes in ankylosing spondylitis and biological pathways associated with those DE genes identified provide valuable information for studying the pathophysiology of ankylosing spondylitis.

  20. Identification of potential transcriptomic markers in developing ankylosing spondylitis: a meta-analysis of gene expression profiles.

    Science.gov (United States)

    Fang, Fang; Pan, Jian; Xu, Lixiao; Li, Gang; Wang, Jian

    2015-01-01

    The goal of this study was to identify potential transcriptomic markers in developing ankylosing spondylitis by a meta-analysis of multiple public microarray datasets. Using the INMEX (integrative meta-analysis of expression data) program, we performed the meta-analysis to identify consistently differentially expressed (DE) genes in ankylosing spondylitis and further performed functional interpretation (gene ontology analysis and pathway analysis) of the DE genes identified in the meta-analysis. Three microarray datasets (26 cases and 29 controls in total) were collected for meta-analysis. 905 consistently DE genes were identified in ankylosing spondylitis, among which 482 genes were upregulated and 423 genes were downregulated. The upregulated gene with the smallest combined rank product (RP) was GNG11 (combined RP=299.64). The downregulated gene with the smallest combined RP was S100P (combined RP=335.94). In the gene ontology (GO) analysis, the most significantly enriched GO term was "immune system process" (P=3.46×10(-26)). The most significant pathway identified in the pathway analysis was antigen processing and presentation (P=8.40×10(-5)). The consistently DE genes in ankylosing spondylitis and biological pathways associated with those DE genes identified provide valuable information for studying the pathophysiology of ankylosing spondylitis.

  1. Analysis of surface hardness of artificially aged resin composites

    Directory of Open Access Journals (Sweden)

    Denise Cremonezzi Tornavoi

    2012-02-01

    Full Text Available This study evaluated the effect of artificially accelerated aging (AAA on the surface hardness of eight composite resins: Filtek Z250, Filtek Supreme, 4 Seasons, Herculite, P60, Tetric Ceram, Charisma, and Filtek Z100. Sixteen specimens were made from the test piece of each material, using an 8.0 × 2.0 mm teflon matrix. After 24 hours, eight specimens from each material were submitted to three surface hardness readings using a Shimadzu Microhardness Tester for 5 seconds at a load of 50 gf. The other eight specimens remained in the artificially accelerated aging machine for 382 hours and were submitted to the same surface hardness analysis. The means of each test specimen were submitted to the Kolmogorov-Smirnov test (p > 0.05, ANOVA and Tukey test (p < 0.05. With regard to hardness (F = 86.74, p < 0.0001 the analysis showed significant differences among the resin composite brands. But aging did not influence the hardness of any of the resin composites (F = 0.39, p = 0.53. In this study, there was interaction between the resin composite brand and the aging factors (F = 4.51, p < 0.0002. It was concluded that notwithstanding the type of resin, AAA did not influence surface hardness. However, with regard to hardness there was a significant difference among the resin brands.

  2. Satellite Based Analysis of Surface Urban Heat Island Intensity

    Directory of Open Access Journals (Sweden)

    Gémes Orsolya

    2016-06-01

    Full Text Available The most obvious characteristics of urban climate are higher air and surface temperatures compared to rural areas and large spatial variation of meteorological parameters within the city. This research examines the long term and seasonal development of urban surface temperature using satellite data during a period of 30 years and within a year. The medium resolution Landsat data were (preprocessed using open source tools. Besides the analysis of the long term and seasonal changes in land surface temperature within a city, also its relationship with changes in the vegetation cover was investigated. Different urban districts and local climate zones showed varying strength of correlation. The temperature difference between urban surfaces and surroundings is defined as surface urban heat island (SUHI. Its development shows remarkable seasonal and spatial anomalies. The satellite images can be applied to visualize and analyze the SUHI, although they were not collected at midday and early afternoon, when the phenomenon is normally at its maximum. The applied methodology is based on free data and software and requires minimal user interaction. Using the results new urban developments (new built up and green areas can be planned, that help mitigate the negative effects of urban climate.

  3. In Vitro Analysis of Fibronectin-Modified Titanium Surfaces

    Science.gov (United States)

    Chang, Yu-Chi; Lee, Wei-Fang; Feng, Sheng-Wei; Huang, Haw-Ming; Lin, Che-Tong; Teng, Nai-Chia; Chang, Wei Jen

    2016-01-01

    Background Glow discharge plasma (GDP) procedure is an effective method for grafting various proteins, including albumin, type I collagen, and fibronectin, onto a titanium surface. However, the behavior and impact of titanium (Ti) surface modification is yet to be unraveled. Purpose The purpose of this study is to evaluate and analyze the biological properties of fibronectin-grafted Ti surfaces treated by GDP. Materials and Methods Grade II Ti discs were initially cleaned and autoclaved to obtain original specimens. Subsequently, the specimens were GDP treated and grafted with fibronectin to form Ar-GDP (Argon GDP treatment only) and GDP-fib (fibronectin coating following GDP treatment) groups. Blood coagulation test and MG-63 cell culture were performed to evaluate the biological effects on the specimen. Results There was no significant difference between Ar-GDP and GDP-fib groups in blood compatibility analysis. While in the MTT test, cellular proliferation was benefited from the presence of fibronectin coating. The numbers of cells on Ar-GDP and GDP-fib specimens were greater than those in the original specimens after 24 h of culturing. Conclusions GDP treatment combined with fibronectin grafting favored MG-63 cell adhesion, migration, and proliferation on titanium surfaces, which could be attributed to the improved surface properties. PMID:26731536

  4. Transcriptome analysis of Houttuynia cordata Thunb. by Illumina paired-end RNA sequencing and SSR marker discovery.

    Directory of Open Access Journals (Sweden)

    Lin Wei

    Full Text Available BACKGROUND: Houttuynia cordata Thunb. is an important traditional medical herb in China and other Asian countries, with high medicinal and economic value. However, a lack of available genomic information has become a limitation for research on this species. Thus, we carried out high-throughput transcriptomic sequencing of H. cordata to generate an enormous transcriptome sequence dataset for gene discovery and molecular marker development. PRINCIPAL FINDINGS: Illumina paired-end sequencing technology produced over 56 million sequencing reads from H. cordata mRNA. Subsequent de novo assembly yielded 63,954 unigenes, 39,982 (62.52% and 26,122 (40.84% of which had significant similarity to proteins in the NCBI nonredundant protein and Swiss-Prot databases (E-value <10(-5, respectively. Of these annotated unigenes, 30,131 and 15,363 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. In addition, 24,434 (38.21% unigenes were mapped onto 128 pathways using the KEGG pathway database and 17,964 (44.93% unigenes showed homology to Vitis vinifera (Vitaceae genes in BLASTx analysis. Furthermore, 4,800 cDNA SSRs were identified as potential molecular markers. Fifty primer pairs were randomly selected to detect polymorphism among 30 samples of H. cordata; 43 (86% produced fragments of expected size, suggesting that the unigenes were suitable for specific primer design and of high quality, and the SSR marker could be widely used in marker-assisted selection and molecular breeding of H. cordata in the future. CONCLUSIONS: This is the first application of Illumina paired-end sequencing technology to investigate the whole transcriptome of H. cordata and to assemble RNA-seq reads without a reference genome. These data should help researchers investigating the evolution and biological processes of this species. The SSR markers developed can be used for construction of high-resolution genetic linkage maps and for

  5. Glycomic and glycoproteomic analysis of serum from patients with stomach cancer reveals potential markers arising from host defense response mechanisms.

    Science.gov (United States)

    Bones, Jonathan; Byrne, Jennifer C; O'Donoghue, Niaobh; McManus, Ciara; Scaife, Caitriona; Boissin, Herve; Nastase, Anca; Rudd, Pauline M

    2011-03-04

    Despite the reduced incidence of gastric cancer in the developed world, a diagnosis of stomach carcinoma still carries a poor prognosis due to the asymptomatic nature of the disease in the early stages, subsequent advanced stage diagnosis, and a low 5 year survival rate. Endoscopy remains the primary standard for diagnosis of stomach carcinoma and the current marker, carbohydrate antigen 19-9 (CA19-9) lacks the levels of sensitivity and specificity required in order to make it clinically useful for diagnostic monitoring. Therefore, there is a current need for additional markers to improve the diagnostic accuracy for the early stages of stomach cancer. Together, glycomic, proteomic, and glycoproteomic analyses of serum have the potential to identify such probable markers. A discovery study is reported here using preoperative serum from 80 stomach cancer patients, 10 patients bearing benign stomach disease, and 20 matched controls. Glycomic analysis of the total and immunoaffinity depleted serum revealed statistically significant increases in the levels of sialyl Lewis X epitopes (SLe(X)) present on triantennary glycans accompanied by increased levels of core fucosylated agalactosyl biantennary glycans present on IgG (referred to as the IgG G0 glycoform) which are associated with increasing disease pathogenesis. Protein expression analysis using 2D-DiGE returned a number of differentially expressed protein candidates in the depleted serum, many of which were shown to carry triantennary SLe(X) during subsequent glycomic investigations. Biological pathway analysis of the experimental data returned complement activation and acute phase response signaling as the most significantly altered pathways in the stomach cancer patient serum. Upon the basis of these findings, it is suggested that increased expression of IgG G0 and complement activation are a host response to the presence of the stomach tumor while the increased expression of SLe(X) and acute phase response

  6. Automated analysis of damages for radiation in plastics surfaces

    International Nuclear Information System (INIS)

    Andrade, C.; Camacho M, E.; Tavera, L.; Balcazar, M.

    1990-02-01

    Analysis of damages done by the radiation in a polymer characterized by optic properties of polished surfaces, of uniformity and chemical resistance that the acrylic; resistant until the 150 centigrade grades of temperature, and with an approximate weight of half of the glass. An objective of this work is the development of a method that analyze in automated form the superficial damages induced by radiation in plastic materials means an images analyst. (Author)

  7. De novo transcriptomic analysis and development of EST-SSR markers in the Siberian tiger (Panthera tigris altaica).

    Science.gov (United States)

    Lu, Taofeng; Sun, Yujiao; Ma, Qin; Zhu, Minghao; Liu, Dan; Ma, Jianzhang; Ma, Yuehui; Chen, Hongyan; Guan, Weijun

    2016-12-01

    The Siberian tiger, Panthera tigris altaica, is an endangered species, and much more work is needed to protect this species, which is still vulnerable to extinction. Conservation efforts may be supported by the genetic assessment of wild populations, for which highly specific microsatellite markers are required. However, only a limited amount of genetic sequence data is available for this species. To identify the genes involved in the lung transcriptome and to develop additional simple sequence repeat (SSR) markers for the Siberian tiger, we used high-throughput RNA-Seq to characterize the Siberian tiger transcriptome in lung tissue (designated 'PTA-lung') and a pooled tissue sample (designated 'PTA'). Approximately 47.5 % (33,187/69,836) of the lung transcriptome was annotated in four public databases (Nr, Swiss-Prot, KEGG, and COG). The annotated genes formed a potential pool for gene identification in the tiger. An analysis of the genes differentially expressed in the PTA lung, and PTA samples revealed that the tiger may have suffered a series of diseases before death. In total, 1062 non-redundant SSRs were identified in the Siberian tiger transcriptome. Forty-three primer pairs were randomly selected for amplification reactions, and 26 of the 43 pairs were also used to evaluate the levels of genetic polymorphism. Fourteen primer pairs (32.56 %) amplified products that were polymorphic in size in P. tigris altaica. In conclusion, the transcriptome sequences will provide a valuable genomic resource for genetic research, and these new SSR markers comprise a reasonable number of loci for the genetic analysis of wild and captive populations of P. tigris altaica.

  8. First Microsatellite Markers Developed from Cupuassu ESTs: Application in Diversity Analysis and Cross-Species Transferability to Cacao

    Science.gov (United States)

    Ferraz dos Santos, Lucas; Moreira Fregapani, Roberta; Falcão, Loeni Ludke; Togawa, Roberto Coiti; Costa, Marcos Mota do Carmo; Lopes, Uilson Vanderlei; Peres Gramacho, Karina; Alves, Rafael Moyses

    2016-01-01

    The cupuassu tree (Theobroma grandiflorum) (Willd. ex Spreng.) Schum. is a fruitful species from the Amazon with great economical potential, due to the multiple uses of its fruit´s pulp and seeds in the food and cosmetic industries, including the production of cupulate, an alternative to chocolate. In order to support the cupuassu breeding program and to select plants presenting both pulp/seed quality and fungal disease resistance, SSRs from Next Generation Sequencing ESTs were obtained and used in diversity analysis. From 8,330 ESTs, 1,517 contained one or more SSRs (1,899 SSRs identified). The most abundant motifs identified in the EST-SSRs were hepta- and trinucleotides, and they were found with a minimum and maximum of 2 and 19 repeats, respectively. From the 1,517 ESTs containing SSRs, 70 ESTs were selected based on their functional annotation, focusing on pulp and seed quality, as well as resistance to pathogens. The 70 ESTs selected contained 77 SSRs, and among which, 11 were polymorphic in cupuassu genotypes. These EST-SSRs were able to discriminate the cupuassu genotype in relation to resistance/susceptibility to witches’ broom disease, as well as to pulp quality (SST/ATT values). Finally, we showed that these markers were transferable to cacao genotypes, and that genome availability might be used as a predictive tool for polymorphism detection and primer design useful for both Theobroma species. To our knowledge, this is the first report involving EST-SSRs from cupuassu and is also a pioneer in the analysis of marker transferability from cupuassu to cacao. Moreover, these markers might contribute to develop or saturate the cupuassu and cacao genetic maps, respectively. PMID:26949967

  9. Genome-Wide DNA Copy Number Analysis of Acute Lymphoblastic Leukemia Identifies New Genetic Markers Associated with Clinical Outcome.

    Directory of Open Access Journals (Sweden)

    Maribel Forero-Castro

    Full Text Available Identifying additional genetic alterations associated with poor prognosis in acute lymphoblastic leukemia (ALL is still a challenge.To characterize the presence of additional DNA copy number alterations (CNAs in children and adults with ALL by whole-genome oligonucleotide array (aCGH analysis, and to identify their associations with clinical features and outcome. Array-CGH was carried out in 265 newly diagnosed ALLs (142 children and 123 adults. The NimbleGen CGH 12x135K array (Roche was used to analyze genetic gains and losses. CNAs were analyzed with GISTIC and aCGHweb software. Clinical and biological variables were analyzed. Three of the patients showed chromothripsis (cth6, cth14q and cth15q. CNAs were associated with age, phenotype, genetic subtype and overall survival (OS. In the whole cohort of children, the losses on 14q32.33 (p = 0.019 and 15q13.2 (p = 0.04 were related to shorter OS. In the group of children without good- or poor-risk cytogenetics, the gain on 1p36.11 was a prognostic marker independently associated with shorter OS. In adults, the gains on 19q13.2 (p = 0.001 and Xp21.1 (p = 0.029, and the loss of 17p (p = 0.014 were independent markers of poor prognosis with respect to OS. In summary, CNAs are frequent in ALL and are associated with clinical parameters and survival. Genome-wide DNA copy number analysis allows the identification of genetic markers that predict clinical outcome, suggesting that detection of these genetic lesions will be useful in the management of patients newly diagnosed with ALL.

  10. First Microsatellite Markers Developed from Cupuassu ESTs: Application in Diversity Analysis and Cross-Species Transferability to Cacao.

    Directory of Open Access Journals (Sweden)

    Lucas Ferraz Dos Santos

    Full Text Available The cupuassu tree (Theobroma grandiflorum (Willd. ex Spreng. Schum. is a fruitful species from the Amazon with great economical potential, due to the multiple uses of its fruit´s pulp and seeds in the food and cosmetic industries, including the production of cupulate, an alternative to chocolate. In order to support the cupuassu breeding program and to select plants presenting both pulp/seed quality and fungal disease resistance, SSRs from Next Generation Sequencing ESTs were obtained and used in diversity analysis. From 8,330 ESTs, 1,517 contained one or more SSRs (1,899 SSRs identified. The most abundant motifs identified in the EST-SSRs were hepta- and trinucleotides, and they were found with a minimum and maximum of 2 and 19 repeats, respectively. From the 1,517 ESTs containing SSRs, 70 ESTs were selected based on their functional annotation, focusing on pulp and seed quality, as well as resistance to pathogens. The 70 ESTs selected contained 77 SSRs, and among which, 11 were polymorphic in cupuassu genotypes. These EST-SSRs were able to discriminate the cupuassu genotype in relation to resistance/susceptibility to witches' broom disease, as well as to pulp quality (SST/ATT values. Finally, we showed that these markers were transferable to cacao genotypes, and that genome availability might be used as a predictive tool for polymorphism detection and primer design useful for both Theobroma species. To our knowledge, this is the first report involving EST-SSRs from cupuassu and is also a pioneer in the analysis of marker transferability from cupuassu to cacao. Moreover, these markers might contribute to develop or saturate the cupuassu and cacao genetic maps, respectively.

  11. First Microsatellite Markers Developed from Cupuassu ESTs: Application in Diversity Analysis and Cross-Species Transferability to Cacao.

    Science.gov (United States)

    Ferraz Dos Santos, Lucas; Moreira Fregapani, Roberta; Falcão, Loeni Ludke; Togawa, Roberto Coiti; Costa, Marcos Mota do Carmo; Lopes, Uilson Vanderlei; Peres Gramacho, Karina; Alves, Rafael Moyses; Micheli, Fabienne; Marcellino, Lucilia Helena

    2016-01-01

    The cupuassu tree (Theobroma grandiflorum) (Willd. ex Spreng.) Schum. is a fruitful species from the Amazon with great economical potential, due to the multiple uses of its fruit´s pulp and seeds in the food and cosmetic industries, including the production of cupulate, an alternative to chocolate. In order to support the cupuassu breeding program and to select plants presenting both pulp/seed quality and fungal disease resistance, SSRs from Next Generation Sequencing ESTs were obtained and used in diversity analysis. From 8,330 ESTs, 1,517 contained one or more SSRs (1,899 SSRs identified). The most abundant motifs identified in the EST-SSRs were hepta- and trinucleotides, and they were found with a minimum and maximum of 2 and 19 repeats, respectively. From the 1,517 ESTs containing SSRs, 70 ESTs were selected based on their functional annotation, focusing on pulp and seed quality, as well as resistance to pathogens. The 70 ESTs selected contained 77 SSRs, and among which, 11 were polymorphic in cupuassu genotypes. These EST-SSRs were able to discriminate the cupuassu genotype in relation to resistance/susceptibility to witches' broom disease, as well as to pulp quality (SST/ATT values). Finally, we showed that these markers were transferable to cacao genotypes, and that genome availability might be used as a predictive tool for polymorphism detection and primer design useful for both Theobroma species. To our knowledge, this is the first report involving EST-SSRs from cupuassu and is also a pioneer in the analysis of marker transferability from cupuassu to cacao. Moreover, these markers might contribute to develop or saturate the cupuassu and cacao genetic maps, respectively.

  12. Surface markers for locating the pulleys and flexor tendon anatomy in the palm and fingers with reference to minimally invasive incisions.

    Science.gov (United States)

    Gordon, Joshua A; Stone, Lindsay; Gordon, Leonard

    2012-05-01

    Palm and finger pulley anatomy has been well described in relation to osseous structures. The goal of this study was to describe skin surface markers that locate the underlying flexor tendon and pulley system. We describe the anatomic detail of these structures and provide a guide for the surgeon for making small incisions. Using this approach, extensile exposure can be avoided, and the integrity of the complex pulley system is maintained. We dissected 12 palms and 48 fingers in 12 cadaver hands. We marked the palm and finger creases with methylene blue before dissection. We removed palm skin, finger skin, and subcutaneous tissue over the flexor tendon sheath and retained a 2-mm strip of each skin crease in its native position. We divided the palm and palmar surface of the fingers into 4 distinct zones and measured the location of the proximal and distal extent of each pulley and the tendon anatomy relative to the proximal and distal skin crease. We documented the location of the proximal and distal extent of the annular and cruciate pulleys as well as the decussation of the flexor digitorum superficialis (FDS) tendon and Camper chiasm. The results allow us to establish a relationship between the skin creases and underlying anatomy by dividing the palm and finger into 4 zones. In zone A, in the palm, the A2 pulley is located in the distal third and the FDS decussation is at the proximal extent of the A2 pulley. Zone B is in the proximal phalanx and A2 lies in the proximal third of this zone, whereas the Camper chiasm lies in the middle third. Zone C is in the middle phalanx and A4 and the insertion of FDS lie in the middle third of this zone. Zone D lies in the distal phalanx and the flexor digitorum profundus tendon inserts into the middle third of this zone. Skin creases can be used as surface markers to accurately locate the underlying pulley and tendon system and plan for limited incisions. These anatomic descriptions can aid surgeons in preoperative planning

  13. Presence of antibodies against a cell-surface protein, cross-reactive with DNA, in systemic lupus erythrematosus: a marker of the disease

    International Nuclear Information System (INIS)

    Jacob, L.; Lety, M.A.; Choquette, D.; Viard, J.P.; Jacob, F.; Louvard, D.; Bach, J.F.

    1987-01-01

    Antibodies against a cell-surface protein, cross-reactive with double-stranded DNA, were detected in the serum of 25 patients with active human systemic lupus erythematosus (SLE), defined on the basis of the revised American Rheumatism Association classification. Among these sera, two did not display anti-DNA antibodies, as shown by Farr assay, solid-phase radioimmunoassay, and Crithidia luciliae test. Five other SLE patients were consecutively studied in active and remission states. Antibodies against the protein were detected in the serum of the 5 SLE patients when they were in active phase but not in the serum of the same patients in inactive phase of the disease. The anti-protein antibodies were not found in the serum of 10 inactive SLE patients or in the sera of 10 normal human controls, 10 patients with rheumatoid arthritis, 5 patients with scleroderma, and 4 patients with primary sicca syndrome. Taken together, these results strongly suggest that antibodies against this cell-surface protein could provide a better diagnosis marker and activity index than anti-DNA antibodies in SLE

  14. Presence of antibodies against a cell-surface protein, cross-reactive with DNA, in systemic lupus erythrematosus: a marker of the disease

    Energy Technology Data Exchange (ETDEWEB)

    Jacob, L.; Lety, M.A.; Choquette, D.; Viard, J.P.; Jacob, F.; Louvard, D.; Bach, J.F.

    1987-05-01

    Antibodies against a cell-surface protein, cross-reactive with double-stranded DNA, were detected in the serum of 25 patients with active human systemic lupus erythematosus (SLE), defined on the basis of the revised American Rheumatism Association classification. Among these sera, two did not display anti-DNA antibodies, as shown by Farr assay, solid-phase radioimmunoassay, and Crithidia luciliae test. Five other SLE patients were consecutively studied in active and remission states. Antibodies against the protein were detected in the serum of the 5 SLE patients when they were in active phase but not in the serum of the same patients in inactive phase of the disease. The anti-protein antibodies were not found in the serum of 10 inactive SLE patients or in the sera of 10 normal human controls, 10 patients with rheumatoid arthritis, 5 patients with scleroderma, and 4 patients with primary sicca syndrome. Taken together, these results strongly suggest that antibodies against this cell-surface protein could provide a better diagnosis marker and activity index than anti-DNA antibodies in SLE.

  15. Market basket analysis visualization on a spherical surface

    Science.gov (United States)

    Hao, Ming C.; Hsu, Meichun; Dayal, Umeshwar; Wei, Shu F.; Sprenger, Thomas; Holenstein, Thomas

    2001-05-01

    This paper discusses the visualization of the relationships in e-commerce transactions. To date, many practical research projects have shown the usefulness of a physics-based mass- spring technique to layout data items with close relationships on a graph. We describe a market basket analysis visualization system using this technique. This system is described as the following: (1) integrates a physics-based engine into a visual data mining platform; (2) use a 3D spherical surface to visualize the cluster of related data items; and (3) for large volumes of transactions, uses hidden structures to unclutter the display. Several examples of market basket analysis are also provided.

  16. Analysis of polymer surfaces and thin-film coatings with Raman and surface enhanced Raman scattering

    CERN Document Server

    McAnally, G D

    2001-01-01

    This thesis investigates the potential of surface-enhanced Raman scattering (SERS) for the analysis and characterisation of polymer surfaces. The Raman and SERS spectra from a PET film are presented. The SERS spectra from the related polyester PBT and from the monomer DMT are identical to PET, showing that only the aromatic signals are enhanced. Evidence from other compounds is presented to show that loss of the carbonyl stretch (1725 cm sup - sup 1) from the spectra is due to a chemical interaction between the silver and surface carbonyl groups. The interaction of other polymer functional groups with silver is discussed. A comparison of Raman and SERS spectra collected from three faces of a single crystal shows the SERS spectra are depolarised. AFM images of the silver films used to obtain SERS are presented. They consist of regular islands of silver, fused together to form a complete film. The stability and reproducibility and of these surfaces is assessed. Band assignments for the SERS spectrum of PET are ...

  17. Unremitted hyperthyroidism following 131I treatment: an analysis of clinical markers in 48 patients

    International Nuclear Information System (INIS)

    Fang Yi; Zhang Xiuli; Liu Jianfeng; Zhang Youren

    2002-01-01

    Objective: To evaluate changes in clinical markers of unremitted hyperthyroidism patients after the first 131 I treatment. Methods: Forth eight unremitted hyperthyroidism patients were selected. Their thyroid function, the peak of 131 I uptake rate and thyroid weight before and after 131 I treatment were compared. Results: TT 3 , TT 4 , TSH were relatively stable and the peak of 131 I uptake rate and thyroid weight were reduced after 131 I treatment. Conclusions: Thyroid volume was reduced after 131 I treatment even if patients' clinical symptoms still existed; the peak of 131 I uptake rate was reduced after 131 I treatment, suggesting that their sensibility to 131 I decreased, so the absorbed dose should be adjusted when the 131 I dosage of second treatment is calculated

  18. The genetic profiles of two salmonid populations from Romania obtained through nuclear markers analysis

    Directory of Open Access Journals (Sweden)

    Ramona Nechifor

    2017-05-01

    Full Text Available The Salmonidae fish family is well represented in Romanian fauna, with a total of six species in the wild and reared in fish farms. Among them, the brown trout (Salmo trutta fario can be found in all major Romanian river basins. However, anthropogenic activities might disrupt salmonids’ habitats, so that inbreeding and genetic isolation might easily occur in the wild populations. We analyzed two wild brown trout populations from rivers targeted by anthropogenic activities, by using nuclear markers and genotyping in order to observe their genetic structure. We analyzed nine microsatellites and we observed their alleles frequencies, number of private alleles, observed and expected heterozygosity, as well as their population structure. The two populations are not in Hardy-Weinberg equilibrium for most of the loci and the inbreeding coefficient for both populations suggests a heterozygote deficit. Further sequencing data are needed in order to have a better view upon their complete genetic structure.

  19. Genetic Diversity Analysis of Iranian Improved Rice Cultivars through RAPD Markers

    Directory of Open Access Journals (Sweden)

    Ghaffar KIANI

    2011-08-01

    Full Text Available The aim of this study was to evaluate the genetic diversity of Iranian improved rice varieties. Sixteen rice varieties of particular interest to breeding programs were evaluated by means of random amplified polymorphic DNA (RAPD technique. The number of amplification products generated by each primer varied from 4 (OPB-04 to 11 (OPD-11 with an average of 8.2 bands per primer. Out of 49 bands, 33 (67.35% were found to be polymorphic for one or more cultivars ranging from 4 to 9 fragments per primer. The size of amplified fragments ranged between 350 to 1800 bp. Pair-wise Nei and Li�s (1979 similarity estimated the range of 0.59 to 0.98 between rice cultivars. Results illustrate the potential of RAPD markers to distinguish improved cultivars at DNA level. The information will facilitate selection of genotypes to serve as parents for effective rice breeding programs in Iran.

  20. Analysis of the genetic diversity of physic nut, Jatropha curcas L. accessions using RAPD markers.

    Science.gov (United States)

    Rafii, M Y; Shabanimofrad, M; Puteri Edaroyati, M W; Latif, M A

    2012-06-01

    A sum of 48 accessions of physic nut, Jatropha curcas L. were analyzed to determine the genetic diversity and association between geographical origin using RAPD-PCR markers. Eight primers generated a total of 92 fragments with an average of 11.5 amplicons per primer. Polymorphism percentages of J. curcas accessions for Selangor, Kelantan, and Terengganu states were 80.4, 50.0, and 58.7%, respectively, with an average of 63.04%. Jaccard's genetic similarity co-efficient indicated the high level of genetic variation among the accessions which ranged between 0.06 and 0.81. According to UPGMA dendrogram, 48 J. curcas accessions were grouped into four major clusters at coefficient level 0.3 and accessions from same and near states or regions were found to be grouped together according to their geographical origin. Coefficient of genetic differentiation (G(st)) value of J. curcas revealed that it is an outcrossing species.

  1. Efficient Software for Multi-marker, Region-Based Analysis of GWAS Data

    Directory of Open Access Journals (Sweden)

    Jaleal S. Sanjak

    2016-04-01

    Full Text Available Genome-wide association studies (GWAS have associated many single variants with complex disease, yet the better part of heritable complex disease risk remains unexplained. Analytical tools designed to work under specific population genetic models are needed. Rare variants are increasingly shown to be important in human complex disease, but most existing GWAS data do not cover rare variants. Explicit population genetic models predict that genes contributing to complex traits and experiencing recurrent, unconditionally deleterious, mutation will harbor multiple rare, causative mutations of subtle effect. It is difficult to identify genes harboring rare variants of large effect that contribute to complex disease risk via the single marker association tests typically used in GWAS. Gene/region-based association tests may have the power detect associations by combining information from multiple markers, but have yielded limited success in practice. This is partially because many methods have not been widely applied. Here, we empirically demonstrate the utility of a procedure based on the rank truncated product (RTP method, filtered to reduce the effects of linkage disequilibrium. We apply the procedure to the Wellcome Trust Case Control Consortium (WTCCC data set, and uncover previously unidentified associations, some of which have been replicated in much larger studies. We show that, in the absence of significant rare variant coverage, RTP based methods still have the power to detect associated genes. We recommend that RTP-based methods be applied to all existing GWAS data to maximize the usefulness of those data. For this, we provide efficient software implementing our procedure.

  2. Effects of fish oil supplementation on inflammatory markers in chronic heart failure: a meta-analysis of randomized controlled trials

    Directory of Open Access Journals (Sweden)

    Xin Wei

    2012-09-01

    Full Text Available Abstract Background Effects of fish oil on systematic inflammation in chronic heart failure remain unclear. In this meta-analysis, we aimed to evaluate the influence of fish oil supplementation on circulating levels of inflammatory markers in patients with chronic heart failure. Methods Human randomized controlled trials, which compared the effects of fish oil supplementation with placebo in patients with chronic heart failure, were identified by systematic search of Medline, Embase, Cochrane’s library and references cited in related reviews and studies up to November 2011. Outcome measures comprised the changes of circulating inflammatory markers. Meta-analysis was performed with the fixed-effect model or random-effect model according to the heterogeneity. Results A total of seven trials with eight study arms were included. The pooled results indicated circulating levels of tumor necrosis factor α (SMD = -0.62, 95% CI -1.08 to -0.16, p = 0.009, interleukin 1 (SMD = -1.24, 95% CI -1.56 to -0.91, p Conclusions Limited evidence suggests anti-inflammation may be a potential mechanism underlying the beneficial effects of fish oil for chronic heart failure. Further large-scale and adequately powered clinical trials are needed to confirm these effects.

  3. Analysis of the genetic structure of the Malay population: Ancestry-informative marker SNPs in the Malay of Peninsular Malaysia.

    Science.gov (United States)

    Yahya, Padillah; Sulong, Sarina; Harun, Azian; Wan Isa, Hatin; Ab Rajab, Nur-Shafawati; Wangkumhang, Pongsakorn; Wilantho, Alisa; Ngamphiw, Chumpol; Tongsima, Sissades; Zilfalil, Bin Alwi

    2017-09-01

    Malay, the main ethnic group in Peninsular Malaysia, is represented by various sub-ethnic groups such as Melayu Banjar, Melayu Bugis, Melayu Champa, Melayu Java, Melayu Kedah Melayu Kelantan, Melayu Minang and Melayu Patani. Using data retrieved from the MyHVP (Malaysian Human Variome Project) database, a total of 135 individuals from these sub-ethnic groups were profiled using the Affymetrix GeneChip Mapping Xba 50-K single nucleotide polymorphism (SNP) array to identify SNPs that were ancestry-informative markers (AIMs) for Malays of Peninsular Malaysia. Prior to selecting the AIMs, the genetic structure of Malays was explored with reference to 11 other populations obtained from the Pan-Asian SNP Consortium database using principal component analysis (PCA) and ADMIXTURE. Iterative pruning principal component analysis (ipPCA) was further used to identify sub-groups of Malays. Subsequently, we constructed an AIMs panel for Malays using the informativeness for assignment (I n ) of genetic markers, and the K-nearest neighbor classifier (KNN) was used to teach the classification models. A model of 250 SNPs ranked by I n , correctly classified Malay individuals with an accuracy of up to 90%. The identified panel of SNPs could be utilized as a panel of AIMs to ascertain the specific ancestry of Malays, which may be useful in disease association studies, biomedical research or forensic investigation purposes. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Selection of an effective microsatellite marker system for genetic control and analysis of gerbil populations in China.

    Science.gov (United States)

    Du, X Y; Li, W; Sa, X Y; Li, C L; Lu, J; Wang, Y Z; Chen, Z W

    2015-09-21

    Although gerbils have been widely used in many areas of biological research over many years, there is currently no effective genetic quality control system available. In the present study, we sought to establish a microsatellite marker system for quality control and conducted an optimized analysis of 137 microsatellite loci in two laboratory gerbil populations and one wild population. Independent sample t-tests on the mean effective allele number, mean of Shannon's information index, and mean HE suggested that 28 of the 137 microsatellite markers were informative for gerbil genetic control. Analysis of 4 laboratory gerbil populations and 1 wild population using the 28 microsatellite loci indicated that allele numbers varied from 1.9639 (Guangzhou, GZ) to 6.6071 (North-West wild, NW). The average of HO versus HE was 0.6236/0.3802, 0.6671/0.4159, 0.4185/0.3464, 0.4592/0.3821, and 0.3972/0.4167 for the Beijing, NW, Hangzhou, Dalian, and GZ populations, respectively. The GZ population showed the greatest differentiation, having higher RST and Nei's standard genetic distances. An AMO-VA revealed high genetic differentiation among the five populations (FST = 0.296). The microsatellite system established here is effective and will be important in future studies for genetic quality control and monitoring of gerbil breeds.

  5. Molecular studies in olive (Olea europaea L.): overview on DNA markers applications and recent advances in genome analysis.

    Science.gov (United States)

    Bracci, T; Busconi, M; Fogher, C; Sebastiani, L

    2011-04-01

    Olive (Olea europaea L.) is one of the oldest agricultural tree crops worldwide and is an important source of oil with beneficial properties for human health. This emblematic tree crop of the Mediterranean Basin, which has conserved a very wide germplasm estimated in more than 1,200 cultivars, is a diploid species (2n = 2x = 46) that is present in two forms, namely wild (Olea europaea subsp. europaea var. sylvestris) and cultivated (Olea europaea subsp. europaea var. europaea). In spite of its economic and nutritional importance, there are few data about the genetic of olive if compared with other fruit crops. Available molecular data are especially related to the application of molecular markers to the analysis of genetic variability in Olea europaea complex and to develop efficient molecular tools for the olive oil origin traceability. With regard to genomic research, in the last years efforts are made for the identification of expressed sequence tag, with particular interest in those sequences expressed during fruit development and in pollen allergens. Very recently the sequencing of chloroplast genome provided new information on the olive nucleotide sequence, opening the olive genomic era. In this article, we provide an overview of the most relevant results in olive molecular studies. A particular attention was given to DNA markers and their application that constitute the most part of published researches. The first important results in genome analysis were reported.

  6. One-chip biosensor for simultaneous disease marker/calibration substance measurement in human urine by electrochemical surface plasmon resonance method.

    Science.gov (United States)

    Nakamoto, Kohei; Kurita, Ryoji; Niwa, Osamu

    2010-12-15

    We have developed a miniaturized electrochemical surface plasmon resonance biosensor for measuring two biomolecules that have very different molecular sizes, one is transferrin (MW=75 kDa) as a disease marker protein, the other is creatinine (MW=113) as a calibration marker for the accurate measurement of human urinary samples. The sensor has a PDMS based microchannel that is 2 mm wide and 20 μm deep. Two gold films were integrated in the microchannel; one was modified with anti-transferrin antibody for immuno-reaction, and the other was modified with osmium-poly-vinylpyridine wired horseradish peroxidase (Os-gel-HRP). We further immobilized a tri-enzyme layer of creatininase, creatinase and sarcosine oxidase in order to measure creatinine by converting it to hydrogen peroxide in the upstream channel. We measured the transferrin concentration from the refractive index change involved in an immuno-complex formation, and we were simultaneously able to measure creatinine by employing the refractive index change in the Os-gel-HRP caused by oxidation with the hydrogen peroxide produced from creatinine by the tri-enzyme. The effects of ascorbic acid and uric acid in urine samples were sufficiently eliminated by adding ascorbate oxidase and uricase to the urine samples during sampling. We were able to measure two analyte concentrations within 15 min by one simple injection of 50 μL of diluted human urine into our sensor. The detectable transferrin and creatinine ranges were 20 ng/mL to 10 μg/mL, and 10 μM to 10 mM, respectively, which are sufficient levels for clinical tests. Finally, we compared the results obtained using our sensor with those obtained with a conventional immunoassay and the Jaffe method. We obtained a similar trend that can reduce the fluctuation in the urinary transferrin concentration from three different samples by calibrating the creatinine concentration. Copyright © 2010 Elsevier B.V. All rights reserved.

  7. Analysis of the Genetic Diversity and Population Structure of Latvian Ash (Fraxinus excelsior L. Stands using Nuclear and Chloroplast SSR Markers

    Directory of Open Access Journals (Sweden)

    Ruņģis Dainis

    2016-06-01

    Full Text Available Common ash (Fraxinus excelsior L. has a widespread distribution throughout Europe, and Latvia is almost at the north eastern edge of the distribution range. In Europe, ash is threatened by ash dieback, a disease caused by the introduced ascomycete Hymenoscyphus fraxineus. Chloroplast and nuclear DNA markers have been used to study the genetic diversity and population structure of ash both in a broader pan-European context as well as in more restricted regions. Some of the markers analysed in these previously published reports were also utilised in this study, enabling comparisons of the genetic parameters calculated from the nuclear SSR marker data and of the haplotypes identified with the chloroplast markers. Analysis of chloroplast markers revealed one dominant haplotype in Latvian stands, which corresponds to the haplotype previously found in Eastern Europe and Scandinavia. A second haplotype, corresponding to a previously reported central European haplotype was found in all individuals from the Ķemeri stand, indicating that this stand was naturally established from introduced germplasm, which was planted in a neighbouring park. The nuclear SSR markers revealed low levels of differentiation of Latvian F. excelsior stands, probably due efficient pollen flow between stands. The analysis of both chloroplast and nuclear DNA markers has revealed different aspects of the structure and provenance of Latvian F. excelsior populations.

  8. Contribution of Microchemical Surface Analysis of Archaeological Artefacts

    Science.gov (United States)

    Mousser, H.; Madani, A.; Amri, R.; Mousser, A.; Darchen, A.

    2009-11-01

    Museum CIRTA of the town of Constantine has a collection of more than 35000 coins and statuettes going back to Numide, Roman, Republican, Vandal and Byzantine times and is struck in the name of the cities, of the kingdoms and the empires. Surface analysis of these coins gives information about the chemical composition and leads to recommendations for restoration and preservations. This work is a contribution of microchemical surface study of coin with the effigy of the Numide King Massinissa (Constantine between 3rd and 2nd century before Jesus Christ). The photographic and scanning electron microscopy coupled with energy dispersive spectrometry (SEM + EDS) and diffraction of X-ray (DRX) was used. The optic microscopy (OMP) and SEM pictures of coins showed heterogeneous surface. Scanning electron microscopy coupled with energy dispersive spectrometry identified three basic metals copper (46.06%), antimony (17.74%) and lead (12.06%), (Weight Percentage). The DRX identifies stages (copper and lead) and their crystalline oxides Bindheimite (Pb2Sb2O7) and Bystromite (MgSb2O6) on the coin's surface.

  9. Coastal surface water suitability analysis for irrigation in Bangladesh

    Science.gov (United States)

    Mahtab, Mohammad Hossain; Zahid, Anwar

    2018-03-01

    Water with adequate quality and quantity is very important for irrigation to ensure the crop yields. Salinity is common problem in the coastal waters in Bangladesh. The intensity of salinity in the coastal zone in Bangladesh is not same. It fluctuates over the year. Sodium is another hazard which may hamper permeability and ultimately affects the fertility. It can reduce the crop yields. Although surface water is available in the coastal zone of Bangladesh, but its quality for irrigation needs to be monitored over the year. This paper will investigate the overall quality of coastal surface waters. Thirty-three water samples from different rivers were collected both in wet period (October-December) and in dry period (February-April). Different physical and chemical parameters are considered for investigation of the adequacy of water with respect to international irrigation water quality standards and Bangladesh standards. A comparison between the dry and wet period coastal surface water quality in Bangladesh will also be drawn here. The analysis shows that coastal surface water in Bangladesh is overall suitable for irrigation during wet period, while it needs treatment (which will increase the irrigation cost) for using for irrigation during dry period. Adaptation to this situation can improve the scenario. An integrated plan should be taken to increase the water storing capacity in the coastal area to harvest water during wet period.

  10. RNA-seq analysis of Quercus pubescens Leaves: de novo transcriptome assembly, annotation and functional markers development.

    Directory of Open Access Journals (Sweden)

    Sara Torre

    Full Text Available Quercus pubescens Willd., a species distributed from Spain to southwest Asia, ranks high for drought tolerance among European oaks. Q. pubescens performs a role of outstanding significance in most Mediterranean forest ecosystems, but few mechanistic studies have been conducted to explore its response to environmental constrains, due to the lack of genomic resources. In our study, we performed a deep transcriptomic sequencing in Q. pubescens leaves, including de novo assembly, functional annotation and the identification of new molecular markers. Our results are a pre-requisite for undertaking molecular functional studies, and may give support in population and association genetic studies. 254,265,700 clean reads were generated by the Illumina HiSeq 2000 platform, with an average length of 98 bp. De novo assembly, using CLC Genomics, produced 96,006 contigs, having a mean length of 618 bp. Sequence similarity analyses against seven public databases (Uniprot, NR, RefSeq and KOGs at NCBI, Pfam, InterPro and KEGG resulted in 83,065 transcripts annotated with gene descriptions, conserved protein domains, or gene ontology terms. These annotations and local BLAST allowed identify genes specifically associated with mechanisms of drought avoidance. Finally, 14,202 microsatellite markers and 18,425 single nucleotide polymorphisms (SNPs were, in silico, discovered in assembled and annotated sequences. We completed a successful global analysis of the Q. pubescens leaf transcriptome using RNA-seq. The assembled and annotated sequences together with newly discovered molecular markers provide genomic information for functional genomic studies in Q. pubescens, with special emphasis to response mechanisms to severe constrain of the Mediterranean climate. Our tools enable comparative genomics studies on other Quercus species taking advantage of large intra-specific ecophysiological differences.

  11. Genetic diversity and structure of the zombi pea (Vigna vexillata (L.) A. Rich) gene pool based on SSR marker analysis.

    Science.gov (United States)

    Dachapak, Sujinna; Somta, Prakit; Poonchaivilaisak, Supalak; Yimram, Tarika; Srinives, Peerasak

    2017-04-01

    Zombi pea (Vigna vexillata (L.) A. Rich) is an underutilized legume species and a useful gene source for resistance to biotic and abiotic stresses, although there is little understanding on its genetic diversity and structure. In this study, 422 (408 wild and 14 cultivated) accessions of zombi pea from diverse origins (201 from Africa, 126 from America, 85 from Australia, 5 from Asia and 5 from unknown origin) were analyzed with 20 simple sequence repeat (SSR) markers to determine its genetic diversity and genetic structure. The SSR markers detected 273 alleles in total with a mean of 13.6 alleles per locus. Polymorphism information content values of the markers varied from 0.58 to 0.90 with an average of 0.76. Overall gene diversity was 0.715. Gene diversity and average allelic richness was highest in Africa (0.749 and 8.08, respectively) and lowest in America (0.435 and 4.10, respectively). Nei's genetic distance analysis revealed that the highest distance was between wild Australia and cultivated Africa (0.559), followed by wild West Africa and wild Australia (0.415). STRUCTURE, neighbor-joining (NJ), and principal coordinate analyses consistently showed that these zombi pea accessions were clustered into three major groups, viz. America, Africa and Asia, and Australia. NJ tree also suggested that American and Australian accessions are originated from East African zombi peas, and that the cultivated accessions from Africa and Asia were genetically distinct, while those from America were clustered with some cultivated accessions from Africa. These results suggest that Africa is the center of origin and diversity of zombi pea, and that domestication of this pea took place more than once in different regions.

  12. Genetic diversity analysis in Malaysian giant prawns using expressed sequence tag microsatellite markers for stock improvement program.

    Science.gov (United States)

    Atin, K H; Christianus, A; Fatin, N; Lutas, A C; Shabanimofrad, M; Subha, B

    2017-08-17

    The Malaysian giant prawn is among the most commonly cultured species of the genus Macrobrachium. Stocks of giant prawns from four rivers in Peninsular Malaysia have been used for aquaculture over the past 25 years, which has led to repeated harvesting, restocking, and transplantation between rivers. Consequently, a stock improvement program is now important to avoid the depletion of wild stocks and the loss of genetic diversity. However, the success of such an improvement program depends on our knowledge of the genetic variation of these base populations. The aim of the current study was to estimate genetic variation and differentiation of these riverine sources using novel expressed sequence tag-microsatellite (EST-SSR) markers, which not only are informative on genetic diversity but also provide information on immune and metabolic traits. Our findings indicated that the tested stocks have inbreeding depression due to a significant deficiency in heterozygotes, and F IS was estimated as 0.15538 to 0.31938. An F-statistics analysis suggested that the stocks are composed of one large panmictic population. Among the four locations, stocks from Johor, in the southern region of the peninsular, showed higher allelic and genetic diversity than the other stocks. To overcome inbreeding problems, the Johor population could be used as a base population in a stock improvement program by crossing to the other populations. The study demonstrated that EST-SSR markers can be incorporated in future marker assisted breeding to aid the proper management of the stocks by breeders and stakeholders in Malaysia.

  13. Intensive Linkage Mapping in a Wasp (Bracon Hebetor) and a Mosquito (Aedes Aegypti) with Single-Strand Conformation Polymorphism Analysis of Random Amplified Polymorphic DNA Markers

    OpenAIRE

    Antolin, M. F.; Bosio, C. F.; Cotton, J.; Sweeney, W.; Strand, M. R.; Black-IV, W. C.

    1996-01-01

    The use of random amplified polymorphic DNA from the polymerase chain reaction (RAPD-PCR) allows efficient construction of saturated linkage maps. However, when analyzed by agarose gel electrophoresis, most RAPD-PCR markers segregate as dominant alleles, reducing the amount of linkage information obtained. We describe the use of single strand conformation polymorphism (SSCP) analysis of RAPD markers to generate linkage maps in a haplodiploid parasitic wasp Bracon (Habrobracon) hebetor and a d...

  14. Database Description - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available Database Description General information of database Database name PGDBj Registered plant list, Marker list,...available URL of Web services - Need for user registration Not available About This Database Database Descri...ption Download License Update History of This Database Site Policy | Contact Us Database Description - PGDBj Regis...switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods

  15. Rate law analysis of water oxidation on a hematite surface.

    Science.gov (United States)

    Le Formal, Florian; Pastor, Ernest; Tilley, S David; Mesa, Camilo A; Pendlebury, Stephanie R; Grätzel, Michael; Durrant, James R

    2015-05-27

    Water oxidation is a key chemical reaction, central to both biological photosynthesis and artificial solar fuel synthesis strategies. Despite recent progress on the structure of the natural catalytic site, and on inorganic catalyst function, determining the mechanistic details of this multiredox reaction remains a significant challenge. We report herein a rate law analysis of the order of water oxidation as a function of surface hole density on a hematite photoanode employing photoinduced absorption spectroscopy. Our study reveals a transition from a slow, first order reaction at low accumulated hole density to a faster, third order mechanism once the surface hole density is sufficient to enable the oxidation of nearest neighbor metal atoms. This study thus provides direct evidence for the multihole catalysis of water oxidation by hematite, and demonstrates the hole accumulation level required to achieve this, leading to key insights both for reaction mechanism and strategies to enhance function.

  16. Statistical Analysis of Magnetic Abrasive Finishing (MAF) On Surface Roughness

    Science.gov (United States)

    Givi, Mehrdad; Tehrani, Alireza Fadaei; Mohammadi, Aminollah

    2010-06-01

    Magnetic assisted finishing is one of the nontraditional methods of polishing that recently has been attractive for the researchers. This paper investigates the effects of some parameters such as rotational speed of the permanent magnetic pole, work gap between the permanent pole and the work piece, number of the cycles and the weight of the abrasive particles on aluminum surface plate finishing. The three levels full factorial method was used as the DOE technique (design of experiments) for studying the selected factors. Analysis of Variance (ANOVA) has been used to determine significant factors and also to obtain an equation based on data regression. Experimental results indicate that for a change in surface roughness ΔRa, number of cycles and working gap are found to be the most significant parameters followed by rotational speed and then weight of powders.

  17. Storage fee analysis for a retrievable surface storage facility

    International Nuclear Information System (INIS)

    Field, B.B.; Rosnick, C.K.

    1973-12-01

    Conceptual design studies are in progress for a Water Basin Concept (WBC) and an alternative Sealed Storage Cask Concept (SSCC) of a Retrievable Surface Storage Facility (RSSF) intended as a Federal government facility for storing high-level radioactive wastes until a permanent disposal method is established. The RSSF will be a man-made facility with a design life of at least 100 y, and will have capacity to store all of the high-level waste from the reprocessing of nuclear power plant spent fuels generated by the industry through the year 2000. This report is a basic version of ARH-2746, ''Retrievable Surface Storage Facility, Water Basin Concept, User Charge Analysis.'' It is concerned with the issue of establishing a fee to cover the cost of storing nuclear wastes both in the RSSF and at the subsequent disposal facility. (U.S.)

  18. Bio-inspired nanotechnology from surface analysis to applications

    CERN Document Server

    Walsh, Tiffany

    2014-01-01

    This book focuses on the use of bio-inspired and biomimetic methods for the fabrication and activation of nanomaterials. This includes studies concerning the binding of the biomolecules to the surface of inorganic structures, structure/function relationships of the final materials, and extensive discussions on the final applications of such biomimetic materials in unique applications including energy harvesting/storage, biomedical diagnostics, and materials assembly. This book also: ·          Covers the sustainable features of bio-inspired nanotechnology ·          Includes studies on the unique applications of biomimetic materials, such as energy harvesting and biomedical diagnostics Bio-Inspired Nanotechnology: From Surface Analysis to Applications is an ideal book for researchers, students, nanomaterials engineers, bioengineers, chemists, biologists, physicists, and medical researchers.

  19. Association Analysis of SSR Markers with Phenology, Grain, and Stover-Yield Related Traits in Pearl Millet (Pennisetum glaucum (L. R. Br.

    Directory of Open Access Journals (Sweden)

    Baskaran Kannan

    2014-01-01

    Full Text Available Pearl millet is a staple food crop for millions of people living in the arid and semi-arid tropics. Molecular markers have been used to identify genomic regions linked to traits of interest by conventional QTL mapping and association analysis. Phenotypic recurrent selection is known to increase frequencies of favorable alleles and decrease those unfavorable for the traits under selection. This study was undertaken (i to quantify the response to recurrent selection for phenotypic traits during breeding of the pearl millet open-pollinated cultivar “CO (Cu 9” and its four immediate progenitor populations and (ii to assess the ability of simple sequence repeat (SSR marker alleles to identify genomic regions linked to grain and stover yield-related traits in these populations by association analysis. A total of 159 SSR alleles were detected across 34 selected single-copy SSR loci. SSR marker data revealed presence of subpopulations. Association analysis identified genomic regions associated with flowering time located on linkage group (LG 6 and plant height on LG4, LG6, and LG7. Marker alleles on LG6 were associated with stover yield, and those on LG7 were associated with grain yield. Findings of this study would give an opportunity to develop marker-assisted recurrent selection (MARS or marker-assisted population improvement (MAPI strategies to increase the rate of gain for pearl millet populations undergoing recurrent selection.

  20. Association of SSR markers with contents of fatty acids in olive oil and genetic diversity analysis of an olive core collection.

    Science.gov (United States)

    Ipek, M; Ipek, A; Seker, M; Gul, M K

    2015-03-27

    The purpose of this research was to characterize an olive core collection using some agronomic characters and simple sequence repeat (SSR) markers and to determine SSR markers associated with the content of fatty acids in olive oil. SSR marker analysis demonstrated the presence of a high amount of genetic variation between the olive cultivars analyzed. A UPGMA dendrogram demonstrated that olive cultivars did not cluster on the basis of their geographic origin. Fatty acid components of olive oil in these cultivars were determined. The results also showed that there was a great amount of variation between the olive cultivars in terms of fatty acid composition. For example, oleic acid content ranged from 57.76 to 76.9% with standard deviation of 5.10%. Significant correlations between fatty acids of olive oil were observed. For instance, a very high negative correlation (-0.812) between oleic and linoleic acids was detected. A structured association analysis between the content of fatty acids in olive oil and SSR markers was performed. STRUCTURE analysis assigned olive cultivars to two gene pools (K = 2). Assignment of olive cultivars to these gene pools was not based on geographical origin. Association between fatty acid traits and SSR markers was evaluated using the general linear model of TASSEL. Significant associations were determined between five SSR markers and stearic, oleic, linoleic, and linolenic acids of olive oil. Very high associations (P olive.

  1. Genetic diversity of native chicken based on analysis of D-Loop mtDNA marker

    Directory of Open Access Journals (Sweden)

    Tike Sartika

    2000-06-01

    Full Text Available Production was carried out using control region/D-loop mtDNA marker. The base population of native chicken was selected from subpopulation at Cianjur, Jatiwangi, Depok, Bogor I, and Bogor 2. Samples from each population was 10 heads and 2 samples Green Jungle Fowl (Gallus various from East Java as out Group samples. Two primers binding conserved tRNA Phenylalanine gene and tRNA Glutamine gene were DNA Heavy stranded HI255 (5'-CATCTTGGCATCTTCAGTGCC-3' and DNA Light stranded Ll6750 (5'-AGGACTACGGCTTGAAAAGC-3' was used to amplify D-Ioop mtDNA chicken. PCR-RFLP methods with 6 restriction enzymes 4 cutter such as, Alul (AG↓CT, Hpall (C↓CGG, Mbol (↓GATC, Rsal (GT↓AC, NlaIII (CATG↓ and HaeIII (GG↓CC were used to detect polymorphism within and between subpopulation. Result of experiment show that mtDNA which was amplified by PCR was 1320 bp, consist of 1227 bp control region/D-loop, 45 bp tRNA Glutamine gene and 48 bp tRNA Phenylalananine gene. PCR product which were digested from 6 endonucleases enzyme show that native chicken within and between population was monomorphic and if its compare with Green Jungle Fowl was polymorphic.

  2. Clothing norms as markers of status in a hospital setting: A Bourdieusian analysis.

    Science.gov (United States)

    Jenkins, Tania M

    2014-09-01

    This article uses a Bourdieusian framework to understand the importance of clothing norms for symbolizing and reproducing social, as well as professional, hierarchy in hospitals. Using data from participant observation, it examines how a complex yet informal dress code has emerged at a community hospital in the Northeastern United States, in a setting where very few formal guidelines exist on how to dress. By conceptualizing professionals as holders of various types of capital (economic, cultural, and symbolic), this article expands previous research which considered clothing only as a marker of professional identity. The findings demonstrate (1) how clothing norms are used in subtle, but purposeful, ways to reflect varying degrees of cultural and economic capital and (2) how these complex norms also reflect professional boundaries in medical authority (symbolic capital), which is important during critical moments where clothing can quickly signal who can take control. The discussion borrows Bourdieu's concepts of habitus and field to explain why subordinates subscribe to these clothing norms, in the absence of a formal organizational dress code. © The Author(s) 2014.

  3. Analysis of genetic diversity of Laeliinae (Orchidaceae) in the State of Sergipe using ISSR markers.

    Science.gov (United States)

    Arrigoni-Blank, M F; Santos, M S; Blank, A F; Rabbani, A R C; Silva-Mann, R; Santos, J B; Costa, A S; Menezes, T S A

    2016-06-03

    The Orchidaceae represent one of the largest and most diverse families on the planet. However, this family is constantly threatened by predators and by the advancement of urban centers over its natural habitats. The objective of this study was to use inter-simple sequence repeat markers to evaluate the genetic diversity between orchid accessions of the Laeliinae subtribe, which comprise part of the Orchidaceae study collection at the Department of Agronomic Engineering of the Federal University of Sergipe. DNA was extracted from each specimen by using an adapted 2% cetyltrimethyl ammonium bromide protocol. Similarity between individuals was calculated using the Jaccard method. Clustering was carried out by the unweighted pair group method with arithmetic mean method, with resampling and 10,000 bootstraps. Eighty-seven fragments were obtained, all of which were polymorphic, revealing high variability between accessions. The mean similarity was 35.77% between Encyclia sp individuals, and 35.90% between specimens of Cattleya tigrina. For Epidendrum secundum, a relationship between geographic and genetic distances was observed, and the accession collected in the southern part of the State of Sergipe (Serra de Itabaiana National Park) was more divergent than that of the other parts of the state. The data generated in this study will guide further research aimed at the ex situ conservation of these materials.

  4. Assessment of Behavioural Markers of Autonoetic Consciousness during Episodic Autobiographical Memory Retrieval: A Preliminary Analysis

    Directory of Open Access Journals (Sweden)

    M. Irish

    2008-01-01

    Full Text Available There is ongoing theoretical debate regarding episodic memory and how it can be accurately measured, in particular if the focus should be content-based recall of episodic details or something more experiential involving the subjective capacity to mentally travel back in time and “re-live” aspects of the original event. The autonoetic subscale of the Episodic Autobiographical Memory Interview (EAMI is presented here as a new test instrument that attempts to redress theoretical and methodological shortcomings in autobiographical memory assessment. The EAMI merges a phenomenological detail-based approach with an assessment of autonoetic consciousness, departing considerably from traditional Remember/Know paradigms used within this field. We present findings from an initial pilot study investigating the potential markers of autonoetic consciousness that may accompany episodic retrieval. Key behavioural indices of autonoetic consciousness, notably those of viewer perspective, visual imagery, and emotional re-experiencing, emerged as being inextricably bound with the level of phenomenological detail recalled and the overall re-living judgment. The autonoetic subscale of the EAMI permits conceptually refined assessment of episodic personal memories and the accompanying subjective experience of mental re-living, characteristic of episodic memory.

  5. Unlocking the diversity of genebanks: whole-genome marker analysis of Swiss bread wheat and spelt

    KAUST Repository

    Müller, Thomas

    2017-11-04

    Genebanks play a pivotal role in preserving the genetic diversity present among old landraces and wild progenitors of modern crops and they represent sources of agriculturally important genes that were lost during domestication and in modern breeding. However, undesirable genes that negatively affect crop performance are often co-introduced when landraces and wild crop progenitors are crossed with elite cultivars, which often limit the use of genebank material in modern breeding programs. A detailed genetic characterization is an important prerequisite to solve this problem and to make genebank material more accessible to breeding. Here, we genotyped 502 bread wheat and 293 spelt accessions held in the Swiss National Genebank using a 15K wheat SNP array. The material included both spring and winter wheats and consisted of old landraces and modern cultivars. Genome- and sub-genome-wide analyses revealed that spelt and bread wheat form two distinct gene pools. In addition, we identified bread wheat landraces that were genetically distinct from modern cultivars. Such accessions were possibly missed in the early Swiss wheat breeding program and are promising targets for the identification of novel genes. The genetic information obtained in this study is appropriate to perform genome-wide association studies, which will facilitate the identification and transfer of agriculturally important genes from the genebank into modern cultivars through marker-assisted selection.

  6. (SSR) markers

    African Journals Online (AJOL)

    SAM

    2014-07-30

    Jul 30, 2014 ... al., 2004; Lefebvre et al., 2001; Moon et al., 2003; Paran et al., 1998; Prince et al., 1992). These markers have proven to be very useful in assessing genetic diversity and phylogeny, characterization of germplasm and detection of duplicates, parental verification in crosses, gene tagging in marker assisted ...

  7. (RAPD) markers

    African Journals Online (AJOL)

    Administrator

    2011-09-21

    Sep 21, 2011 ... RAPD markers reveal polymorphism among some Iranian pomegranate genotypes. Sci. Hortic. 111: 24-29. Shasany AK, Darokar MP, Dhawan S, Gupta AK, Gupta S, Shukla AK,. Patra NK, Khanuja SPS (2005). Use of RAPD and AFLP Markers to. Identify Inter- and Intraspecific Hybrids of Mentha. J. Hered.

  8. Analysis and design of functional micro/nano structured surfaces

    Science.gov (United States)

    Xu, Zhenzhen; Kong, Lingbao; Xu, Min

    2016-03-01

    In recent years, more and more attention has been paid to the bionic structure and functional materials. The theoretical research and fabricating ways of the Super-hydrophobic surface have sound achievements. However, the existing methods largely depend on the precision of the equipment and complex chemical substances, and it is hard to ensure the consistence of the material surface. Therefore, construction of microstructure on the surface of the material by using the method of mechanical processing to make the scale of the Super-hydrophobic surface to promote the popularization and application of Super-hydrophobic surface is of great significance. In order to put forward the innovative microstructure and to provide theoretical basis for the subsequent mechanical processing, based on the analysis of the classical theory of Super-hydrophobic, the super-hydrophobic film was by sol gel method. To explore the effects of different ratio of materials on the hydrophobicity, a micro/nano-structured super-hydrophobic coating was obtained by coating a film improved by hexamethyldisilazane (HMDS) after a film improved by polyethylene glycol (PEG) was coated. The microstructure of bilayer films is analyzed, and the double-layer film structure is simplified to design two kinds of microstructure models. For the design of the two models based on the Wenzel and Cassie equations, a roughness factor is adopted to establish the quantitative relationship between the contact angle and the microstructure parameters, and the microstructure parameters is also analyzed by using MATLAB software, and hence the optimized microstructure parameters is obtained.

  9. Morphological characteristics of primary enamel surfaces versus permanent enamel surfaces: SEM digital analysis.

    Science.gov (United States)

    Lucchese, A; Storti, E

    2011-09-01

    The morphology of permanent and primary enamel surface merits further analysis. The objective of this study was to illustrate a method of SEM digital image processing able to quantify and discriminate between the morphological characteristics of primary and permanent tooth enamel. Sixteen extracted teeth, 8 primary teeth and 8 permanent teeth, kept in saline solution, were analysed. The teeth were observed under SEM. The SEM images were analysed by means of digitally processed algorithms. The two algorithms used were: Local standard deviation to measure surface roughness with the roughness index (RI); Hough's theorem to identify linear structures with the linear structure index (LSI). The SEM images of primary teeth enamel show smooth enamel with little areas of irregularity. No linear structures are apparent. The SEM images of permanent enamel show a not perfectly smooth surface; there are furrows and irregularities of variable depth and width. In the clinical practice a number of different situations require the removal of a thin layer of enamel. Only a good morphological knowledge of both permanent and primary tooth enamel gives the opportunity to identify and exploit the effects of rotary tools on enamel, thus allowing for a correct finishing technique.

  10. Multi-channel Analysis of Passive Surface Waves (MAPS)

    Science.gov (United States)

    Xia, J.; Cheng, F. Mr; Xu, Z.; Wang, L.; Shen, C.; Liu, R.; Pan, Y.; Mi, B.; Hu, Y.

    2017-12-01

    Urbanization is an inevitable trend in modernization of human society. In the end of 2013 the Chinese Central Government launched a national urbanization plan—"Three 100 Million People", which aggressively and steadily pushes forward urbanization. Based on the plan, by 2020, approximately 100 million people from rural areas will permanently settle in towns, dwelling conditions of about 100 million people in towns and villages will be improved, and about 100 million people in the central and western China will permanently settle in towns. China's urbanization process will run at the highest speed in the urbanization history of China. Environmentally friendly, non-destructive and non-invasive geophysical assessment method has played an important role in the urbanization process in China. Because human noise and electromagnetic field due to industrial life, geophysical methods already used in urban environments (gravity, magnetics, electricity, seismic) face great challenges. But humanity activity provides an effective source of passive seismic methods. Claerbout pointed out that wavefileds that are received at one point with excitation at the other point can be reconstructed by calculating the cross-correlation of noise records at two surface points. Based on this idea (cross-correlation of two noise records) and the virtual source method, we proposed Multi-channel Analysis of Passive Surface Waves (MAPS). MAPS mainly uses traffic noise recorded with a linear receiver array. Because Multi-channel Analysis of Surface Waves can produces a shear (S) wave velocity model with high resolution in shallow part of the model, MPAS combines acquisition and processing of active source and passive source data in a same flow, which does not require to distinguish them. MAPS is also of ability of real-time quality control of noise recording that is important for near-surface applications in urban environment. The numerical and real-world examples demonstrated that MAPS can be

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

    Science.gov (United States)

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

    2002-04-26

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

  12. Noise filtering and nonparametric analysis of microarray data underscores discriminating markers of oral, prostate, lung, ovarian and breast cancer

    Directory of Open Access Journals (Sweden)

    Dermody James J

    2004-11-01

    Full Text Available Abstract Background A major goal of cancer research is to identify discrete biomarkers that specifically characterize a given malignancy. These markers are useful in diagnosis, may identify potential targets for drug development, and can aid in evaluating treatment efficacy and predicting patient outcome. Microarray technology has enabled marker discovery from human cells by permitting measurement of steady-state mRNA levels derived from thousands of genes. However many challenging and unresolved issues regarding the acquisition and analysis of microarray data remain, such as accounting for both experimental and biological noise, transcripts whose expression profiles are not normally distributed, guidelines for statistical assessment of false positive/negative rates and comparing data derived from different research groups. This study addresses these issues using Affymetrix HG-U95A and HG-U133 GeneChip data derived from different research groups. Results We present here a simple non parametric approach coupled with noise filtering to identify sets of genes differentially expressed between the normal and cancer states in oral, breast, lung, prostate and ovarian tumors. An important feature of this study is the ability to integrate data from different laboratories, improving the analytical power of the individual results. One of the most interesting findings is the down regulation of genes involved in tissue differentiation. Conclusions This study presents the development and application of a noise model that suppresses noise, limits false positives in the results, and allows integration of results from individual studies derived from different research groups.

  13. Integrating marker-assisted background analysis with foreground selection for pyramiding bacterial blight resistance genes into Basmati rice.

    Science.gov (United States)

    Baliyan, Nikita; Malik, Rekha; Rani, Reema; Mehta, Kirti; Vashisth, Urvashi; Dhillon, Santosh; Boora, Khazan Singh

    2018-01-01

    Bacterial leaf blight (BB), caused by the bacterium Xanthomonas oryzae pv. Oryzae (Xoo), is the major constraint amongst rice diseases in India. CSR-30 is a very popular high-yielding, salt-tolerant Basmati variety widely grown in Haryana, India, but highly susceptible to BB. In the present study, we have successfully introgressed three BB resistance genes (Xa21, xa13 and xa5) from BB-resistant donor variety IRBB-60 into the BB-susceptible Basmati variety CSR-30 through marker-assisted selection (MAS) exercised with stringent phenotypic selection without compromising the Basmati traits. Background analysis using 131 polymorphic SSR markers revealed that recurrent parent genome (RPG) recovery ranged up to 97.1% among 15 BC 3 F 1 three-gene-pyramided genotypes. Based on agronomic evaluation, BB reaction, aroma, percentage recovery of RPG, and grain quality evaluation, four genotypes, viz., IC-R28, IC-R68, IC-R32, and IC-R42, were found promising and advanced to BC 3 F 2 generation. Copyright © 2017 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.

  14. Genotypic and Phenotypic Analysis of Dairy Lactococcus lactis Biodiversity in Milk: Volatile Organic Compounds as Discriminating Markers

    Science.gov (United States)

    Dhaisne, Amandine; Guellerin, Maeva; Laroute, Valérie; Laguerre, Sandrine; Le Bourgeois, Pascal; Loubiere, Pascal

    2013-01-01

    The diversity of nine dairy strains of Lactococcus lactis subsp. lactis in fermented milk was investigated by both genotypic and phenotypic analyses. Pulsed-field gel electrophoresis and multilocus sequence typing were used to establish an integrated genotypic classification. This classification was coherent with discrimination of the L. lactis subsp. lactis bv. diacetylactis lineage and reflected clonal complex phylogeny and the uniqueness of the genomes of these strains. To assess phenotypic diversity, 82 variables were selected as important dairy features; they included physiological descriptors and the production of metabolites and volatile organic compounds (VOCs). Principal-component analysis (PCA) demonstrated the phenotypic uniqueness of each of these genetically closely related strains, allowing strain discrimination. A method of variable selection was developed to reduce the time-consuming experimentation. We therefore identified 20 variables, all associated with VOCs, as phenotypic markers allowing discrimination between strain groups. These markers are representative of the three metabolic pathways involved in flavor: lipolysis, proteolysis, and glycolysis. Despite great phenotypic diversity, the strains could be divided into four robust phenotypic clusters based on their metabolic orientations. Inclusion of genotypic diversity in addition to phenotypic characters in the classification led to five clusters rather than four being defined. However, genotypic characters make a smaller contribution than phenotypic variables (no genetic distances selected among the most contributory variables). This work proposes an original method for the phenotypic differentiation of closely related strains in milk and may be the first step toward a predictive classification for the manufacture of starters. PMID:23709512

  15. Linkage Map Construction and QTL Analysis of Fruit Traits in Melon (Cucumis melo L.) Based on CAPS Markers

    International Nuclear Information System (INIS)

    Baloch, A. M.; Liu, S.; Wang, X.; Luan, F.; Baloch, A. W.; Baloch, M. J.

    2016-01-01

    In the current experiment, the quantitative trait loci (QTL) analysis was done by composite interval mapping method to detect QTLs in edge, central parts and fruit shape of melon. In this context, 235 F/sub 2/ populations along with their parents were evaluated for fruit size, shape and color under replicated trail at Horticulture Experimental Station of Northeast Agricultural University, Harbin, China, during the growing year 2014. Moreover, 96 pairs of CAPS markers were used to construct a linkage map using F/sub 2/ population that was derived from the cross between two contrasting parents (MR-1 and Topmark). The total length of linkage map was found to be 4984.1cM with an average of 51.9177 cM between the markers. In a total, we detected ten QTLs, in which one was major, while others were minor. Five QTLs were detected in the edge part of melon fruit and three QTLs were detected in central parts of melon and all were considered as Brix content. Two QTLs were related with fruit shape. Our present genetic and QTLs mapping would be proved useful in plant breeding programs for the improvement of economically important horticultural traits. (author)

  16. Contribution to the study of markers in lungs carcinogenesis and analysis of factors predicting the benefit of chemotherapy

    International Nuclear Information System (INIS)

    Olaussen, K.A.

    2006-06-01

    A better definition of early bio markers in lung carcinogenesis should enhance the development of molecular means to perform screening, diagnostic, and chemo-prevention of patients at high risk of lung cancer. We studied epigenetic deregulation of multiple promoters (p16(INK4a), HOX A9, MAGE A 1 et MAGE B2) in sputum samples from smokers at high risk and from patients with non-small cell lung cancer (N.S.C.L.C.). This molecular test, based on easily accessible sample,s can be modulated according to the aims of the investigator (e.g. screening or confirmation of diagnosis). Secondly, we have studied two candidate proteins as predictive markers of the benefit of adjuvant chemotherapy in patients with resected lung cancer. The multivariate analysis shows that tumor expression of the catalytic sub-unit of telomerase is not able to predict survival in patients included in the lAL T study' of adjuvant chemotherapy. However, tumor expression of the DNA repair protein ERCC1 identifies a sub-group of patients (ERCC1 negative) whose chances of survival are increased by 35% by means of cisplatin-based adjuvant chemotherapy. Further, tumor ERCC1 expression has a positive prognostic value in the non-treated control group. The need for a deeper understanding in cancerology of the physiological role of the ERCC1 endonuclease is discussed in this thesis. (author)

  17. Adlayers of dimannoside thiols on gold: surface chemical analysis.

    Science.gov (United States)

    Dietrich, Paul M; Horlacher, Tim; Girard-Lauriault, Pierre-Luc; Gross, Thomas; Lippitz, Andreas; Min, Hyegeun; Wirth, Thomas; Castelli, Riccardo; Seeberger, Peter H; Unger, Wolfgang E S

    2011-04-19

    Carbohydrate films on gold based on dimannoside thiols (DMT) were prepared, and a complementary surface chemical analysis was performed in detail by X-ray photoelectron spectroscopy (XPS), time-of-flight secondary ion mass spectrometry (ToF-SIMS), near-edge X-ray absorption fine structure (NEXAFS), FT-IR, and contact angle measurements in order to verify formation of ω-carbohydrate-functionalized alkylthiol films. XPS (C 1s, O 1s, and S 2p) reveals information on carbohydrate specific alkoxy (C-O) and acetal moieties (O-C-O) as well as thiolate species attached to gold. Angle-resolved synchrotron XPS was used for chemical speciation at ultimate surface sensitivity. Angle-resolved XPS analysis suggests the presence of an excess top layer composed of unbound sulfur components combined with alkyl moieties. Further support for DMT attachment on Au is given by ToF-SIMS and FT-IR analysis. Carbon and oxygen K-edge NEXAFS spectra were interpreted by applying the building block model supported by comparison to data of 1-undecanethiol, poly(vinyl alcohol), and polyoxymethylene. No linear dichroism effect was observed in the angle-resolved C K-edge NEXAFS. © 2011 American Chemical Society

  18. An intelligent hybrid system for surface coal mine safety analysis

    Energy Technology Data Exchange (ETDEWEB)

    Lilic, N.; Obradovic, I.; Cvjetic, A. [University of Belgrade, Belgrade (Serbia)

    2010-06-15

    Analysis of safety in surface coal mines represents a very complex process. Published studies on mine safety analysis are usually based on research related to accidents statistics and hazard identification with risk assessment within the mining industry. Discussion in this paper is focused on the application of AI methods in the analysis of safety in mining environment. Complexity of the subject matter requires a high level of expert knowledge and great experience. The solution was found in the creation of a hybrid system PROTECTOR, whose knowledge base represents a formalization of the expert knowledge in the mine safety field. The main goal of the system is the estimation of mining environment as one of the significant components of general safety state in a mine. This global goal is subdivided into a hierarchical structure of subgoals where each subgoal can be viewed as the estimation of a set of parameters (gas, dust, climate, noise, vibration, illumination, geotechnical hazard) which determine the general mine safety state and category of hazard in mining environment. Both the hybrid nature of the system and the possibilities it offers are illustrated through a case study using field data related to an existing Serbian surface coal mine.

  19. Identification and validation of multiple cell surface markers of clinical-grade adipose-derived mesenchymal stromal cells as novel release criteria for good manufacturing practice-compliant production

    NARCIS (Netherlands)

    Camilleri, Emily T.; Gustafson, Michael P.; Dudakovic, Amel; Riester, Scott M.; Garces, Catalina Galeano; Paradise, Christopher R.; Takai, Hideki; Karperien, Marcel; Cool, Simon; Sampen, Hee Jeong Im; Larson, A. Noelle; Qu, Wenchun; Smith, Jay; Dietz, Allan B.; van Wijnen, Andre J.

    2016-01-01

    Background: Clinical translation of mesenchymal stromal cells (MSCs) necessitates basic characterization of the cell product since variability in biological source and processing of MSCs may impact therapeutic outcomes. Although expression of classical cell surface markers (e.g., CD90, CD73, CD105,

  20. Subdivisions of the adult zebrafish pallium based on molecular marker analysis [version 2; referees: 2 approved, 1 approved with reservations

    Directory of Open Access Journals (Sweden)

    Julia Ganz

    2015-11-01

    Full Text Available Background: The telencephalon shows a remarkable structural diversity among vertebrates. In particular, the everted telencephalon of ray-finned fishes has a markedly different morphology compared to the evaginated telencephalon of all other vertebrates. This difference in development has hampered the comparison between different areas of the pallium of ray-finned fishes and the pallial nuclei of all other vertebrates. Various models of homology between pallial subdivisions in ray-finned fishes and the pallial nuclei in tetrapods have been proposed based on connectional, neurochemical, gene expression and functional data. However, no consensus has been reached so far. In recent years, the analysis of conserved developmental marker genes has assisted the identification of homologies for different parts of the telencephalon among several tetrapod species. Results: We have investigated the gene expression pattern of conserved marker genes in the adult zebrafish (Danio rerio pallium to identify pallial subdivisions and their homology to pallial nuclei in tetrapods. Combinatorial expression analysis of ascl1a, eomesa, emx1, emx2, emx3, and Prox1 identifies four main divisions in the adult zebrafish pallium. Within these subdivisions, we propose that Dm is homologous to the pallial amygdala in tetrapods and that the dorsal subdivision of Dl is homologous to part of the hippocampal formation in mouse. We have complemented this analysis be examining the gene expression of emx1, emx2 and emx3 in the zebrafish larval brain. Conclusions: Based on our gene expression data, we propose a new model of subdivisions in the adult zebrafish pallium and their putative homologies to pallial nuclei in tetrapods. Pallial nuclei control sensory, motor, and cognitive functions, like memory, learning and emotion. The identification of pallial subdivisions in the adult zebrafish and their homologies to pallial nuclei in tetrapods will contribute to the use of the zebrafish

  1. Genetic diversity analysis of cyanogenic potential (CNp) of root among improved genotypes of cassava using simple sequence repeat markers.

    Science.gov (United States)

    Moyib, O K; Mkumbira, J; Odunola, O A; Dixon, A G

    2012-12-01

    Cyanogenic potential (CNp) of cassava constitutes a serious problem for over 500 million people who rely on the crop as their main source of calories. Genetic diversity is a key to successful crop improvement for breeding new improved variability for target traits. Forty-three improved genotypes of cassava developed by International Institute of Tropical Agriculture (ITA), Ibadan, were characterized for CNp trait using 35 Simple Sequence.Repeat (SSR) markers. Essential colorimetry picric test was used for evaluation of CNp on a color scale of 1 to 14. The CNp scores obtained ranged from 3 to 9, with a mean score of 5.48 (+/- 0.09) based on Statistical Analysis System (SAS) package. TMS M98/ 0068 (4.0 +/- 0.25) was identified as the best genotype with low CNp while TMS M98/0028 (7.75 +/- 0.25) was the worst. The 43 genotypes were assigned into 7 phenotypic groups based on rank-sum analysis in SAS. Dissimilarity analysis representatives for windows generated a phylogenetic tree with 5 clusters which represented hybridizing groups. Each of the clusters (except 4) contained low CNp genotypes that could be used for improving the high CNp genotypes in the same or near cluster. The scatter plot of the genotypes showed that there was little or no demarcation for phenotypic CNp groupings in the molecular groupings. The result of this study demonstrated that SSR markers are powerful tools for the assessment of genetic variability, and proper identification and selection of parents for genetic improvement of low CNp trait among the IITA cassava collection.

  2. Semiautomated quantitative image analysis of glomerular immunohistochemistry markers desmin, vimentin, podocin, synaptopodin and WT-1 in acute and chronic rat kidney disease models.

    Science.gov (United States)

    Funk, J; Ott, V; Herrmann, A; Rapp, W; Raab, S; Riboulet, W; Vandjour, A; Hainaut, E; Benardeau, A; Singer, T; Jacobsen, B

    2016-03-01

    Five different glomerular immunohistochemistry markers were evaluated and compared in four different acute and chronic rat kidney disease models. Progression of glomerular or podocyte damage was shown in the puromycin aminonucleoside nephrosis (PAN) and Zucker fatty/spontaneously hypertensive heart failure F1 hybrid (ZSF1) rat model. Progression and prevention of glomerular damage was demonstrated in the Zucker diabetic fatty (ZDF) and Dahl salt-sensitive (Dahl SS) rat. Immunohistochemistry was performed for desmin, vimentin, podocin, synaptopodin and Wilms tumor protein-1 (WT-1), and evaluation of glomerular immunohistochemistry markers was done by semiautomated quantitative image analysis. We found desmin and WT-1 as the most sensitive markers for podocyte damage in both acute and chronic glomerular damage followed by vimentin, podocin and synaptopodin. We were able to demonstrate that early podocyte damage as shown by increased desmin and vimentin staining together with either a phenotypic podocyte change or podocyte loss (reduced numbers of WT-1-stained podocytes) drives the progression of glomerular damage. This is followed by a reduction in podocyte-specific proteins such as podocin and synaptopodin. Our report describes the different sensitivity of glomerular or podocyte markers and gives future guidance for the selection of the most sensitive markers for efficacy testing of new drugs as well as for the selection of tissue-based toxicity markers for glomerular or podocyte injury. In addition to functional clinical chemistry markers, desmin and WT-1 immunohistochemistry offers reliable and valuable data on the morphologic state of podocytes.

  3. Surface proteome analysis and characterization of surface cell antigen (Sca or autotransporter family of Rickettsia typhi.

    Directory of Open Access Journals (Sweden)

    Khandra T Sears

    Full Text Available Surface proteins of the obligate intracellular bacterium Rickettsia typhi, the agent of murine or endemic typhus fever, comprise an important interface for host-pathogen interactions including adherence, invasion and survival in the host cytoplasm. In this report, we present analyses of the surface exposed proteins of R. typhi based on a suite of predictive algorithms complemented by experimental surface-labeling with thiol-cleavable sulfo-NHS-SS-biotin and identification of labeled peptides by LC MS/MS. Further, we focus on proteins belonging to the surface cell antigen (Sca autotransporter (AT family which are known to be involved in rickettsial infection of mammalian cells. Each species of Rickettsia has a different complement of sca genes in various states; R. typhi, has genes sca1 thru sca5. In silico analyses indicate divergence of the Sca paralogs across the four Rickettsia groups and concur with previous evidence of positive selection. Transcripts for each sca were detected during infection of L929 cells and four of the five Sca proteins were detected in the surface proteome analysis. We observed that each R. typhi Sca protein is expressed during in vitro infections and selected Sca proteins were expressed during in vivo infections. Using biotin-affinity pull down assays, negative staining electron microscopy, and flow cytometry, we demonstrate that the Sca proteins in R. typhi are localized to the surface of the bacteria. All Scas were detected during infection of L929 cells by immunogold electron microscopy. Immunofluorescence assays demonstrate that Scas 1-3 and 5 are expressed in the spleens of infected Sprague-Dawley rats and Scas 3, 4 and 5 are expressed in cat fleas (Ctenocephalides felis. Sca proteins may be crucial in the recognition and invasion of different host cell types. In short, continuous expression of all Scas may ensure that rickettsiae are primed i to infect mammalian cells should the flea bite a host, ii to remain

  4. Moessbauer backscattering spectrometer for mineralogical analysis of the Mars surface

    International Nuclear Information System (INIS)

    Klingelhoefer, G.; Foh, J.; Held, P.; Jaeger, H.; Kankeleit, E.; Teucher, R.

    1992-01-01

    A Moessbauer spectrometer for the mineralogical analysis of the Mars surface is under development. This instrument will be installed on a Mars-Rover, included in the Soviet Union Mars-94/96 Mars mission. Due to power and mass restrictions the electromechanical drive and the electronic components have been extremely miniaturized in comparison to standard systems. Solid state detectors (PIN-diodes) are used for γ- and x-ray detection. The whole spectrometer is controlled by a microprocessor (transputer). An additional application as X-ray fluorescence spectrometer is proposed. (orig.)

  5. Transcriptome Analysis Reveals Markers of Aberrantly Activated Innate Immunity in Vitiligo Lesional and Non-Lesional Skin

    Science.gov (United States)

    Huang, Yuanshen; Wang, Yang; Yu, Jie; Gao, Min; Levings, Megan; Wei, Shencai; Zhang, Shengquan; Xu, Aie; Su, Mingwan; Dutz, Jan; Zhang, Xuejun; Zhou, Youwen

    2012-01-01

    Background Vitiligo is characterized by the death of melanocytes in the skin. This is associated with the presence of T cell infiltrates in the lesional borders. However, at present, there is no detailed and systematic characterization on whether additional cellular or molecular changes are present inside vitiligo lesions. Further, it is unknown if the normal appearing non-lesional skin of vitiligo patients is in fact normal. The purpose of this study is to systematically characterize the molecular and cellular characteristics of the lesional and non-lesional skin of vitiligo patients. Methods and Materials Paired lesional and non-lesional skin biopsies from twenty-three vitiligo patients and normal skin biopsies from sixteen healthy volunteers were obtained with informed consent. The following aspects were analyzed: (1) transcriptome changes present in vitiligo skin using DNA microarrays and qRT-PCR; (2) abnormal cellular infiltrates in vitiligo skin explant cultures using flow cytometry; and (3) distribution of the abnormal cellular infiltrates in vitiligo skin using immunofluorescence microscopy. Results Compared with normal skin, vitiligo lesional skin contained 17 genes (mostly melanocyte-specific genes) whose expression was decreased or absent. In contrast, the relative expression of 13 genes was up-regulated. The up-regulated genes point to aberrant activity of the innate immune system, especially natural killer cells in vitiligo. Strikingly, the markers of heightened innate immune responses were also found to be up-regulated in the non-lesional skin of vitiligo patients. Conclusions and Clinical Implications As the first systematic transcriptome characterization of the skin in vitiligo patients, this study revealed previously unknown molecular markers that strongly suggest aberrant innate immune activation in the microenvironment of vitiligo skin. Since these changes involve both lesional and non-lesional skin, our results suggest that therapies targeting

  6. Transcriptome analysis reveals markers of aberrantly activated innate immunity in vitiligo lesional and non-lesional skin.

    Directory of Open Access Journals (Sweden)

    Richard Yu

    Full Text Available BACKGROUND: Vitiligo is characterized by the death of melanocytes in the skin. This is associated with the presence of T cell infiltrates in the lesional borders. However, at present, there is no detailed and systematic characterization on whether additional cellular or molecular changes are present inside vitiligo lesions. Further, it is unknown if the normal appearing non-lesional skin of vitiligo patients is in fact normal. The purpose of this study is to systematically characterize the molecular and cellular characteristics of the lesional and non-lesional skin of vitiligo patients. METHODS AND MATERIALS: Paired lesional and non-lesional skin biopsies from twenty-three vitiligo patients and normal skin biopsies from sixteen healthy volunteers were obtained with informed consent. The following aspects were analyzed: (1 transcriptome changes present in vitiligo skin using DNA microarrays and qRT-PCR; (2 abnormal cellular infiltrates in vitiligo skin explant cultures using flow cytometry; and (3 distribution of the abnormal cellular infiltrates in vitiligo skin using immunofluorescence microscopy. RESULTS: Compared with normal skin, vitiligo lesional skin contained 17 genes (mostly melanocyte-specific genes whose expression was decreased or absent. In contrast, the relative expression of 13 genes was up-regulated. The up-regulated genes point to aberrant activity of the innate immune system, especially natural killer cells in vitiligo. Strikingly, the markers of heightened innate immune responses were also found to be up-regulated in the non-lesional skin of vitiligo patients. CONCLUSIONS AND CLINICAL IMPLICATIONS: As the first systematic transcriptome characterization of the skin in vitiligo patients, this study revealed previously unknown molecular markers that strongly suggest aberrant innate immune activation in the microenvironment of vitiligo skin. Since these changes involve both lesional and non-lesional skin, our results suggest that

  7. Genome analysis and DNA marker-based characterisation of pathogenic trypanosomes

    NARCIS (Netherlands)

    Agbo, Edwin Chukwura

    2003-01-01

    The advances in genomics technologies and genome analysis methods that offer new leads for accelerating discovery of putative targets for developing overall control tools are reviewed in Chapter 1. In Chapter 2, a PCR typing method based on restriction fragment length polymorphism analysis of the

  8. Identification of Cell Surface Targets through Meta-analysis of Microarray Data

    Directory of Open Access Journals (Sweden)

    Henry Haeberle

    2012-07-01

    Full Text Available High-resolution image guidance for resection of residual tumor cells would enable more precise and complete excision for more effective treatment of cancers, such as medulloblastoma, the most common pediatric brain cancer. Numerous studies have shown that brain tumor patient outcomes correlate with the precision of resection. To enable guided resection with molecular specificity and cellular resolution, molecular probes that effectively delineate brain tumor boundaries are essential. Therefore, we developed a bioinformatics approach to analyze micro-array datasets for the identification of transcripts that encode candidate cell surface biomarkers that are highly enriched in medulloblastoma. The results identified 380 genes with greater than a two-fold increase in the expression in the medulloblastoma compared with that in the normal cerebellum. To enrich for targets with accessibility for extracellular molecular probes, we further refined this list by filtering it with gene ontology to identify genes with protein localization on, or within, the plasma membrane. To validate this meta-analysis, the top 10 candidates were evaluated with immunohistochemistry. We identified two targets, fibrillin 2 and EphA3, which specifically stain medulloblastoma. These results demonstrate a novel bioinformatics approach that successfully identified cell surface and extracellular candidate markers enriched in medulloblastoma versus adjacent cerebellum. These two proteins are high-value targets for the development of tumor-specific probes in medulloblastoma. This bioinformatics method has broad utility for the identification of accessible molecular targets in a variety of cancers and will enable probe development for guided resection.

  9. Microsatellite marker analysis reveals the complex phylogeographic history of Rhododendron ferrugineum (Ericaceae in the Pyrenees.

    Directory of Open Access Journals (Sweden)

    Olivia Charrier

    Full Text Available Genetic variation within plant species is determined by a number of factors such as reproductive mode, breeding system, life history traits and climatic events. In alpine regions, plants experience heterogenic abiotic conditions that influence the population's genetic structure. The aim of this study was to investigate the genetic structure and phylogeographic history of the subalpine shrub Rhododendron ferrugineum across the Pyrenees and the links between the populations in the Pyrenees, the Alps and Jura Mountains. We used 27 microsatellite markers to genotype 645 samples from 29 Pyrenean populations, three from the Alps and one from the Jura Mountains. These data were used to estimate population genetics statistics such as allelic richness, observed heterozygosity, expected heterozygosity, fixation index, inbreeding coefficient and number of migrants. Genetic diversity was found to be higher in the Alps than in the Pyrenees suggesting colonization waves from the Alps to the Pyrenees. Two separate genetic lineages were found in both the Alps and Pyrenees, with a substructure of five genetic clusters in the Pyrenees where a loss of genetic diversity was noted. The strong differentiation among clusters is maintained by low gene flow across populations. Moreover, some populations showed higher genetic diversity than others and presented rare alleles that may indicate the presence of alpine refugia. Two lineages of R. ferrugineum have colonized the Pyrenees from the Alps. Then, during glaciation events R. ferrugineum survived in the Pyrenees in different refugia such as lowland refugia at the eastern part of the chain and nunataks at high elevations leading to a clustered genetic pattern.

  10. The Analysis of Pandanus Relationship of Purwodadi Botanical Garden Collections Based on Morphological Character and Molecular Marker (trnL and trnL-F

    Directory of Open Access Journals (Sweden)

    Risca Adiyani Rachma

    2017-10-01

    Full Text Available The morphological characteristics of plant vegetative organ has the potential to be the defining factor of pandanus family collection at Purwodadi Botanical Garden (PBG. However, the information is not enough to confirm the identity of pandanus at the type-level. This problem happened at the collection of PBG. It is an urgent issue considering PBG as one of the most important ex-situ plant conservation institute that also has function as a study source for plant taxonomy science in Indonesia. Therefore, the use of molecular technology analysis using molecular marker (primer is incredibly important to identify the member of pandanus family by identifying its family relationship pattern. This information was expected to give a clarity about the identity of Pandanus family at PBG which will support further research and activity for pandanus conservation. The plant sample includes 16 specimens of pandanus with one member of the family from Freycinetia as the outgroup. Morphological analysis of the 50 characteristics of vegetative organs (leaf, stem, and root was conducted. Molecular analysis of DNA using primer of trnL and trnL-F. The data sequence as a result of the analysis was then tested using homology test with BLAST. All of the DNA sequence was paralleled using Clustal W analysis, the tree construction relationship was analysed using Maximum Parsimony (MP method with MEGA 6.0 program. The results of morphological studies showed the character vegetative that is the position of the spines on the leaves, the shape of apex leaf and the condition of the root surface above the soil. Molecularly, appears 1 new genera that has not been previously identified by PBG researcher is Benstonea.

  11. Surface recombination analysis in silicon-heterojunction solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Barrio, R.; Gandia, J.J.; Carabe, J.; Gonzalez, N.; Torres, I. [CIEMAT, Madrid (Spain); Munoz, D.; Voz, C. [Universitat Politecnica de Catalunya, Barcelona (Spain)

    2010-02-15

    The origin of this work is the understanding of the correlation observed between efficiency and emitter-deposition temperature in single silicon-heterojunction solar cells prepared by depositing an n-doped hydrogenated-amorphous-silicon thin film onto a p-type crystalline-silicon wafer. In order to interpret these results, surface-recombination velocities have been determined by two methods, i.e. by fitting the current-voltage characteristics to a theoretical model and by means of the Quasi-Steady-State Photoconductance Technique (QSSPC). In addition, effective diffusion lengths have been estimated from internal quantum efficiencies. The analysis of these data has led to conclude that the performance of the cells studied is limited by back-surface recombination rather than by front-heterojunction quality. A 12%-efficient cell has been prepared by combining optimum emitter-deposition conditions with back-surface-field (BSF) formation by vacuum annealing of the back aluminium contact. This result has been achieved without using any transparent conductive oxide. (author)

  12. Thermal Desorption Analysis of Effective Specific Soil Surface Area

    Science.gov (United States)

    Smagin, A. V.; Bashina, A. S.; Klyueva, V. V.; Kubareva, A. V.

    2017-12-01

    A new method of assessing the effective specific surface area based on the successive thermal desorption of water vapor at different temperature stages of sample drying is analyzed in comparison with the conventional static adsorption method using a representative set of soil samples of different genesis and degree of dispersion. The theory of the method uses the fundamental relationship between the thermodynamic water potential (Ψ) and the absolute temperature of drying ( T): Ψ = Q - aT, where Q is the specific heat of vaporization, and a is the physically based parameter related to the initial temperature and relative humidity of the air in the external thermodynamic reservoir (laboratory). From gravimetric data on the mass fraction of water ( W) and the Ψ value, Polyanyi potential curves ( W(Ψ)) for the studied samples are plotted. Water sorption isotherms are then calculated, from which the capacity of monolayer and the target effective specific surface area are determined using the BET theory. Comparative analysis shows that the new method well agrees with the conventional estimation of the degree of dispersion by the BET and Kutilek methods in a wide range of specific surface area values between 10 and 250 m2/g.

  13. Static stability analysis of embedded flexoelectric nanoplates considering surface effects

    Science.gov (United States)

    Ebrahimi, Farzad; Barati, Mohammad Reza

    2017-10-01

    In this paper, electromechanical buckling behavior of size-dependent flexoelectric nanoplates is investigated based on nonlocal and surface elasticity theories. Flexoelectricity represents the coupling between strain gradients and electrical polarizations. Flexoelectric nanoplates can tolerate higher buckling loads compared with conventional piezoelectric nanoplates, especially at lower thicknesses. The flexoelectric nanoplate is in contact with a two-parameter elastic foundation, which consists of infinite linear springs and a shear layer. Nonlocal elasticity theory of Eringen is applied in the analysis of flexoelectric nanoplates for the first time. The residual surface stresses which are usually neglected in the modeling of flexoelectric nanoplates are incorporated into nonlocal elasticity to provide better understanding of the physics of the problem. Applying an analytical solution which satisfies various boundary conditions, the governing equations obtained from Hamilton's principle are solved. The reliability of the present approach is verified by comparing the obtained results with those provided in literature. Finally, the influences of nonlocal parameter, surface effect, plate geometrical parameters, elastic foundation and boundary conditions on the buckling characteristics of flexoelectric nanoplates are explored.

  14. Surface analysis in steel nitrides by using Moessbauer spectroscopy

    International Nuclear Information System (INIS)

    Figueiredo, R.S. de.

    1991-07-01

    The formation of iron nitride layer at low temperatures, 600-700 K, by Moessbauer spectroscopy is studied. These layers were obtained basically through two different processes: ion nitriding and ammonia gas nitriding. A preliminary study about post-discharge nitriding was made using discharge in hollow cathode as well as microwave excitation. The assembly of these chambers is also described. The analysis of the nitrided samples was done by CEMS and CXMS, aided by optical microscopy, and the CEMS and CXMS detectors were constructed by ourselves. We also made a brief study about these detectors, testing as acetone as the mixture 80% He+10% C H 4 as detection gases for the use of CEMS. The surface analysis of the samples showed that in the ammonia gas process nitriding the nitrided layer starts by the superficial formation of an iron nitride rich nitrogen. By thermal evolution this nitride promotes the diffusion of nitrogen and the formation of other more stable nitrides. (author)

  15. Genetic diversity analysis of Amomum tsao-ko in Jinping County of Yunnan Province using SSR markers

    Science.gov (United States)

    Ma, Mengli; Wang, Tiantao; Lei, En; Meng, Hengling; Xie, Linyan; Zhu, Kunlong; Duan, Shaoze; Li, Wenqiang; Lu, Bingyue

    2017-08-01

    Genetic diversity analysis is very important for germplasm resources conservation and utilization. The objective of this study was to assess the genetic diversity among 44 individuals of Amomum tsao-ko from Jinping County of Yunnan Province using 5 selected SSR (simple sequence repeat) markers. A total of 23 polymorphic loci were detected among these germplasms, with an average of 4.6 polymorphic loci per SSR primer combination. The percentage of polymorphic loci was 100%, whereas the mean effective number of alleles (Ne), observed heterozygosity(Ho), expected heterozygosity (He), Shannon's information index (I), and the mean polymorphism information content (PIC) were 3. 410, 0. 491, 0. 679, 1.266 and 0. 672, respectively, indicating that the Amomum tsao-ko germplasms from Jinping County had high genetic diversity.

  16. Comparative analysis of chromosomal localization of ribosomal and telomeric DNA markers in three species of Pyrgomorphidae grasshoppers.

    Science.gov (United States)

    Buleu, Olesya G; Jetybayev, Ilyas Y; Bugrov, Alexander G

    2017-01-01

    The karyotypes of three species of Pyrgomorphidae grasshoppers were studied: Zonocerus elegans (Thunberg, 1815), Pyrgomorpha guentheri (Burr, 1899) and Atractomorpha lata (Mochulsky, 1866). Data on karyotypes of P. guentheri and Z. elegans are reported here for the first time. All species have karyotypes consisting of 19 acrocentric chromosomes in males and 20 acrocentric chromosomes in females (2n♂=19, NF=19; 2n♀=20, NF=20) and X0/XX sex determination system. A comparative analysis of the localization of C-heterochromatin, clusters of ribosomal DNA, and telomere repeats revealed inter-species diversity in these cytogenetic markers. These differences indicate that the karyotype divergence in the species studied is not associated with structural chromosome rearrangements, but with the evolution of repeated DNA sequences.

  17. Comparative analysis of chromosomal localization of ribosomal and telomeric DNA markers in three species of Pyrgomorphidae grasshoppers

    Directory of Open Access Journals (Sweden)

    Olesya G. Buleu

    2017-09-01

    Full Text Available The karyotypes of three species of Pyrgomorphidae grasshoppers were studied: Zonocerus elegans (Thunberg, 1815, Pyrgomorpha guentheri (Burr, 1899 and Atractomorpha lata (Mochulsky, 1866. Data on karyotypes of P. guentheri and Z. elegans are reported here for the first time. All species have karyotypes consisting of 19 acrocentric chromosomes in males and 20 acrocentric chromosomes in females (2n♂=19, NF=19; 2n♀=20, NF=20 and X0/XX sex determination system. A comparative analysis of the localization of C-heterochromatin, clusters of ribosomal DNA, and telomere repeats revealed inter-species diversity in these cytogenetic markers. These differences indicate that the karyotype divergence in the species studied is not associated with structural chromosome rearrangements, but with the evolution of repeated DNA sequences.

  18. Markers of subclinical atherosclerosis in patients with aortic valve sclerosis: A meta-analysis of literature studies.

    Science.gov (United States)

    Di Minno, Matteo Nicola Dario; Di Minno, Alessandro; Songia, Paola; Ambrosino, Pasquale; Gripari, Paola; Ravani, Alessio; Pepi, Mauro; Rubba, Paolo Osvaldo; Medda, Emanuela; Tremoli, Elena; Baldassarre, Damiano; Poggio, Paolo

    2016-11-15

    Growing evidence suggested an association between aortic valve sclerosis (AVSc) and cardiovascular (CV) events. However, little is known about the association of AVSc with major markers of subclinical atherosclerosis. We performed a meta-analysis of literature studies to address this issue. Studies on the relationship between AVSc and common carotid artery intima-media thickness (IMT), prevalence of carotid plaques (CPs), flow-mediated dilation (FMD), aortic pulse wave velocity (PWV) and augmentation index (AIx) were systematically searched in electronic databases. Thirteen studies enrolling 1086 AVSc patients and 2124 controls were included. Compared to controls, AVSc patients showed higher IMT (MD: 0.32mm; 95%CI: 0.07, 0.58; p=0.014), and higher prevalence of CPs (OR: 4.06; 95%CI: 2.38, 6.93; patherosclerosis, thus supporting the concept that AVSc and atherosclerosis share common etiopathological mechanism and/or risk factors. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  19. Quantitative and pattern recognition analysis of five marker compounds in Raphani semen using high-performance liquid chromatography

    Energy Technology Data Exchange (ETDEWEB)

    Jung, Yeon Woo; Lee, Joo Sang; Zhao, Bing Tian; Woo, Mi Hee; Min, Byung Sun [College of Pharmacy, Drug Research and Development Center, Catholic University of Daegu, Gyeongsan (Korea, Republic of); Kim, Jeong Ah [College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu (Korea, Republic of); Eun, Rhan Woo [College of Pharmacy, Chosun University, Gwangju (Korea, Republic of)

    2015-09-15

    A rapid and simple high-performance liquid chromatography (HPLC)-photodiode array (PDA) analytical method was developed for the quantitative analysis of Raphani Semen (RS). This method was successfully used to determine the five main phenolic compounds found in RS specimens from different production regions. The compounds included sinapine thiocyanate (1), β-d-fructofuranosyl-α-d-(6-O-sinapoyl)-glucopyranoside (2), isorhamnetin 3,4′-di-O-β-d-glucoside (3), β-d-(3-O-sinapoyl)-fructofuranosyl-α-d-(6-O-sinapoyl)-glucopyranoside (4), and β-d-(3,4-O-disinapoyl)-fructofuranosyl-α-d-(6-O-sinapoyl)-glucopyranoside (5). The marker compounds were separated using an Agilent Eclipse XDB-C18 column (5.0 µm, 150 × 4.6 mm i.d.) by gradient elution with acetonitrile/water/0.1% trifluoroacetic acid (TFA) as the mobile phase (flow rate, 1.0 mL/min). This method was fully validated with respect to linearity, precision, accuracy, stability, and robustness. The HPLC analytical method was validated to conduct a pattern recognition analysis by repeatedly analyzing 56 seed samples including 55 RS (C01–C49 and K50–K55) and 1 Brassicae Semen samples. In addition, a content standard for RS was proposed. Compounds 1 and 4 were revealed as major components in the HPLC chromatogram, and their contents ranged from 0.06 to 0.20 and 0.02 to 0.35 mg/g, respectively. These results demonstrate the successful development of an analytical method suitable for evaluating the quality and distinguishing the origin of RS. In addition, we briefly describe the crucial liquid chromatography-tandem mass spectrometry (LC-MS/MS) analytical conditions for the precise simultaneous quantification of the marker compounds.

  20. Analysis of expressed sequence tags from Prunus mume flower and fruit and development of simple sequence repeat markers

    Directory of Open Access Journals (Sweden)

    Gao Zhihong

    2010-07-01

    Full Text Available Abstract Background Expressed Sequence Tag (EST has been a cost-effective tool in molecular biology and represents an abundant valuable resource for genome annotation, gene expression, and comparative genomics in plants. Results In this study, we constructed a cDNA library of Prunus mume flower and fruit, sequenced 10,123 clones of the library, and obtained 8,656 expressed sequence tag (EST sequences with high quality. The ESTs were assembled into 4,473 unigenes composed of 1,492 contigs and 2,981 singletons and that have been deposited in NCBI (accession IDs: GW868575 - GW873047, among which 1,294 unique ESTs were with known or putative functions. Furthermore, we found 1,233 putative simple sequence repeats (SSRs in the P. mume unigene dataset. We randomly tested 42 pairs of PCR primers flanking potential SSRs, and 14 pairs were identified as true-to-type SSR loci and could amplify polymorphic bands from 20 individual plants of P. mume. We further used the 14 EST-SSR primer pairs to test the transferability on peach and plum. The result showed that nearly 89% of the primer pairs produced target PCR bands in the two species. A high level of marker polymorphism was observed in the plum species (65% and low in the peach (46%, and the clustering analysis of the three species indicated that these SSR markers were useful in the evaluation of genetic relationships and diversity between and within the Prunus species. Conclusions We have constructed the first cDNA library of P. mume flower and fruit, and our data provide sets of molecular biology resources for P. mume and other Prunus species. These resources will be useful for further study such as genome annotation, new gene discovery, gene functional analysis, molecular breeding, evolution and comparative genomics between Prunus species.

  1. Multivariate analysis of complex gene expression and clinical phenotypes with genetic marker data.

    Science.gov (United States)

    Beyene, Joseph; Tritchler, David; Bull, Shelley B; Cartier, Kevin C; Jonasdottir, Gudrun; Kraja, Aldi T; Li, Na; Nock, Nora L; Parkhomenko, Elena; Rao, J Sunil; Stein, Catherine M; Sutradhar, Rinku; Waaijenborg, Sandra; Wang, Ke-Sheng; Wang, Yuanjia; Wolkow, Pavel

    2007-01-01

    This paper summarizes contributions to group 12 of the 15th Genetic Analysis Workshop. The papers in this group focused on multivariate methods and applications for the analysis of molecular data including genotypic data as well as gene expression microarray measurements and clinical phenotypes. A range of multivariate techniques have been employed to extract signals from the multi-feature data sets that were provided by the workshop organizers. The methods included data reduction techniques such as principal component analysis and cluster analysis; latent variable models including structural equations and item response modeling; joint multivariate modeling techniques as well as multivariate visualization tools. This summary paper categorizes and discusses individual contributions with regard to multiple classifications of multivariate methods. Given the wide variety in the data considered, the objectives of the analysis and the methods applied, direct comparison of the results of the various papers is difficult. However, the group was able to make many interesting comparisons and parallels between the various approaches. In summary, there was a consensus among authors in group 12 that the genetic research community should continue to draw experiences from other fields such as statistics, econometrics, chemometrics, computer science and linear systems theory. (c) 2007 Wiley-Liss, Inc.

  2. Mediation analysis for logistic regression with interactions: Application of a surrogate marker in ophthalmology.

    Science.gov (United States)

    Jensen, Signe M; Hauger, Hanne; Ritz, Christian

    2018-01-01

    Mediation analysis is often based on fitting two models, one including and another excluding a potential mediator, and subsequently quantify the mediated effects by combining parameter estimates from these two models. Standard errors of such derived parameters may be approximated using the delta method. For a study evaluating a treatment effect on visual acuity, a binary outcome, we demonstrate how mediation analysis may conveniently be carried out by means of marginally fitted logistic regression models in combination with the delta method. Several metrics of mediation are estimated and results are compared to findings using existing methods.

  3. Tumors markers

    International Nuclear Information System (INIS)

    Yamaguchi-Mizumoto, N.H.

    1989-01-01

    In order to study blood and cell components alterations (named tumor markers) that may indicate the presence of a tumor, several methods are presented. Aspects as diagnostic, prognostic, therapeutic value and clinical evaluation are discussed. (M.A.C.)

  4. Tumor Markers

    Science.gov (United States)

    ... only a small number of people will test positive for the disease who do not have it—in other words, it will result in very few false-positive results. Although tumor markers are extremely useful in ...

  5. Bone Markers

    Science.gov (United States)

    ... and Iron-binding Capacity (TIBC, UIBC) Trichomonas Testing Triglycerides Troponin Tryptase Tumor Markers Uric Acid Urinalysis Urine ... Replacement or Calcium Supplementation. Journal of Clinical Endocrinology & Metabolism Vol. 82, No. 6 1904-1910, 1997. N. ...

  6. Mediation analysis for logistic regression with interactions: Application of a surrogate marker in ophthalmology

    DEFF Research Database (Denmark)

    Jensen, Signe Marie; Hauger, Hanne; Ritz, Christian

    2018-01-01

    method. For a study evaluating a treatment effect on visual acuity, a binary outcome, we demonstrate how mediation analysis may conveniently be carried out by means of marginally fitted logistic regression models in combination with the delta method. Several metrics of mediation are estimated and results...

  7. Mapping cellular hierarchy by single-cell analysis of the cell surface repertoire.

    Science.gov (United States)

    Guo, Guoji; Luc, Sidinh; Marco, Eugenio; Lin, Ta-Wei; Peng, Cong; Kerenyi, Marc A; Beyaz, Semir; Kim, Woojin; Xu, Jian; Das, Partha Pratim; Neff, Tobias; Zou, Keyong; Yuan, Guo-Cheng; Orkin, Stuart H

    2013-10-03

    Stem cell differentiation pathways are most often studied at the population level, whereas critical decisions are executed at the level of single cells. We have established a highly multiplexed, quantitative PCR assay to profile in an unbiased manner a panel of all commonly used cell surface markers (280 genes) from individual cells. With this method, we analyzed over 1,500 single cells throughout the mouse hematopoietic system and illustrate its utility for revealing important biological insights. The comprehensive single cell data set permits mapping of the mouse hematopoietic stem cell differentiation hierarchy by computational lineage progression analysis. Further profiling of 180 intracellular regulators enabled construction of a genetic network to assign the earliest differentiation event during hematopoietic lineage specification. Analysis of acute myeloid leukemia elicited by MLL-AF9 uncovered a distinct cellular hierarchy containing two independent self-renewing lineages with different clonal activities. The strategy has broad applicability in other cellular systems. Copyright © 2013 Elsevier Inc. All rights reserved.

  8. Genetic diversity and structure analysis in wild and landraces of barley from Jordan by using ISJ markers

    International Nuclear Information System (INIS)

    Baloch, A. W.; Balogh, M. J.; Baloch, M.; Baloch, I. A.

    2016-01-01

    The present experiment was carried out to estimate genetic diversity and genetic structure in cultivated and wild barley populations collected from Jordan which is considered as primary gene pool of barley. In a total, 94 cultivated barley accessions composed of 4 populations and 52 wild barley accessions consisted of 3 populations were used for genetic analysis using 7 Intron Splice Junction (ISJ) markers. The genetic diversity index (He) of cultivated barley ranged between 0.049 and 0.060; whereas that of wild barley populations ranged between 0.084 and 0.146, suggesting that wild resources of barley harbored greater genetic diversity than its domesticated counterpart, reflecting that barley domestication occurred with genetic bottleneck. Analysis of molecular variance showed high genetic variations among rather than within populations, referring that high genetic differentiation of barley populations caused by genetic and geographical separation of the populations in the harsh growing conditions of Fertile Crescent. Principal coordinate, clustering and structure analysis not only separated cultivated and wild barley, but also each single population, showing their genetic basis and original sample site. The obtained Results also revealed that there is lesser genetic communication between cultivated and wild barley under natural environments. The current findings can better be exploited for collection and utilization of plant germplasms. (author)

  9. Multicolor in situ hybridization and linkage analysis order Charcot-Marie-Tooth type I (CMTIA) gene-region markers

    Energy Technology Data Exchange (ETDEWEB)

    Lebo, R.V.; Lynch, E.D.; Golbus, M.S. (Univ. of California, San Francisco (United States)); Bird, T.D. (Univ. of Washington, Seattle (United States)); Barker, D.F.; O' Connell, P.; Chance, P.F. (Univ. of Utah, Salt Lake City (United States))

    1992-01-01

    This study demonstrates a clear and current role for multicolor in situ hybridization in expediting positional cloning studies of unknown disease genes. Nine polymorphic DNA cosmids have been mapped to eight ordered locations spanning the Charcot-Marie-Tooth type 1 (CMT1A) disease gene region in distal band 17p11.2, by multicolor in situ hybridization. When used with linkage analysis, these methods have generated a fine physical map and have firmly assigned the CMT1A gene to distal band 17p11.2. Linkage analysis with four CMT1A pedigrees mapped the CMT1A gene with respect to two flanking markers. Additional loci were physically mapped and ordered by in situ hybridization and analysis of phase-known recombinants in CMT1A pedigrees. These data demonstrate the ability of in situ hybridization to resolve loci within 0.5 Mb on early-metaphase chromosomes. Multicolor in situ hybridization also excluded the possibility of pericentric inversions in two unrelated patients with CMT1 and neurofibromatosis type 1. When used with pulsed-field gel electrophoresis, multicolor in situ hybridization can establish physical location, order, and distance in closely spaced chromosome loci.

  10. The origin of T cells in permanently reconstituted old athymic nude rats. Analysis using chromosome or allotype markers.

    Science.gov (United States)

    Bell, E B; Sparshott, S M; Drayson, M T; Hunt, S V

    1989-12-01

    Athymic PVG-rnu/rnu rats receiving a single intravenous injection of syngeneic euthymic thoracic duct lymphocytes (TDL) develop normal levels of CD4+ T lymphocytes and survive for more than 2 years in a conventional animal house. We investigated the origin of the T cells (and B cells) in reconstituted nude recipients by transferring TDL carrying either the 3T chromosome marker or the RT6b + Igk-1b allotype or the RT7b (leucocyte-common) allotype markers. Karyotype analysis of spleen and lymph node (LN) cells from 1- to 2-year-old PVG-3T/3T-reconstituted nude recipients, stimulated in vitro with phytohaemagglutinin (PHA), unexpectedly revealed that a majority (79-97%) of dividing cells were of nude origin. However, extensive nude cell division was also recorded in PHA-stimulated cultures using mixtures of euthymic (PVG-3T/3T) and unreconstituted nude spleen cells; the assumption that only T cells divide in PHA-stimulated cultures thus appears to be erroneous. In contrast to the karyotype analysis, sIg- RT6b+ LN cells obtained from nude recipients reconstituted 2 years earlier with PVG-RT6b allotype-marked TDL, were all of donor origin with no indication of a nude-derived sIg- RT6a+ population. Igk-1b+ donor B cells were not found in these same recipients. Dual fluorescence analysis of TDL from 18- to 20-month RT7b-reconstituted nudes showed that 91-100% of CD4+ cells were donor-derived. When tested functionally, sIg- RT7b+ (donor) cells, but not sIg- RT7b- (nude-derived) cells, were able to reject skin allografts and induce local graft-versus-host (GVH) responses. Donor T cells, in contrast to CD4+ cells of nude origin, divided extensively in nude recipients; FACS-purified RT7b+ (donor) TDL retransferred from 17-month primary reconstituted nude rats, expanded further (60-100-fold) in secondary nude recipients. In conclusion, only the donor-derived CD4+ cells in reconstituted nude rats displayed T-cell function; evidence to the contrary from karyotype analysis was

  11. Gas chromatography/trace analysis of derivatized azelaic acid as a stability marker.

    Science.gov (United States)

    Alzweiri, Muhammed; Tarawneh, Ruba; Khanfar, Mohammad A

    2013-10-01

    Azelaic acid, a naturally occurring saturated dicarboxylic acid, is found in many topical formulations for its various medical benefits or as a byproduct of the oxidative decomposition of unsaturated fatty acids. The poor volatility of azelaic acid hinders its applicability in GC analysis. Therefore, azelaic acid was derivatized by methylation and silylation procedures to enhance its volatility for GC analysis. Accordingly, dimethyl azelate (DMA) and di(trimethylsilyl) azelate were synthesized and characterized by GC-MS. Subsequently, a GC with flame ionization detection method was developed and validated to analyze trace amounts of azelaic acid in some marketed skin creams. Unlike DMA, di(trimethylsilyl) azelate was chemically unstable and degraded within few hours. Nonane was used as a stable internal standard. Variability due to derivatization and extraction was controlled by a standard addition procedure. DMA analysis was linear in a wide concentration range (100 ng/mL to 100 mg/mL). Moreover, the method was accurate (96.4-103.4%) and precise with inter- and intraday variability <2.0% and LOQ and LOD of 100 and 10 ng/mL, respectively. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Search for potential gastric cancer markers using miRNA databases and gene expression analysis.

    Science.gov (United States)

    Volkomorov, V; Grigoryeva, E; Krasnov, G; Litviakov, N; Tsyganov, M; Karbyshev, M; Zavyalova, M; Afanasуev, S; Cherdyntseva, N; Lisitsyn, N; Beresten, S

    2013-03-01

    The aim of this study was to identify genes that are differentially expressed in gastric tumors and to analyze the association of their expression level with tumor clinicopathologic features. In the present research, we used bioinformatic-driven search to identify miRNA that are down-regulated in gastric tumors and to find their potential targets. Then, the expression levels of some of the target mRNAs were investigated using reverse transcription polymerase chain reaction (RT-PCR) analysis. As a result of the bioinformatics analysis, fifteen genes were found to be potentially differentially expressed between the tumors and normal gastric tissue. Five of them were chosen for the further analysis (WNT4, FGF12, EFEMP1, CTGF, and HSPG2) due to their important role in cell proliferation and differentiation. Expression levels of these genes were evaluated in our collection of frozen tissue samples of gastric tumor and paired normal stomach epithelia. Increased FGF12 expression was observed in diffuse type of gastric cancer while WNT4 mRNA was found to be down-regulated in intestinal type of gastric cancer. Besides, CTGF gene overexpression was revealed in diffuse type of stomach cancer in comparison with that in intestinal type. Up-regulation of CTGF was also associated with lymph node metastasis. The findings show its expedient to perform further investigations in order to clarify diagnostic and prognostic value of CTGF, FGF12, and WNT4's in stomach cancer as well as the role of these genes in carcinogenesis.

  13. Global phylogeography with mixed-marker analysis reveals male-mediated dispersal in the endangered scalloped hammerhead shark (Sphyrna lewini.

    Directory of Open Access Journals (Sweden)

    Toby S Daly-Engel

    Full Text Available The scalloped hammerhead shark, Sphyrna lewini, is a large endangered predator with a circumglobal distribution, observed in the open ocean but linked ontogenetically to coastal embayments for parturition and juvenile development. A previous survey of maternal (mtDNA markers demonstrated strong genetic partitioning overall (global Φ(ST = 0.749 and significant population separations across oceans and between discontinuous continental coastlines.We surveyed the same global range with increased sample coverage (N = 403 and 13 microsatellite loci to assess the male contribution to dispersal and population structure. Biparentally inherited microsatellites reveal low or absent genetic structure across ocean basins and global genetic differentiation (F(ST = 0.035 over an order of magnitude lower than the corresponding measures for maternal mtDNA lineages (Φ(ST = 0.749. Nuclear allelic richness and heterozygosity are high throughout the Indo-Pacific, while genetic structure is low. In contrast, allelic diversity is low while population structure is higher for populations at the ends of the range in the West Atlantic and East Pacific.These data are consistent with the proposed Indo-Pacific center of origin for S. lewini, and indicate that females are philopatric or adhere to coastal habitats while males facilitate gene flow across oceanic expanses. This study includes the largest sampling effort and the most molecular loci ever used to survey the complete range of a large oceanic predator, and findings emphasize the importance of incorporating mixed-marker analysis into stock assessments of threatened and endangered shark species.

  14. Inter-simple sequence repeat (ISSR) marker analysis in Parkia timoriana (DC.) Merr. populations from Northeast India.

    Science.gov (United States)

    Thangjam, Robert

    2014-02-01

    Genetic variation in three populations of Parkia timoriana (DC.) Merr. grown in the Manipur state of northeast India was analysed using inter-simple sequence repeat (ISSR) markers. A total of 30 individual trees representing three populations were sampled and studied using 22 University of British Columbia (UBC set no. 9) primers in the present study. Of the total 22 primers, 19 primers produced distinct, reproducible and well-resolved fragments. Overall, a total number of 111 fragments were generated by the 19 primers and of which, 51 were polymorphic (45.94 %). The average number of loci and polymorphic loci generated per primer were 5.84 and 2.68, respectively. The genetic variation generated by ISSR markers within the three populations studied ranges from 33.33 to 18.92 %. The overall genetic differentiation (Gst) among populations was estimated to be 0.29, and the number of gene flow (Nm) was estimated to be 1.23 per generation between populations. Of the total genetic variance, 70.04 % was attributed to within-population diversity while 4.72 % differences to the among-populations. The genetic similarity across the individuals belonging to the three populations was represented by the dendrogram showing the grouping of the individuals into three major groups which is also supported by the principle component analysis. The present finding asserts the effectiveness of ISSR procedure for assessing genetic variations of P. timoriana populations and provides valuable genetic information that can be utilized for breeding and conservation strategies.

  15. Analysis of simple sequence repeats in the Gaeumannomyces graminis var. tritici genome and the development of microsatellite markers.

    Science.gov (United States)

    Li, Wei; Feng, Yanxia; Sun, Haiyan; Deng, Yuanyu; Yu, Hanshou; Chen, Huaigu

    2014-11-01

    Understanding the genetic structure of Gaeumannomyces graminis var. tritici is essential for the establishment of efficient disease control strategies. It is becoming clear that microsatellites, or simple sequence repeats (SSRs), play an important role in genome organization and phenotypic diversity, and are a large source of genetic markers for population genetics and meiotic maps. In this study, we examined the G. graminis var. tritici genome (1) to analyze its pattern of SSRs, (2) to compare it with other plant pathogenic filamentous fungi, such as Magnaporthe oryzae and M. poae, and (3) to identify new polymorphic SSR markers for genetic diversity. The G. graminis var. tritici genome was rich in SSRs; a total 13,650 SSRs have been identified with mononucleotides being the most common motifs. In coding regions, the densities of tri- and hexanucleotides were significantly higher than in noncoding regions. The di-, tri-, tetra, penta, and hexanucleotide repeats in the G. graminis var. tritici genome were more abundant than the same repeats in M. oryzae and M. poae. From 115 devised primers, 39 SSRs are polymorphic with G. graminis var. tritici isolates, and 8 primers were randomly selected to analyze 116 isolates from China. The number of alleles varied from 2 to 7 and the expected heterozygosity (He) from 0.499 to 0.837. In conclusion, SSRs developed in this study were highly polymorphic, and our analysis indicated that G. graminis var. tritici is a species with high genetic diversity. The results provide a pioneering report for several applications, such as the assessment of population structure and genetic diversity of G. graminis var. tritici.

  16. Response surface analysis to improve dispersed crude oil biodegradation

    Energy Technology Data Exchange (ETDEWEB)

    Zahed, Mohammad A.; Aziz, Hamidi A.; Mohajeri, Leila [School of Civil Engineering, Universiti Sains Malaysia, Nibong Tebal, Penang (Malaysia); Isa, Mohamed H. [Civil Engineering Department, Universiti Teknologi PETRONAS, Tronoh, Perak (Malaysia)

    2012-03-15

    In this research, the bioremediation of dispersed crude oil, based on the amount of nitrogen and phosphorus supplementation in the closed system, was optimized by the application of response surface methodology and central composite design. Correlation analysis of the mathematical-regression model demonstrated that a quadratic polynomial model could be used to optimize the hydrocarbon bioremediation (R{sup 2} = 0.9256). Statistical significance was checked by analysis of variance and residual analysis. Natural attenuation was removed by 22.1% of crude oil in 28 days. The highest removal on un-optimized condition of 68.1% were observed by using nitrogen of 20.00 mg/L and phosphorus of 2.00 mg/L in 28 days while optimization process exhibited a crude oil removal of 69.5% via nitrogen of 16.05 mg/L and phosphorus 1.34 mg/L in 27 days therefore optimization can improve biodegradation in shorter time with less nutrient consumption. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  17. XPS analysis of nanostructured materials and biological surfaces

    International Nuclear Information System (INIS)

    Baer, D.R.; Engelhard, M.H.

    2010-01-01

    This paper examines the types of information that XPS can provide about a variety of nanostructured materials. Although it is sometimes not considered a 'nanoscale analysis method,' XPS can provide a great deal of information about elemental distributions, layer or coating structure and thicknesses, surface functionality, and even particles sizes on the 1-20 nm scale for sample types that may not be readily analyzed by other methods. This information is important for both synthetic nanostructured or nanosized materials and a variety of natural materials with nanostructure. Although the links between nanostructure materials and biological systems may not at first be obvious, many biological molecules and some organisms are the sizes of nanoparticles. The nanostructure of cells and microbes plays a significant role in how they interact with their environment. The interaction of biomolecules with nanoparticles is important for medical and toxicity studies. The interaction of biomolecules is important for sensor function and many nanomaterials are now the active elements in sensors. This paper first discusses how nanostructures influences XPS data as a part of understanding how simple models of sample structure and data analysis can be used to extract information about the physical and chemical structures of the materials being analyzed. Equally important, aspects of sample and analysis limitations and challenges associated with understanding nanostructured materials are indicated. Examples of the application of XPS to nanostructured and biological systems and materials are provided.

  18. Monitoring regulatory T cells in clinical samples: consensus on an essential marker set and gating strategy for regulatory T cell analysis by flow cytometry.

    Science.gov (United States)

    Santegoets, Saskia J A M; Dijkgraaf, Eveline M; Battaglia, Alessandra; Beckhove, Philipp; Britten, Cedrik M; Gallimore, Awen; Godkin, Andrew; Gouttefangeas, Cecile; de Gruijl, Tanja D; Koenen, Hans J P M; Scheffold, Alexander; Shevach, Ethan M; Staats, Janet; Taskén, Kjetil; Whiteside, Theresa L; Kroep, Judith R; Welters, Marij J P; van der Burg, Sjoerd H

    2015-10-01

    Regulatory T cell (Treg)-mediated immunosuppression is considered a major obstacle for successful cancer immunotherapy. The association between clinical outcome and Tregs is being studied extensively in clinical trials, but unfortunately, no consensus has been reached about (a) the markers and (b) the gating strategy required to define human Tregs in this context, making it difficult to draw final conclusions. Therefore, we have organized an international workshop on the detection and functional testing of Tregs with leading experts in the field, and 40 participants discussing different analyses and the importance of different markers and context in which Tregs were analyzed. This resulted in a rationally composed ranking list of "Treg markers". Subsequently, the proposed Treg markers were tested to get insight into the overlap/differences between the most frequently used Treg definitions and their utility for Treg detection in various human tissues. Here, we conclude that the CD3, CD4, CD25, CD127, and FoxP3 markers are the minimally required markers to define human Treg cells. Staining for Ki67 and CD45RA showed to provide additional information on the activation status of Tregs. The use of markers was validated in a series of PBMC from healthy donors and cancer patients, as well as in tumor-draining lymph nodes and freshly isolated tumors. In conclusion, we propose an essential marker set comprising antibodies to CD3, CD4, CD25, CD127, Foxp3, Ki67, and CD45RA and a corresponding robust gating strategy for the context-dependent analysis of Tregs by flow cytometry.

  19. SEM Analysis of Surface Impact on Biofilm Antibiotic Treatment.

    Science.gov (United States)

    Gomes, Luciana Calheiros; Mergulhão, Filipe José

    2017-01-01

    The aim of this work was to use scanning electron microscopy (SEM) to investigate the effect of ampicillin treatment on Escherichia coli biofilms formed on two surface materials with different properties, silicone (SIL) and glass (GLA). Epifluorescence microscopy (EM) was initially used to assess biofilm formation and killing efficiency on both surfaces. This technique showed that higher bacterial colonization was obtained in the hydrophobic SIL than in the hydrophilic GLA. It has also shown that higher biofilm inactivation was attained for GLA after the antibiotic treatment (7-log reduction versus 1-log reduction for SIL). Due to its high resolution and magnification, SEM enabled a more detailed analysis of the antibiotic effect on biofilm cells, complementing the killing efficiency information obtained by EM. SEM micrographs revealed that ampicillin-treated cells have an elongated form when compared to untreated cells. Additionally, it has shown that different materials induced different levels of elongation on cells exposed to antibiotic. Biofilms formed on GLA showed a 37% higher elongation than those formed on SIL. Importantly, cell elongation was related to viability since ampicillin had a higher bactericidal effect on GLA-formed biofilms. These findings raise the possibility of using SEM for understanding the efficacy of antimicrobial treatments by observation of biofilm morphology.

  20. Proteomic analysis of the shistosome tegument and its surface membranes

    Directory of Open Access Journals (Sweden)

    Simon Braschi

    2006-10-01

    Full Text Available The tegument surface of the adult schistosome, bounded by a normal plasma membrane overlain by a secreted membranocalyx, holds the key to understanding how schistosomes evade host immune responses. Recent advances in mass spectrometry (MS, and the sequencing of the Schistosoma mansoni transcriptome/genome, have facilitated schistosome proteomics. We detached the tegument from the worm body and enriched its surface membranes by differential extraction, before subjecting the preparation to liquid chromatography-based proteomics to identify its constituents. The most exposed proteins on live worms were labelled with impearmeant biotinylation reagents, and we also developed methods to isolate the membranocalyx for analysis. We identified transporters for sugars, amino acids, inorganic ions and water, which confirm the importance of the tegument plasma membrane in nutrient acquisition and solute balance. Enzymes, including phosphohydrolases, esterases and carbonic anhydrase were located with their catalytic domains external to the plasma membrane, while five tetraspanins, annexin and dysferlin were implicated in membrane architecture. In contrast, few parasite proteins could be assigned to the membranocalyx but mouse immune response proteins, including three immunoglobulins and two complement factors, were detected, plus host membrane proteins such as CD44, integrin and a complement regulatory protein, testifying to the acquisitive properties of the secreted bilayer.

  1. Use of microsatellite markers in molecular analysis of segregating populations of papaya (Carica papaya L.) derived from backcrossing.

    Science.gov (United States)

    Pinto, F O; Pereira, M G; Luz, L N; Cardozo, D L; Ramos, H C C; Macedo, C M P

    2013-07-08

    Brazil is the world leader in papaya production. However, only a small number of cultivars are registered for commercial planting, mainly owing to delays in obtaining cultivars and the high costs of the field phase of breeding programs. These costs can be reduced when molecular tools are combined with conventional breeding methods. In the present study, we conducted a molecular analysis of a self-fertilized population of a first backcrossing generation of BC1S1 papaya plants via microsatellite markers both to monitor the level of homozygosity and the gene/allele transfer that confers the Golden trait (fruit color) and to assess the parental genomic proportion in the genotypes studied. Based on the analysis of 20 polymorphic microsatellite loci, 19 genotypes with the Golden trait belonging to BC1S1 were evaluated in addition to the parental genotypes. Genetic distance was estimated through weighted index. The genotypes were then grouped using the hierarchical nearest neighbor method, and the analysis of principal coordinates was used to measure the proportion of parental genomes in the segregating genotypes. The mean value of the inbreeding coefficient was 0.36. The analysis of the principal coordinates revealed that on average, 64% of the recurrent parent genome was present in the population. Together, the analyses allowed the selection of 3 individuals for the next backcross cycle (33BC1S1-18, 34BC1S1-16, and 37BC1S1-10). These individuals had a higher proportion of the recurrent parent and were grouped close to the recurrent parent in the cluster analysis.

  2. Hygrothermal analysis of surface layers of historical masonry

    Science.gov (United States)

    Kočí, Václav; Maděra, Jiří; Keppert, Martin; Černý, Robert

    2017-11-01

    The paper deals with the hygrothermal analysis of surface layers of historical masonry. Solid brick provided with a traditional and two modified lime-based plasters is studied. The heat and moisture transport in the envelope is induced by an exposure of the wall from the exterior side to dynamic climatic conditions of Olomouc, Czech Republic. The transport processes are described using diffusion type of mathematical model based on experimentally determined material properties. The computational results indicate that hygric transport and accumulation properties of exterior plasters affect the hygrothermal performance of the underlying solid brick in a very significant way, being able to regulate the amount of transported moisture. The modified lime plasters are not found generally superior to the traditional lime plasters in that respect. Therefore, their suitability for historical masonry should be assessed case by case, with a particular attention to the climatic conditions and to the properties of the load bearing structure.

  3. Analysis of MAGSAT and surface data of the Indian region

    Science.gov (United States)

    Agarwal, G. C. (Principal Investigator)

    1983-01-01

    Techniques and significant results of an analysis of MAGSAT and surface data of the Indian region are described. Specific investigative tasks included: (1) use of the multilevel data at different altitudes to develop a model for variation of magnetic anomaly with altitude; (2) development of the regional model for the description of main geomagnetic field for the Indian sub-continent using MAGSAT and observatory data; (3) development of regional mathematical model of secular variations over the Indian sub-continent; and (4) downward continuation of the anomaly field obtained from MAGSAT and its combination with the existing observatory data to produce a regional anomaly map for elucidating tectonic features of the Indian sub-continent.

  4. Evaluation of flyash surface phenomena and the application of surface analysis technology. Summary report: Phase I. [44 elements; 86 references

    Energy Technology Data Exchange (ETDEWEB)

    Smith, R.D.

    1981-06-01

    The factors governing the formation of flyash surfaces during and following coal combustion are reviewed. The competing chemical and physical processes during the evolution of inorganic material in coal during combustion into flyash are described with respect to various surface segregation processes. Two mechanisms leading to surface enrichment are volatilization-condensation processes and diffusion processes within individual flyash particles. The experimental evidence for each of these processes is reviewed. It is shown that the volatilization-condensation process is the major factor leading to trace element enrichment in smaller flyash particles. Evidence also exists from surface analyses of flyash and representative mineral matter that diffusion processes may lead to surface enrichment of elements not volatilized or cause transport of surface-condensed elements into the flyash matrix. The semiquantitative determination of the relative importance of these two processes can be determined by comparison of concentration versus particle size profiles with surface-depth profiles obtained using surface analysis techniques. A brief description of organic transformations on flyash surfaces is also presented. The various surface analytical techniques are reviewed and the relatively new technique of Static-Secondary Ion Mass Spectroscopy is suggested as having significant advantages in studies of surfaces and diffusion processes in model systems. Several recommendations are made for research relevant to flyash formation and processes occurring on flyash surfaces.

  5. Generation and analysis of ESTs from the eastern oyster, Crassostrea virginica Gmelin and identification of microsatellite and SNP markers

    Directory of Open Access Journals (Sweden)

    Wallace Richard

    2007-06-01

    Full Text Available Abstract Background The eastern oyster, Crassostrea virginica (Gmelin 1791, is an economically important species cultured in many areas in North America. It is also ecologically important because of the impact of its filter feeding behaviour on water quality. Populations of C. virginica have been threatened by overfishing, habitat degradation, and diseases. Through genome research, strategies are being developed to reverse its population decline. However, large-scale expressed sequence tag (EST resources have been lacking for this species. Efficient generation of EST resources from this species has been hindered by a high redundancy of transcripts. The objectives of this study were to construct a normalized cDNA library for efficient EST analysis, to generate thousands of ESTs, and to analyze the ESTs for microsatellites and potential single nucleotide polymorphisms (SNPs. Results A normalized and subtracted C. virginica cDNA library was constructed from pooled RNA isolated from hemocytes, mantle, gill, gonad and digestive tract, muscle, and a whole juvenile oyster. A total of 6,528 clones were sequenced from this library generating 5,542 high-quality EST sequences. Cluster analysis indicated the presence of 635 contigs and 4,053 singletons, generating a total of 4,688 unique sequences. About 46% (2,174 of the unique ESTs had significant hits (E-value ≤ 1e-05 to the non-redundant protein database; 1,104 of which were annotated using Gene Ontology (GO terms. A total of 35 microsatellites were identified from the ESTs, with 18 having sufficient flanking sequences for primer design. A total of 6,533 putative SNPs were also identified using all existing and the newly generated EST resources of the eastern oysters. Conclusion A high quality normalized cDNA library was constructed. A total of 5,542 ESTs were generated representing 4,688 unique sequences. Putative microsatellite and SNP markers were identified. These genome resources provide the

  6. Diagnostic value of tumor markers for lung adenocarcinoma-associated malignant pleural effusion: a validation study and meta-analysis.

    Science.gov (United States)

    Feng, Mei; Zhu, Jing; Liang, Liqun; Zeng, Ni; Wu, Yanqiu; Wan, Chun; Shen, Yongchun; Wen, Fuqiang

    2017-04-01

    Pleural effusion is one of the most common complications of lung adenocarcinoma and is diagnostically challenging. This study aimed to investigate the diagnostic performance of carcinoembryonic antigen (CEA), cytokeratin fragment (CYFRA) 21-1, and cancer antigen (CA) 19-9 for lung adenocarcinoma-associated malignant pleural effusion (MPE) through a validation study and meta-analysis. Pleural effusion samples were collected from 81 lung adenocarcinoma-associated MPEs and 96 benign pleural effusions. CEA, CYFRA 21-1, and CA19-9 were measured by electrochemiluminescence immunoassay. The capacity of tumor markers was assessed with receiver operating characteristic curve analyses and the area under the curve (AUC) was calculated. Standard methods for meta-analysis of diagnostic studies were used to summarize the diagnostic performance of CEA, CYFRA 21-1, and CA19-9 for lung adenocarcinoma-associated MPE. The pleural levels of CEA, CYFRA 21-1, and CA19-9 were significantly increased in lung adenocarcinoma-associated MPE compared to benign pleural effusion. The cut-off points for CEA, CYFRA 21-1, and CA19-9 were optimally set at 4.55 ng/ml, 43.10 μg/ml, and 12.89 U/ml, and corresponding AUCs were 0.93, 0.85, and 0.81, respectively. The combination of CEA, CYFRA 21-1, and CA19-9 increased the sensitivity to 95.06%, with an AUC of 0.95. Eight studies were included in this meta-analysis. CEA showed the best diagnostic performance with pooled sensitivity, specificity, positive/negative likelihood ratio, and diagnostic odds ratio of 0.75, 0.96, 16.01, 0.23, and 81.49, respectively. The AUC was 0.93. CEA, CYFRA 21-1, and CA19-9 play a role in the diagnosis of lung adenocarcinoma-associated MPE. The combination of these tumor markers increases the diagnostic accuracy.

  7. The genetic diversity and evolution of field pea (Pisum studied by high throughput retrotransposon based insertion polymorphism (RBIP marker analysis

    Directory of Open Access Journals (Sweden)

    Smýkal Petr

    2010-02-01

    Full Text Available Abstract Background The genetic diversity of crop species is the result of natural selection on the wild progenitor and human intervention by ancient and modern farmers and breeders. The genomes of modern cultivars, old cultivated landraces, ecotypes and wild relatives reflect the effects of these forces and provide insights into germplasm structural diversity, the geographical dimension to species diversity and the process of domestication of wild organisms. This issue is also of great practical importance for crop improvement because wild germplasm represents a rich potential source of useful under-exploited alleles or allele combinations. The aim of the present study was to analyse a major Pisum germplasm collection to gain a broad understanding of the diversity and evolution of Pisum and provide a new rational framework for designing germplasm core collections of the genus. Results 3020 Pisum germplasm samples from the John Innes Pisum germplasm collection were genotyped for 45 retrotransposon based insertion polymorphism (RBIP markers by the Tagged Array Marker (TAM method. The data set was stored in a purpose-built Germinate relational database and analysed by both principal coordinate analysis and a nested application of the Structure program which yielded substantially similar but complementary views of the diversity of the genus Pisum. Structure revealed three Groups (1-3 corresponding approximately to landrace, cultivar and wild Pisum respectively, which were resolved by nested Structure analysis into 14 Sub-Groups, many of which correlate with taxonomic sub-divisions of Pisum, domestication related phenotypic traits and/or restricted geographical locations. Genetic distances calculated between these Sub-Groups are broadly supported by principal coordinate analysis and these, together with the trait and geographical data, were used to infer a detailed model for the domestication of Pisum. Conclusions These data provide a clear picture

  8. Facial trauma as physical violence markers against elderly Brazilians: A comparative analysis between genders.

    Science.gov (United States)

    de Sousa, Rayanne Izabel Maciel; de Macedo Bernardino, Ítalo; Castro, Ricardo Dias; Cavalcanti, Alessandro Leite; Bento, Patricia Meira; d'Ávila, Sérgio

    2016-01-01

    The aim of this study was to characterize the profile of elderly Brazilians with injuries resulting from physical violence and identify victimization differences. A descriptive and exploratory study was conducted involving the analysis of medico-legal and social records of 259 elderly victims of physical violence treated at an Institute of Forensic Medicine and Dentistry over four years (from January 2008 to December 2011). The forensic service database was evaluated by researchers properly trained and calibrated to perform this function between January and March 2013. Socio-demographic variables of victims, aggression characteristics, aggressor's profile and types of lesions were evaluated. Descriptive and multivariate statistics using Multiple Correspondence Analysis (MCA) were performed. The prevalence of facial trauma was 42.9%. Based on the MCA results, two groups with different victimization profiles were identified: married men aged 70-79 years, victims of community violence at night, suffering facial injuries; and single, widowed or separated women aged 60-69 years, victims of domestic violence during the day, suffering trauma in other areas of the body. The results suggest that there is a high prevalence of facial injuries among elderly Brazilians victims of physical violence and there are important differences related to victimization characteristics according to gender. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  9. Combined Scintigraphy and Tumor Marker Analysis Predicts Unfavorable Histopathology of Neuroblastic Tumors with High Accuracy.

    Directory of Open Access Journals (Sweden)

    Wolfgang Peter Fendler

    Full Text Available Our aim was to improve the prediction of unfavorable histopathology (UH in neuroblastic tumors through combined imaging and biochemical parameters.123I-MIBG SPECT and MRI was performed before surgical resection or biopsy in 47 consecutive pediatric patients with neuroblastic tumor. Semi-quantitative tumor-to-liver count-rate ratio (TLCRR, MRI tumor size and margins, urine catecholamine and NSE blood levels of neuron specific enolase (NSE were recorded. Accuracy of single and combined variables for prediction of UH was tested by ROC analysis with Bonferroni correction.34 of 47 patients had UH based on the International Neuroblastoma Pathology Classification (INPC. TLCRR and serum NSE both predicted UH with moderate accuracy. Optimal cut-off for TLCRR was 2.0, resulting in 68% sensitivity and 100% specificity (AUC-ROC 0.86, p < 0.001. Optimal cut-off for NSE was 25.8 ng/ml, resulting in 74% sensitivity and 85% specificity (AUC-ROC 0.81, p = 0.001. Combination of TLCRR/NSE criteria reduced false negative findings from 11/9 to only five, with improved sensitivity and specificity of 85% (AUC-ROC 0.85, p < 0.001.Strong 123I-MIBG uptake and high serum level of NSE were each predictive of UH. Combined analysis of both parameters improved the prediction of UH in patients with neuroblastic tumor. MRI parameters and urine catecholamine levels did not predict UH.

  10. Toxicogenomic markers for corticosteroid treatment in beef cattle: integrated analysis of transcriptomic data.

    Science.gov (United States)

    Pegolo, Sara; Di Camillo, Barbara; Montesissa, Clara; Cannizzo, Francesca Tiziana; Biolatti, Bartolomeo; Bargelloni, Luca

    2015-03-01

    In the present work, an integrated analysis was performed on DNA-microarray data of bovine muscle samples belonging to controls, animals treated with various growth promoters (GPs) and unknown commercial samples. The aim was identify a robust gene expression signature of corticosteroid treatment for the classification of commercial samples, despite the effects of biological variation and other confounding factors. DNA-Microarray data from 5 different batches of bovine skeletal muscle samples were analyzed (146 samples). After preprocessing, expression data from animals treated with corticosteroids and controls from the different batches (89 samples) were used to train a Support Vector Machines (SVMs) classifier. The optimal number of gene probes chosen by our classification framework was 73. The SVMs with linear kernel built on these 73 biomarker genes was predicted to perform on novel samples with a high classification accuracy (Matthew's correlation coefficient equal to 0.77) and an average percentage of false positive and false negative equal to 5% and 6%, respectively. Concluding, a relatively small set of genes was able to discriminate between controls and corticosteroid-treated animals, despite different breeds, animal ages, and combination of GPs. The results are extremely promising, suggesting that integrated analysis provides robust transcriptomic signatures for GP abuse. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. Surface-Source Downhole Seismic Analysis in R

    Science.gov (United States)

    Thompson, Eric M.

    2007-01-01

    This report discusses a method for interpreting a layered slowness or velocity model from surface-source downhole seismic data originally presented by Boore (2003). I have implemented this method in the statistical computing language R (R Development Core Team, 2007), so that it is freely and easily available to researchers and practitioners that may find it useful. I originally applied an early version of these routines to seismic cone penetration test data (SCPT) to analyze the horizontal variability of shear-wave velocity within the sediments in the San Francisco Bay area (Thompson et al., 2006). A more recent version of these codes was used to analyze the influence of interface-selection and model assumptions on velocity/slowness estimates and the resulting differences in site amplification (Boore and Thompson, 2007). The R environment has many benefits for scientific and statistical computation; I have chosen R to disseminate these routines because it is versatile enough to program specialized routines, is highly interactive which aids in the analysis of data, and is freely and conveniently available to install on a wide variety of computer platforms. These scripts are useful for the interpretation of layered velocity models from surface-source downhole seismic data such as deep boreholes and SCPT data. The inputs are the travel-time data and the offset of the source at the surface. The travel-time arrivals for the P- and S-waves must already be picked from the original data. An option in the inversion is to include estimates of the standard deviation of the travel-time picks for a weighted inversion of the velocity profile. The standard deviation of each travel-time pick is defined relative to the standard deviation of the best pick in a profile and is based on the accuracy with which the travel-time measurement could be determined from the seismogram. The analysis of the travel-time data consists of two parts: the identification of layer-interfaces, and the

  12. Single strand conformation polymorphism based SNP and Indel markers for genetic mapping and synteny analysis of common bean (Phaseolus vulgaris L.).

    Science.gov (United States)

    Galeano, Carlos H; Fernández, Andrea C; Gómez, Marcela; Blair, Matthew W

    2009-12-23

    Expressed sequence tags (ESTs) are an important source of gene-based markers such as those based on insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). Several gel based methods have been reported for the detection of sequence variants, however they have not been widely exploited in common bean, an important legume crop of the developing world. The objectives of this project were to develop and map EST based markers using analysis of single strand conformation polymorphisms (SSCPs), to create a transcript map for common bean and to compare synteny of the common bean map with sequenced chromosomes of other legumes. A set of 418 EST based amplicons were evaluated for parental polymorphisms using the SSCP technique and 26% of these presented a clear conformational or size polymorphism between Andean and Mesoamerican genotypes. The amplicon based markers were then used for genetic mapping with segregation analysis performed in the DOR364 x G19833 recombinant inbred line (RIL) population. A total of 118 new marker loci were placed into an integrated molecular map for common bean consisting of 288 markers. Of these, 218 were used for synteny analysis and 186 presented homology with segments of the soybean genome with an e-value lower than 7 x 10-12. The synteny analysis with soybean showed a mosaic pattern of syntenic blocks with most segments of any one common bean linkage group associated with two soybean chromosomes. The analysis with Medicago truncatula and Lotus japonicus presented fewer syntenic regions consistent with the more distant phylogenetic relationship between the galegoid and phaseoloid legumes. The SSCP technique is a useful and inexpensive alternative to other SNP or Indel detection techniques for saturating the common bean genetic map with functional markers that may be useful in marker assisted selection. In addition, the genetic markers based on ESTs allowed the construction of a transcript map and given their high conservation

  13. Single strand conformation polymorphism based SNP and Indel markers for genetic mapping and synteny analysis of common bean (Phaseolus vulgaris L.

    Directory of Open Access Journals (Sweden)

    Gómez Marcela

    2009-12-01

    Full Text Available Abstract Background Expressed sequence tags (ESTs are an important source of gene-based markers such as those based on insertion-deletions (Indels or single-nucleotide polymorphisms (SNPs. Several gel based methods have been reported for the detection of sequence variants, however they have not been widely exploited in common bean, an important legume crop of the developing world. The objectives of this project were to develop and map EST based markers using analysis of single strand conformation polymorphisms (SSCPs, to create a transcript map for common bean and to compare synteny of the common bean map with sequenced chromosomes of other legumes. Results A set of 418 EST based amplicons were evaluated for parental polymorphisms using the SSCP technique and 26% of these presented a clear conformational or size polymorphism between Andean and Mesoamerican genotypes. The amplicon based markers were then used for genetic mapping with segregation analysis performed in the DOR364 × G19833 recombinant inbred line (RIL population. A total of 118 new marker loci were placed into an integrated molecular map for common bean consisting of 288 markers. Of these, 218 were used for synteny analysis and 186 presented homology with segments of the soybean genome with an e-value lower than 7 × 10-12. The synteny analysis with soybean showed a mosaic pattern of syntenic blocks with most segments of any one common bean linkage group associated with two soybean chromosomes. The analysis with Medicago truncatula and Lotus japonicus presented fewer syntenic regions consistent with the more distant phylogenetic relationship between the galegoid and phaseoloid legumes. Conclusion The SSCP technique is a useful and inexpensive alternative to other SNP or Indel detection techniques for saturating the common bean genetic map with functional markers that may be useful in marker assisted selection. In addition, the genetic markers based on ESTs allowed the construction

  14. Ten-year survival and prognostic markers in one thousand patients with advanced heart failure. A single-centre analysis.

    Science.gov (United States)

    Lesny, Peter; Luknar, Milan; Matejka, Martin; Varga, Ivan; Solik, Peter; Wimmerova, Sona; Goncalvesova, Eva

    2016-06-01

    Patients with advanced heart failure (HF) represent a pool of candidates for heart transplantation and long-term mechanical circulatory support devices. The aim of our study was to determine simple and reliable markers of one-year mortality for selection of the most suitable patients for heart replacement therapy. One thousand consecutive patients with HF (mean age 49 ± 10.9 years; 86.8% males) referred to a single tertiary centre from January 1998 to January 2010 in order to assess the indication for heart transplantation were enrolled. Kaplan-Meier survival analysis was performed. Independent mortality predictors were established using logistic regression analysis. The mean follow-up was 4.3 ± 2.7 years (range 1-12 years). Cumulative survival was as follows: 1-year survival 83%, 3-year 63%, 5-year 50%, 7-year 39%, and 10-year 23%. Independent predictors of 1-year mortality included coronary artery disease, left ventricular diastolic diameter >79 mm, plasma sodium 240 mg/day. Short-term prognosis of HF patient can be estimated based on simple parameters. Patients with signs of poor prognosis should be referred to tertiary centres to be considered for heart replacement therapy.

  15. Analysis of genetic diversity of Tunisian caprifig (Ficus caricaL.) accessions using simple sequence repeat (SSR) markers.

    Science.gov (United States)

    Essid, Awatef; Aljane, Fateh; Ferchichi, Ali; Hormaza, Jose Ignacio

    2015-01-01

    The common fig ( Ficus carica L.) is a gynodioecious species with two sexual forms: male trees (caprifigs) with male and female flowers and female trees that produce only female flowers that will result in the edible fig syconium. In this study the genetic diversity of 20 Tunisian accessions of caprifig is analyzed using SSR markers previously developed for this crop. The results revealed that the 13 pairs of primers used amplified a total of 37 alleles in the accessions studied. The number of alleles per locus ranged from two to six, with a mean value of 2.85 alleles per locus. Observed and expected heterozygosities showed mean values of 0.33 and 0.29 respectively. UPGMA cluster analysis and Principal Component Analysis grouped the caprifig accessions analyzed in three groups. The results obtained show a low genetic diversity in the Tunisian accessions of caprifig studied and, in spite of analyzing samples from different geographic regions, no clear groupings based on geographical origin are observed suggesting widespread exchange of caprifig plant material through vegetative propagation among different areas in Tunisia.

  16. Time From Smoking Cessation and Inflammatory Markers: New Evidence From a Cross-Sectional Analysis of ELSA-Brasil.

    Science.gov (United States)

    Peres, Flávia Soares; Barreto, Sandhi Maria; Camelo, Lidyane V; Ribeiro, Antonio Luiz P; Vidigal, Pedro Guatimosim; Duncan, Bruce Bartholow; Giatti, Luana

    2017-07-01

    The time for inflammatory markers of former smokers to revert to never smoker levels is still controversial, ranging from 5 to 20 years. We aimed to determine the time from smoking cessation for white blood cell (WBC) count and serum C-reactive protein (CRP) levels to return to those of never-smokers, after adjusting for confounding factors and for secondhand smoke (SHS) exposure among participants of the Brazilian Longitudinal Study of Adult Health (ELSA-Brasil). Cross-sectional analysis of baseline participants of ELSA-Brasil. We used linear regression analysis and generalized linear models with gamma distribution and logarithmic link function to estimate the association of WBC count and CRP levels with time from smoking cessation. The following confounding factors were considered: sex, age, education, SHS, alcohol consumption, leisure-time physical activity, BMI, total cholesterol/HDL ratio, hypertension, diabetes, cardiovascular disease, and chronic obstructive pulmonary disease (COPD). Results: After all adjustments, time from smoking cessation smoking cessation ≥ 5 and smoking cessation smoking cessation for CRP and 10 years after for WBC. The results may add to the arsenal health professionals have to encourage their patients to quit smoking, as some harms from smoking appear to revert to never-smokers' level sooner than previously reported. Longitudinal studies should confirm our findings. © The Author 2017. Published by Oxford University Press on behalf of the Society for Research on Nicotine and Tobacco. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  17. Surface topography analysis for dimensional quality control of replication at the micrometre scale

    DEFF Research Database (Denmark)

    Balcon, M.; Marinello, F.; Tosello, Guido

    2011-01-01

    and replica surfaces must be quantitatively analysed and compared. In the present work, reference simulated surfaces were considered and studied in order to evaluate the effectiveness and traceability of different analysis tools for replication quality control. Topographies were analysed simulating different...... surface mapping techniques, such as optical profilometry, scanning probe microscopy and scanning electron microscopy. Different strategies for surface analysis and comparison are proposed and discussed taking into account the instrument, the measuring range and the functionality of the surface....

  18. Surface return direction-of-arrival analysis for radar ice sounding surface clutter suppression

    DEFF Research Database (Denmark)

    Nielsen, Ulrik; Dall, Jørgen

    2015-01-01

    Airborne radar ice sounding is challenged by surface clutter masking the depth signal of interest. Surface clutter may even be prohibitive for potential space-based ice sounding radars. To some extent the radar antenna suppresses the surface clutter, and a multi-phase-center antenna in combination...

  19. Evaluation of toxicological monitoring markers using proteomic analysis in rats exposed to formaldehyde.

    Science.gov (United States)

    Im, Hosub; Oh, Eunha; Mun, Joohee; Khim, Jin-Young; Lee, Eunil; Kang, Hyung-Sik; Kim, Eunmi; Kim, Hyunsuk; Won, Nam-Hee; Kim, Young-Hwan; Jung, Woon-Won; Sul, Donggeun

    2006-06-01

    Formaldehyde (FA) is known as a low molecule weight organic compound and one of major components that causes sick building syndrome (SBS), and it has been reported that FA has cytotoxic, hemotoxic, immunotoxic, and genotoxic properties. The International Agency for Research on Cancer (IARC) has characterized FA as a carcinogen. In this study, we investigated the effects of FA on rat plasma proteins by using proteomic approach. Rats were exposed to three different concentrations of FA (0, 5, 10 ppm) for 2 weeks at 6 hours/day and 5 days/week in an inhalation chamber. Malondialdehyde (MDA) assay and carbonyl spectrometric assay were conducted to determine lipid peroxidation and protein oxidation levels and Comet assays were used for genotoxicity evaluation. Level of MDA, carbonyl insertion and DNA damage in plasma, livers, and in the lymphocytes of rats exposed to FA were found to be dose dependently increased. Proteomic analysis using three different pI ranges (3.5-5.6, 5.3-6.9, 6-9) and large size two-dimensional gel electrophoresis (2-DE) showed the presence of 3491 protein spots. A total of 32 (19 up- and 13 down-regulated) proteins were identified as biomarkers of FA, all showed dose dependent expressions in the plasma of rats exposed to FA and of these, 27 protein spots were identified by MALDI-TOF/MS. Several differentiated protein groups were found. Proteins involved in apoptosis, transportation, signaling, energy metabolism, and cell structure and motility were found to be up- or down-regulated. Among these, the identities of SNAP 23, apolipoprotein A-1 and E, clusterin, kinesin, and fibrinogen gamma were confirmed by Western blot assay, and apo E was further analyzed by using 2-DE immunoblot assays to determine isoform patterns. Two cytokine including IL4 and INF-gamma were measured in plasma with respect to fibrinogen gamma changes. In summary, cytotoxicity, and genotoxicity assays, namely MDA lipid peroxidation assay, the carbonyl protein oxidation assay

  20. Ambient Surface Analysis of Organic Monolayers using Direct Analysis in Real Time Orbitrap Mass Spectrometry

    NARCIS (Netherlands)

    Manova, R.K.; Joshi, S.; Debrassi, A.; Bhairamadgi, N.S.; Roeven, E.; Gagnon, J.; Tahir, M.N.; Claassen, F.W.; Scheres, L.M.W.; Wennekes, T.; Schroën, C.G.P.H.; Beek, van T.A.; Zuilhof, H.; Nielen, M.W.F.

    2014-01-01

    A better characterization of nanometer-thick organic layers (monolayers) as used for engineering surface properties, biosensing, nanomedicine, and smart materials will widen their application. The aim of this study was to develop direct analysis in real time high-resolution mass spectrometry

  1. Gis-Based Surface Analysis of Archaeological Finds

    Science.gov (United States)

    Kovács, K.; Hanke, K.; Moser, M.

    2011-09-01

    The international research project HiMAT (History of Mining Activities in the Tyrol and adjacent areas) is dedicated to the study of mining history in the Eastern Alps by various scientific disciplines. The aim of this program is the analysis of the mining activities' impacts on environment and human societies. Unfortunately, there is only a limited number of specific regions (e.g. Mitterberg) to offer possibilities to investigate the former mining expansions. Within this multidisciplinary project, the archaeological sites and finds are analyzed by the Surveying and Geoinformation Unit at the University of Innsbruck. This paper shows data fusion of different surveying and post-processing methods to achieve a photo-realistic digital 3D model of one of these most important finds, the Bronze Age sluice box from the Mitterberg. The applied workflow consists of four steps: 1. Point cloud processing, 2. Meshing of the point clouds and editing of the models, 3. Image orientation, bundle and image adjustment, 4. Model texturing. In addition, a short range laser scanning survey was organized before the conservation process of this wooden find. More accurate research opportunities were offered after this detailed documentation of the sluice box, for example the reconstruction of the broken parts and the surface analysis of this archaeological object were implemented using these high-resolution datasets. In conclusion, various unperceived patterns of the wooden boards were visualized by the GIS-based tool marks investigation.

  2. GIS-BASED SURFACE ANALYSIS OF ARCHAEOLOGICAL FINDS

    Directory of Open Access Journals (Sweden)

    K. Kovács

    2012-09-01

    Full Text Available The international research project HiMAT (History of Mining Activities in the Tyrol and adjacent areas is dedicated to the study of mining history in the Eastern Alps by various scientific disciplines. The aim of this program is the analysis of the mining activities’ impacts on environment and human societies. Unfortunately, there is only a limited number of specific regions (e.g. Mitterberg to offer possibilities to investigate the former mining expansions. Within this multidisciplinary project, the archaeological sites and finds are analyzed by the Surveying and Geoinformation Unit at the University of Innsbruck. This paper shows data fusion of different surveying and post-processing methods to achieve a photo-realistic digital 3D model of one of these most important finds, the Bronze Age sluice box from the Mitterberg. The applied workflow consists of four steps: 1. Point cloud processing, 2. Meshing of the point clouds and editing of the models, 3. Image orientation, bundle and image adjustment, 4. Model texturing. In addition, a short range laser scanning survey was organized before the conservation process of this wooden find. More accurate research opportunities were offered after this detailed documentation of the sluice box, for example the reconstruction of the broken parts and the surface analysis of this archaeological object were implemented using these high-resolution datasets. In conclusion, various unperceived patterns of the wooden boards were visualized by the GIS-based tool marks investigation.

  3. Numerical analysis of surface subsidence in asymmetric parallel highway tunnels

    Directory of Open Access Journals (Sweden)

    Ratan Das

    2017-02-01

    Full Text Available Tunnelling related hazards are very common in the Himalayan terrain and a number of such instances have been reported. Several twin tunnels are being planned for transportation purposes which will require good understanding for prediction of tunnel deformation and surface settlement during the engineering life of the structure. The deformational behaviour, design of sequential excavation and support of any jointed rock mass are challenging during underground construction. We have raised several commonly assumed issues while performing stability analysis of underground opening at shallow depth. For this purpose, Kainchi-mod Nerchowck twin tunnels (Himachal Pradesh, India are taken for in-depth analysis of the stability of two asymmetric tunnels to address the influence of topography, twin tunnel dimension and geometry. The host rock encountered during excavation is composed mainly of moderately to highly jointed grey sandstone, maroon sandstone and siltstones. In contrast to equidimensional tunnels where the maximum subsidence is observed vertically above the centreline of the tunnel, the result from the present study shows shifting of the maximum subsidence away from the tunnel centreline. The maximum subsidence of 0.99 mm is observed at 4.54 m left to the escape tunnel centreline whereas the maximum subsidence of 3.14 mm is observed at 8.89 m right to the main tunnel centreline. This shifting clearly indicates the influence of undulating topography and in-equidimensional noncircular tunnel.

  4. Analysis of variability of tropical Pacific sea surface temperatures

    Science.gov (United States)

    Davies, Georgina; Cressie, Noel

    2016-11-01

    Sea surface temperature (SST) in the Pacific Ocean is a key component of many global climate models and the El Niño-Southern Oscillation (ENSO) phenomenon. We shall analyse SST for the period November 1981-December 2014. To study the temporal variability of the ENSO phenomenon, we have selected a subregion of the tropical Pacific Ocean, namely the Niño 3.4 region, as it is thought to be the area where SST anomalies indicate most clearly ENSO's influence on the global atmosphere. SST anomalies, obtained by subtracting the appropriate monthly averages from the data, are the focus of the majority of previous analyses of the Pacific and other oceans' SSTs. Preliminary data analysis showed that not only Niño 3.4 spatial means but also Niño 3.4 spatial variances varied with month of the year. In this article, we conduct an analysis of the raw SST data and introduce diagnostic plots (here, plots of variability vs. central tendency). These plots show strong negative dependence between the spatial standard deviation and the spatial mean. Outliers are present, so we consider robust regression to obtain intercept and slope estimates for the 12 individual months and for all-months-combined. Based on this mean-standard deviation relationship, we define a variance-stabilizing transformation. On the transformed scale, we describe the Niño 3.4 SST time series with a statistical model that is linear, heteroskedastic, and dynamical.

  5. Sequential analysis of variable markers for predicting outcomes in pediatric patients with acute liver failure.

    Science.gov (United States)

    Uchida, Hajime; Sakamoto, Seisuke; Fukuda, Akinari; Sasaki, Kengo; Shigeta, Takanobu; Nosaka, Shunsuke; Kubota, Masaya; Nakazawa, Atsuko; Nakagawa, Satoshi; Kasahara, Mureo

    2017-11-01

    Our aim was to analyze serial changes in the predictive variables and a scoring system retrospectively adapted to evaluate outcomes in pediatric patients with acute liver failure (ALF). We retrospectively collected data on 65 patients with ALF. The 65 patients were divided into two groups according to the need for liver transplantation (LT) as follows: LT group (n = 54) and non-LT group (n = 11). The early determination scoring system of the indications for LT proposed by the Intractable Hepato-Biliary Diseases Study Group of Japan (JIHBDSG) was used in our study. The area under the receiver operating characteristic curve (AUROC) was calculated for the JIHBDSG score between the LT group and non-LT group at the time of diagnosis (day 0) and day 3, and day 5 after the diagnosis. A JIHBDSG score of >3 at day 5 was found to identify the patients requiring LT with 83.7% sensitivity, 81.8% specificity, and 83.3% diagnostic accuracy. Based on a comparison of AUROC values, the JIHBDSG score on day 5 (AUROC 0.91) was higher than that on day 0 (AUROC 0.75) and day 3 (AUROC 0.84). We showed that a serial analysis of the JIHBDSG score might be useful for predicting outcomes of ALF in pediatric patients who fulfilled the criteria of LT indication in our center. However, further studies are needed to validate our results. © 2016 The Japan Society of Hepatology.

  6. Experimental analysis of surface finish in normal conducting cavities

    Science.gov (United States)

    Zarrebini-Esfahani, A.; Aslaninejad, M.; Ristic, M.; Long, K.

    2017-10-01

    A normal conducting 805 MHz test cavity with an in built button shaped sample is used to conduct a series of surface treatment experiments. The button enhances the local fields and influences the likelihood of an RF breakdown event. Because of their smaller sizes, compared to the whole cavity surface, they allow practical investigations of the effects of cavity surface preparation in relation to RF breakdown. Manufacturing techniques and steps for preparing the buttons to improve the surface quality are described in detail. It was observed that even after the final stage of the surface treatment, defects on the surface of the cavities still could be found.

  7. A Cross Cultural Analysis of Textual and Interpersonal Metadiscourse Markers: The Case of Economic Articles in English and Persian Newspapers

    Directory of Open Access Journals (Sweden)

    Abbas Mehrabi Boshrabadi

    2014-04-01

    Full Text Available This study was an attempt to investigate the functional role of textual and interpersonal metadiscourse markers in English and Persian Economic news reports. To this end, 10 news articles, 5 in each language, were randomly selected from the Economic sections of the leading newspapers published in 2013-2014 in Iran and the United States. Based on Kopple’s (1985 taxonomy, the type and frequency of metadiscourse markers used in the texts were analyzed to find out their functions in the text. The findings revealed that the textual markers used by Persian authors were considerably more frequent than those employed by the American writers. Interestingly, unlike the Persian writers, the American authors enlisted a larger number of interpersonal markers, which made their angle of the subject treatment different. It is evident that the differential use of metadiscourse markers by nationally different authors could be attributed to culture-specific norms governing the development and organization of discourse.

  8. Forensic ancestry analysis with two capillary electrophoresis ancestry informative marker (AIM) panels: Results of a collaborative EDNAP exercise.

    Science.gov (United States)

    Santos, C; Fondevila, M; Ballard, D; Banemann, R; Bento, A M; Børsting, C; Branicki, W; Brisighelli, F; Burrington, M; Capal, T; Chaitanya, L; Daniel, R; Decroyer, V; England, R; Gettings, K B; Gross, T E; Haas, C; Harteveld, J; Hoff-Olsen, P; Hoffmann, A; Kayser, M; Kohler, P; Linacre, A; Mayr-Eduardoff, M; McGovern, C; Morling, N; O'Donnell, G; Parson, W; Pascali, V L; Porto, M J; Roseth, A; Schneider, P M; Sijen, T; Stenzl, V; Court, D Syndercombe; Templeton, J E; Turanska, M; Vallone, P M; Oorschot, R A H van; Zatkalikova, L; Carracedo, Á; Phillips, C

    2015-11-01

    There is increasing interest in forensic ancestry tests, which are part of a growing number of DNA analyses that can enhance routine profiling by obtaining additional genetic information about unidentified DNA donors. Nearly all ancestry tests use single nucleotide polymorphisms (SNPs), but these currently rely on SNaPshot single base extension chemistry that can fail to detect mixed DNA. Insertion-deletion polymorphism (Indel) tests have been developed using dye-labeled primers that allow direct capillary electrophoresis detection of PCR products (PCR-to-CE). PCR-to-CE maintains the direct relationship between input DNA and signal strength as each marker is detected with a single dye, so mixed DNA is more reliably detected. We report the results of a collaborative inter-laboratory exercise of 19 participants (15 from the EDNAP European DNA Profiling group) that assessed a 34-plex SNP test using SNaPshot and a 46-plex Indel test using PCR-to-CE. Laboratories were asked to type five samples with different ancestries and detect an additional mixed DNA sample. Statistical inference of ancestry was made by participants using the Snipper online Bayes analysis portal plus an optional PCA module that analyzes the genotype data alongside calculation of Bayes likelihood ratios. Exercise results indicated consistent genotyping performance from both tests, reaching a particularly high level of reliability for the Indel test. SNP genotyping gave 93.5% concordance (compared to the organizing laboratory's data) that rose to 97.3% excluding one laboratory with a large number of miscalled genotypes. Indel genotyping gave a higher concordance rate of 99.8% and a reduced no-call rate compared to SNP analysis. All participants detected the mixture from their Indel peak height data and successfully assigned the correct ancestry to the other samples using Snipper, with the exception of one laboratory with SNP miscalls that incorrectly assigned ancestry of two samples and did not obtain

  9. Gene expression analysis of urine sediment: evaluation for potential noninvasive markers of interstitial cystitis/bladder pain syndrome.

    Science.gov (United States)

    Blalock, Eric M; Korrect, Garrett S; Stromberg, Arnold J; Erickson, Deborah R

    2012-02-01

    We determined whether gene expression profiles in urine sediment could provide noninvasive markers for interstitial cystitis/bladder pain syndrome with and/or without Hunner lesions. Fresh catheterized urine was collected and centrifuged from 5 controls, and 5 Hunner lesion-free and 5 Hunner lesion bearing patients. RNA was extracted from pelleted material and quantified by gene expression microarray using the GeneChip® Human Gene ST Array. Three biologically likely hypotheses were tested, including 1) all 3 groups are distinct from each other, 2) controls are distinct from the 2 types combined of patients with interstitial cystitis/bladder pain syndrome and 3) patients with Hunner lesion-interstitial cystitis/bladder pain syndrome are distinct from controls and patients with nonHunner-lesion interstitial cystitis/bladder pain syndrome combined. For statistical parity an unlikely fourth hypothesis was included, that is patients with nonHunner-lesion interstitial cystitis/bladder pain syndrome are distinct from controls and patients with Hunner lesion-interstitial cystitis/bladder pain syndrome combined. Analysis supported selective up-regulation of genes in the Hunner lesion interstitial cystitis/bladder pain syndrome group (hypothesis 3), which were primarily associated with inflammation. The inflammatory profile was statistically similar to that reported in a prior Hunner lesion interstitial cystitis/bladder pain syndrome bladder biopsy study. Gene expression analysis of urine sediment was feasible in this pilot study. Expression profiles failed to discriminate nonHunner-lesion interstitial cystitis/bladder pain syndrome from controls and they are unlikely to be a noninvasive marker for nonHunner-lesion interstitial cystitis/bladder pain syndrome. In contrast, patients with Hunner lesion had increased proinflammatory gene expression in urine sediment, similar to that in a prior microarray study of bladder biopsies. If these preliminary results are validated in

  10. Transcriptome analysis between invasive Pomacea canaliculata and indigenous Cipangopaludina cahayensis reveals genomic divergence and diagnostic microsatellite/SSR markers.

    Science.gov (United States)

    Mu, Xidong; Hou, Guangyuan; Song, Hongmei; Xu, Peng; Luo, Du; Gu, Dangen; Xu, Meng; Luo, Jianren; Zhang, Jiaen; Hu, Yinchan

    2015-02-11

    Pomacea canaliculata is an important invasive species worldwide. However, little is known about the molecular mechanisms behind species displacement, adaptational abilities, and pesticide resistance, partly because of the lack of genomic information that is available