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Sample records for cell gel electrophoresis

  1. The application of single cell gel electrophoresis or comet assay to human monitoring studies

    Directory of Open Access Journals (Sweden)

    Valverde Mahara

    1999-01-01

    Full Text Available Objective. In the search of new human genotoxic biomarkers, the single cell gel electrophoresis assay has been proposed as a sensible alternative. Material and methods. This technique detects principally single strand breaks as well as alkali-labile and repair-retarded sites. Results. Herein we present our experience using the single cell gel electrophoresis assay in human population studies, both occupationally and environmentally exposed. Conclusions. We discuss the assay feasibility as a genotoxic biomarker.

  2. Diversity in the applications of the single cell gel electrophoresis (comet) assay / Cristal Huysamen

    OpenAIRE

    Huysamen, Cristal

    2005-01-01

    The development of the single cell gel electrophoresis assay (Comet assay) as a powerful method for measuring DNA strand breakage and repair, has lead to a broader understanding of the impact of certain internal and external factors on DNA damage. This study describes the establishment of the Comet assay in our laboratory and its application in a diversity of studies. These studies include the monitoring of the effect of exercise on DNA damage and repair with the purpose of ...

  3. Denaturing gradient gel electrophoresis

    International Nuclear Information System (INIS)

    It is worthwhile considering that only some 30 species make up the bulk of the bacterial population in human faeces at any one time based on the classical cultivation-based approach. The situation in the rumen is similar. Thus, it is practical to focus on specific groups of interest within the complex community. These may be the predominant or the most active species, specific physiological groups or readily identifiable (genetic) clusters of phylogenetically related organisms. Several 16S rDNA fingerprinting techniques can be invaluable for selecting and monitoring sequences or phylogenetic groups of interest and are described below. Over the past few decades, considerable attention was focussed on the identification of pure cultures of microbes on the basis of genetic polymorphisms of DNA encoding rRNA such as ribotyping, amplified fragment length polymorphism and randomly amplified polymorphic DNA. However, many of these methods require prior cultivation and are less suitable for use in analysis of complex mixed populations although important in describing cultivated microbial diversity in molecular terms. Much less attention was given to molecular characterization of complex communities. In particular, research into diversity and community structure over time has been revolutionized by the advent of molecular fingerprinting techniques for complex communities. Denaturing or temperature gradient gel electrophoresis (DGGE/TGGE) methods have been successfully applied to the analysis of human, pig, cattle, dog and rodent intestinal populations

  4. Application of the Single Cell Gel Electrophoresis (SCGE) Assay to Genotoxicity Evaluation in Plants and Animals

    International Nuclear Information System (INIS)

    Application of the Single Cell Gel Electrophoresis (SCGE) Assay to Genotoxicity Evaluation in Plants and Animals. Recently, the importance of ionizing radiation and chemicals has been recognized since radio- and chemical therapy is directly related to the control of various diseases such as cancer. Radiation and the chemicals can cause biological damages while they have great applicability. It is of necessity to analyze rapidly, easily and accurately the biological effects, especially DNA damage due to those factors. Recently SCGE (single cell gel electrophoresis assay, alias comet assay) has been developed for the efficient evaluation of DNA damage. In this report, the comprehensive review will be given on the rationale, the technical applications and the advantages and shortcomings of SCGE assay. This method can be directly applied to study on toxicity, cancer, and aging in terms of the evaluation of DNA damages due to radiation and chemicals on human cellular level. It is also suggested that comet assay be used for testing genotoxicity of suspected substances, detecting irradiated foods, screening radioprotective candidates, and studying DNA repair process in various biological systems

  5. Application of the Single Cell Gel Electrophoresis (SCGE) Assay to Genotoxicity Evaluation in Plants and Animals

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jin Kyu

    2007-10-15

    Application of the Single Cell Gel Electrophoresis (SCGE) Assay to Genotoxicity Evaluation in Plants and Animals. Recently, the importance of ionizing radiation and chemicals has been recognized since radio- and chemical therapy is directly related to the control of various diseases such as cancer. Radiation and the chemicals can cause biological damages while they have great applicability. It is of necessity to analyze rapidly, easily and accurately the biological effects, especially DNA damage due to those factors. Recently SCGE (single cell gel electrophoresis assay, alias comet assay) has been developed for the efficient evaluation of DNA damage. In this report, the comprehensive review will be given on the rationale, the technical applications and the advantages and shortcomings of SCGE assay. This method can be directly applied to study on toxicity, cancer, and aging in terms of the evaluation of DNA damages due to radiation and chemicals on human cellular level. It is also suggested that comet assay be used for testing genotoxicity of suspected substances, detecting irradiated foods, screening radioprotective candidates, and studying DNA repair process in various biological systems.

  6. Two-dimensional polyacrylamide gel electrophoresis analysis of indomethacin-treated human colon cancer cells

    Institute of Scientific and Technical Information of China (English)

    Yan-Li Cheng; Gui-Ying Zhang; Zhi-Qiang Xiao; Fa-Qing Tang

    2005-01-01

    AIM: To establish the two-dimensional gel electrophoresis (2-DE) profiles of indomethacin (IN)-treated human colon cancer cell line HCT116, and to provide a new way to study its anti-tumor molecular mechanism through analyzing a variety of protein maps.METHODS: Two-DE profiles of HCT116 were established in IN-treated and untreated groups. Total proteins were separated by immobilized pH gradient-based 2-DE. The gels were stained by silver, scanned by ImageScanner,and analyzed with Image Master software.RESULTS: Clear background, well-resolved and reproducible 2-DE patterns of HCT116 cells were acquired in IN-treated and untreated group. The average deviation of spot position was 0.896±0.177 mm in IEF direction and 1.106±0.289 mm in SDS-PAGE direction respectively. In IN-treated group,1 169±36 spots were detected and 1 061±32 spots were matched, the average matching rate was 90.6% in three gels. In untreated group, 1 256±50 spots were detected and 1 168±46 spots were matched, the average matching rate was 93.0% in three gels. Forty-five differential protein spots were displayed between IN-treated and untreated groups. Of which, 34 protein spots decreased and 9showed higher expression in IN-treated group, and only two protein spots showed an expression in untreated cells.CONCLUSION: Two-DE profiles of IN-treated and untreated HCT116 cells were established. Apparent 45 different protein spots were detected in IN-treated and untreated HCT116 cells. The analysis on differential protein spots may serve as a new way to study the molecule mechanism of IN-treated colon cancer.

  7. Analysis of Differential Gel Electrophoresis of Paclitaxol Resistant and Sensitive Lung Adenocarcinoma Cells' Secretome

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    Tianqing CHU

    2009-07-01

    Full Text Available Background and objective Paclitaxol (PTX resistance is one of main factors which affect the outcome of chemotherapy of lung adenocarcinoma. The aim of this study is to compare the secreted protein expression profiles between Paclitaxol (PTX resistant and sensitive lung adenocarcinoma cells by proteomic research method, so as to provide evidence of choosing individual chemotherapy drugs in clinical treatment. Methods Total secreted proteins extracted from a PTX sensitive cell line A549 and a PTX resistant cell line A549-Taxol were separated by fluorscent differential gel electrophoresis (DIGE. High quality 2-DE profiles were obtained and analyzed by Decyder 6.5 analysis software to screen differentially expressed protein spots. Those spots were identified by mass spectrometry. Results 2-DE patterns of lung adenocarcinoma cells with high-resolution and reproducibility were obtained. 76 significantly differentially expressed protein spots were screened, 19 proteins were identified by mass spectrometry. The identified proteins could be classified into different catogories: metabolic enzyme, extracellular matrix (ECM degradation enzyme, cytokine, signal transducer, cell adhesion, and so on. Conclusion Multiple secreted proteins related to chemoresistance of A549-Taxol cells were identified in this study for the first time. The results presented here would provide clues to identify new serologic chemoresistant biomarkers of NSCLC.

  8. Radiation-induced DNA damage and repair in radiosensitive and radioresistant human tumour cells measured by field inversion gel electrophoresis

    International Nuclear Information System (INIS)

    Radiation-induced DNA damage induction and repair was measured in two human squamous carcinoma cell lines with differing radiosensitivities. Experiments were carried out with field inversion gel electrophoresis (FIGE), adapted to measure DNA double strand break (DSB) induction and repair in unlabelled cells. The sensitivity of the method was increased by introducing a hybridization membrane into the agarose gel. Damaged DNA accumulated on one spot on the membrane resulting in high local concentrations. This DNA was quantified using radioactively-labelled total human DNA as a probe. Radiosensitivity differences at physiological temperatures could not be explained by differences in either induction or repair of DNA damage as measured by pulsed field gel electrophoresis. (author)

  9. Mapping and identification of interferon gamma-regulated HeLa cell proteins separated by immobilized pH gradient two-dimensional gel electrophoresis

    DEFF Research Database (Denmark)

    Shaw, AC; Rossel Larsen, M; Roepstorff, P;

    1999-01-01

    magnitude of IFN-gamma responsive genes has been reported previously. Our goal is to identify and map IFN-gamma-regulated HeLa cell proteins to the two-dimensional polyacrylamide gel electrophoresis with the immobilized pH gradient (IPG) two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) system...

  10. Detection of connexins in liver cells using sodiumdodecylsulfate polyacrylamide gel electrophoresis and immunoblot analysis

    Science.gov (United States)

    Willebrords, Joost; Maes, Michaël; Yanguas, Sara Crespo; Cogliati, Bruno; Vinken, Mathieu

    2016-01-01

    Summary Since connexin expression is partly regulated at the protein level, immunoblot analysis represents a frequently addressed technique in the connexin research field. The present chapter describes the set-up of an immunoblot procedure, including protein extraction and quantification from biological samples, gel electrophoresis, protein transfer and immunoblotting, which is optimized for analysis of connexins in liver tissue. In essence, proteins are separated on a polyacrylamide gel using sodiumdodecylsulfate followed by transfer of proteins on a nitrocellulose membrane. The latter allows specific detection of connexins with antibodies combined with revelation through enhanced chemiluminescence. PMID:27207285

  11. Analysis of cell wall extracts of Candida albicans by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blot techniques.

    OpenAIRE

    Ponton, J; J. M. Jones

    1986-01-01

    Cell walls of intact yeast- and mycelial-phase Candida albicans B311 were extracted with different compounds: dithiothreitol, dithiothreitol with protease, dithiothreitol with lyticase, and dithiothreitol with protease followed by beta-glucuronidase with chitinase. Extracts were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blot techniques. Dithiothreitol extracts contained the most satisfactory array of components for study. Analysis of these extracts demo...

  12. Conducting polymer electrodes for gel electrophoresis.

    Directory of Open Access Journals (Sweden)

    Katarina Bengtsson

    Full Text Available In nearly all cases, electrophoresis in gels is driven via the electrolysis of water at the electrodes, where the process consumes water and produces electrochemical by-products. We have previously demonstrated that π-conjugated polymers such as poly(3,4-ethylenedioxythiophene (PEDOT can be placed between traditional metal electrodes and an electrolyte to mitigate electrolysis in liquid (capillary electroosmosis/electrophoresis systems. In this report, we extend our previous result to gel electrophoresis, and show that electrodes containing PEDOT can be used with a commercial polyacrylamide gel electrophoresis system with minimal impact to the resulting gel image or the ionic transport measured during a separation.

  13. Two-dimensional gel electrophoresis data for proteomic profiling of Sporothrix yeast cells

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    Anderson Messias Rodrigues

    2015-03-01

    Full Text Available Sporotrichosis is a chronic infection of the skin and subcutaneous tissues of human and other mammals caused by a complex of cryptic dimorphic fungi in the plant-associated order Ophiostomatales. With major differences between routes of transmission, Sporothrix infections are emerging as new threat in tropical and subtropical areas, particularly in form of outbreaks. The mechanisms underlying the pathogenesis and invasion of Sporothrix spp. are still poorly understood and many virulence factors remain unidentified. In this scenario, a global analysis of proteins expressed by clinical Sporothrix species combined with the identification of seroreactive proteins is overdue. Optimization of sample preparation and electrophoresis conditions are key steps toward reproducibility of gel-based proteomics assays. We provide the data generated using an efficient protocol of protein extraction for rapid and large-scale proteome analysis using two-dimensional gel electrophoresis. The protocol was established and optimized for pathogenic and non-pathogenic Sporothrix spp. including Sporothrix brasiliensis (CBS 132990, Sporothrix schenckii sensu stricto (CBS 132974, Sporothrix globosa (CBS 132922, and Sporothrix mexicana (CBS 120341. The data, supplied in this article, are related to the research article entitled “Immunoproteomic analysis reveals a convergent humoral response signature in the Sporothrix schenckii complex” (Rodrigues et al., 2014 [1].

  14. Assessing CMT cell line stability by two dimensional polyacrylamide gel electrophoresis and mass spectrometry based proteome analysis

    DEFF Research Database (Denmark)

    Zhang, Kelan; Wrzesinski, Krzysztof; Fey, Stephen J;

    2008-01-01

    Two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) followed by mass spectrometric identification of the proteins in the protein spots has become a central tool in proteomics. CMT167(H), CMT64(M) and CMT170(L) cell lines, selected from a spontaneous mouse lung adenocarcinoma, with high-...... to be a useful tool for assessing differences in cell line stability. This approach provided a tool to select the best cell line and optimal subculture period for studies of cancer related phenomena and for testing the effect of potential anticancer drugs....

  15. DNA damaging effects of carbofuran and its main metabolites on mice by micronucleus test and single cell gel electrophoresis

    Institute of Scientific and Technical Information of China (English)

    ZHOU; Pei; LIU; Baofeng; LU; Yitong

    2005-01-01

    The DNA damaging effects of the carbamate pesticide carbofuran and its four metabolites (carbofuranphenol, 3-ketocarbofuran, 3-hydrocarbofuran and nitrosocarbofuran) on mice were evaluated by single cell gel electrophoresis (SCGE) assay and micronucleus test. KM mice were exposed to test compounds with different doses of 0.1, 0.2 and 0.4mg/kg through intraperitoneal injection two times with an internal of 24 h, and then killed by cervical dislocation 6 h after the second injection. In SCGE assay, isolated mice peripheral blood lymphocytes were employed to determine DNA damaging degree after a 1 h treatment by test compounds and a following electrophoresis. Carbofuran and carbofuranphenol showed negative results in both test and had no obvious toxicity. 3-hydrocarbofuran and nitrosocarbofuran were positive.3-ketocarbofuran could not induce micronucleus formation but caused significant DNA migration in SCGE test. These tests revealed that 3-ketocarbofuran, 3-hydrocarbofuran and nitrosocarbofuran are potential mutagesis and further research is needed.

  16. Avoiding acidic region streaking in two-dimensional gel electrophoresis: Case study with two bacterial whole cell protein extracts

    Indian Academy of Sciences (India)

    Arnab Roy; Umesh Varshney; Debnath Pal

    2014-09-01

    Acidic region streaking (ARS) is one of the lacunae in two-dimensional gel electrophoresis (2DE) of bacterial proteome. This streaking is primarily caused by nucleic acid (NuA) contamination and poses major problem in the downstream processes like image analysis and protein identification. Although cleanup and nuclease digestion are practiced as remedial options, these strategies may incur loss in protein recovery and perform incomplete removal of NuA. As a result, ARS has remained a common observation across publications, including the recent ones. In this work, we demonstrate how ultrasound wave can be used to shear NuA in plain ice-cooled water, facilitating the elimination of ARS in the 2DE gels without the need for any additional sample cleanup tasks. In combination with a suitable buffer recipe, IEF program and frequent paper-wick changing approach, we are able to reproducibly demonstrate the production of clean 2DE gels with improved protein recovery and negligible or no ARS. We illustrate our procedure using whole cell protein extracts from two diverse organisms, Escherichia coli and Mycobacterium smegmatis. Our designed protocols are straightforward and expected to provide good 2DE gels without ARS, with comparable times and significantly lower cost.

  17. Single Cell Gel Electrophoresis Assay of Porcine Leydig Cell DNA Damage Induced by Zearalenone

    Institute of Scientific and Technical Information of China (English)

    Jianwei ZHEN; Qincl LIU; Jianhong GU; Yan YUAN; Xuezhong LIU; Handong WANG; Zongping LIU; Jianchun BIAN

    2012-01-01

    Abstract [Objective] This study aimed to investigate the effect of zearalenone (ZEN) on DNA damage of porcine leydig cells. [Method] Porcine leydig cells cultured in vitro were collected to determine the median lethal dose (LD~o) of ZEN with tetra- zolium-based colorimetric assay (MTT assay). Comet assay was carried out to de- tect the DNA damage of porcine leydig cells exposed to at 0 (negative group), 1, 5, 10, 20, 40 tJmol/L of ZEN. [Result] The percentage of cell tail was 16.67%, 34.00%, 40.67%. 52.00% and 64.67% under 0, 1, 5, 10 and 20 ~mo~/L o~ ZEN, respectively; the differences between the percentages of celt tail in various experimental groups had extremely significant statistical significance compared with the negative group (P〈0.01), showing a significant dose-effect relationship; Tail length in various groups was 57.60_+4.78, 57.75_+6.25, 78.97_+5.83, 100.50~6.94 and 146.83_+12.31 ~m, re- spectively; Tail DNA % in various groups was 21.29_+2.25%, 22.24_+2.43%, 31.21_+ 6.27%, 37.45_+4.33% and 60.68_+9.83%, respectively; Tail length and Tail DNA % in experimental groups with ZEN concentration above 5 ~mo~/L showed significant dif- ferences (P〈0.05) compared with the negative group, which showed an upward trend with the increase of ZEN concentration. [Conclusion] ZEN has genotoxic effect on porcine leydig cells, which can cause DNA damage, with a significant dose-effect relationship.

  18. 44. Study the level of DNA breakage in workers exposed to styrene by single cell gel electrophoresis

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Objective: Study the level of DNA breakage in workers exposed to styrene. Methods: 35 workers aging from 18 to 40 exposed to styrene half a year above were observed as exposed group, in the mean time, 57 workers in the same district who hadn't been exposed to known genotoxicant were selected as control. Bloods of them were sampled and DNA lesions were detected by single cell gel electrophoresis. Results: Compared with control, the ratio between the length of Comet tail and the total length of Comet in exposed group significantly increased, especially it raised following the styrene concentration exposed, but it was not different among different working age groups. Conclusions: DNA is damaged by styrene, and it appears as dose-response relationship.

  19. Matching Two-dimensional Gel Electrophoresis' Spots

    DEFF Research Database (Denmark)

    Dos Anjos, António; AL-Tam, Faroq; Shahbazkia, Hamid Reza;

    2012-01-01

    This paper describes an approach for matching Two-Dimensional Electrophoresis (2-DE) gels' spots, involving the use of image registration. The number of false positive matches produced by the proposed approach is small, when compared to academic and commercial state-of-the-art approaches. This ar......This paper describes an approach for matching Two-Dimensional Electrophoresis (2-DE) gels' spots, involving the use of image registration. The number of false positive matches produced by the proposed approach is small, when compared to academic and commercial state-of-the-art approaches...

  20. Feasibility of measuring radiation-induced DNA double strand breaks and their repair by pulsed field gel electrophoresis in freshly isolated cells from the mouse RIF-1 tumor

    NARCIS (Netherlands)

    vanWaarde, MAWH; vanAssen, AJ; Konings, AWT; Kampinga, HH

    1996-01-01

    Purpose: To examine the technical feasibility of pulsed field gel electrophoresis (PFGE) as a predictive assay for the radioresponsiveness of tumors. Induction and repair of DNA double strand breaks (DSBs) in a freshly prepared cell suspension from a RIF-1 tumor (irradiated ex vivo) was compared wit

  1. DNA DAMAGE QUANTITATION BY ALKALINE GEL ELECTROPHORESIS.

    Energy Technology Data Exchange (ETDEWEB)

    SUTHERLAND,B.M.; BENNETT,P.V.; SUTHERLAND, J.C.

    2004-03-24

    Physical and chemical agents in the environment, those used in clinical applications, or encountered during recreational exposures to sunlight, induce damages in DNA. Understanding the biological impact of these agents requires quantitation of the levels of such damages in laboratory test systems as well as in field or clinical samples. Alkaline gel electrophoresis provides a sensitive (down to {approx} a few lesions/5Mb), rapid method of direct quantitation of a wide variety of DNA damages in nanogram quantities of non-radioactive DNAs from laboratory, field, or clinical specimens, including higher plants and animals. This method stems from velocity sedimentation studies of DNA populations, and from the simple methods of agarose gel electrophoresis. Our laboratories have developed quantitative agarose gel methods, analytical descriptions of DNA migration during electrophoresis on agarose gels (1-6), and electronic imaging for accurate determinations of DNA mass (7-9). Although all these components improve sensitivity and throughput of large numbers of samples (7,8,10), a simple version using only standard molecular biology equipment allows routine analysis of DNA damages at moderate frequencies. We present here a description of the methods, as well as a brief description of the underlying principles, required for a simplified approach to quantitation of DNA damages by alkaline gel electrophoresis.

  2. Analysis of differentially expressed mitochondrial proteins in chromophobe renal cell carcinomas and renal oncocytomas by 2-D gel electrophoresis

    Directory of Open Access Journals (Sweden)

    Maria V. Yusenko, Thomas Ruppert, Gyula Kovacs

    2010-01-01

    Full Text Available Renal oncocytomas (RO and chromophobe renal cell carcinomas (RCC display morphological and functional alterations of the mitochondria. Previous studies showed that accumulation of mitochondria in ROs is associated with somatic mutations of mitochondrial DNA (mtDNA resulting in decreased activity of the respiratory chain complex I, whereas in chromophobe RCC only heteroplasmic mtDNA mutations were found. To identify proteins associated with these changes, for the first time we have compared the mitochondrial proteomes of mitochondria isolated from ROs and chromophobe RCCs as well as from normal kidney tissues by two-dimensional polyacrylamide gel electrophoresis. The proteome profiles were reproducible within the same group of tissues in subsequent experiments. The expression patterns within each group of samples were compared and 81 in-gel digested spots were subjected to nanoLC-MS/MS-based identification of proteins. Although the list of mitochondrial proteins identified in this study is incomplete, we identified the downregulation of NDUFS3 from complex I of the respiratory chain and upregulation of COX5A, COX5B, and ATP5H from complex IV and V in ROs. In chromophobe RCCs downregulation of ATP5A1, the alpha subunit of complex V, has been observed, but no changes in expression of other complexes of the respiratory chain were detected. To confirm the role of respiratory chain complex alterations in the morphological and/or functional changes in chromophobe RCCs and ROs, further studies will be necessary.

  3. Proteomic analysis of docetaxel resistance in human nasopharyngeal carcinoma cells using the two-dimensional gel electrophoresis method.

    Science.gov (United States)

    Peng, Xingchen; Gong, Fengming M; Ren, Min; Ai, Ping; Wu, ShaoYong; Tang, Jie; Hu, XiaoLin

    2016-09-01

    Docetaxel-based chemotherapy has been recommended for advanced nasopharyngeal carcinoma (NPC). However, treatment failure often occurs because of acquired drug resistance. In this study, a docetaxel-resistant NPC cell line CNE-2R was established with increasing doses of docetaxel for more than 6 months. Two-dimensional gel electrophoresis and ESI-Q-TOF-MS were used to compare the differential expression of docetaxel-resistance-associated proteins between human NPC CNE-2 cells and docetaxel-resistant CNE-2R cells. As a result, 24 differentially expressed proteins were identified, including 11 proteins with increased expression and 13 proteins with decreased expression. These proteins function in diverse biological processes such as metabolism, signal transduction, calcium ion binding, immune response, proteolysis, and so on. Among these, α-enolase (ENO1), significantly upregulated in CNE-2R, was selected for detailed analysis. Inhibition of ENO1 by shRNA restored CNE-2R cells' sensitivity to docetaxel. Moreover, overexpression of ENO1 could facilitate the development of acquired resistance of docetaxel in CNE-2 cells. Western blot and reverse-transcription PCR data of clinical samples confirmed that α-enolase was upregulated in docetaxel-resistant human NPC tissues. Finding such proteins might improve interpretation of the molecular mechanisms leading to the acquisition of docetaxel chemoresistance. PMID:27333594

  4. Identification of ataxia telangiectasia heterozygotes, a cancer-prone population, using the single-cell gel electrophoresis (Comet) assay.

    Science.gov (United States)

    Djuzenova, C S; Schindler, D; Stopper, H; Hoehn, H; Flentje, M; Oppitz, U

    1999-06-01

    Heterozygotes of ataxia telangiectasia (AT) may comprise up to 1% of the general population. Because these individuals have no clinical expression of AT but may be highly radiosensitive and strongly predisposed for several forms of cancer, identification of AT carriers represents a considerable interest in cancer epidemiology and radiotherapy. We report a new approach for the in vitro identification of AT-heterozygotes based on the evaluation of the radiosensitivity and DNA damage repair ability of peripheral blood mononuclear cells using the single-cell gel electrophoresis (Comet) assay. The assay was performed on cells isolated from four different groups of individuals: (1) apparently healthy donors (n = 10); (2) patients with breast cancer showing a normal reaction to radiotherapy (n = 10); (3) a group of obligate AT carriers (parents of AT-homozygotes, n = 20); and (4) AT-homozygotes (n = 4). Cells irradiated with 3 Gy of x-rays were assayed for three parameters: (1) the initial and (2) residual DNA damage and (3) the kinetics of DNA damage repair. Both AT-heterozygotes' and AT-homozygotes' cells were found to be highly sensitive to x-irradiation. Quantitative evaluation of the single-cell electrophoregrams revealed that the average initial DNA damage in AT-heterozygous and AT-homozygous cells was almost three times higher than that in control non-AT cells. In addition, the DNA repair process in irradiated AT carrier cells was almost three times slower, and the extent of irreparable DNA damage in these cells was three times greater than in controls. Simultaneous assessment of the three parameters enabled correct identification of all tested AT carriers. This method seems to be a sensitive and useful tool for populational studies as a rapid prescreening test for a mutated AT status. The approach can also be extended for prediction of the in vivo radiosensitivity, which would enable optimization of individual radiotherapy schedules. PMID:10378512

  5. Pulsed field gel electrophoresis a practical guide

    CERN Document Server

    Birren, Bruce

    1993-01-01

    Pulsed Field Gel Electrophoresis: A Practical Guide is the first laboratory manual to describe the theory and practice of this technique. Based on the authors' experience developing pulsed field gel instruments and teaching procedures, this book provides everything a researcher or student needs to know in order to understand and carry out pulsed field gel experiments. Clear, well-tested protocols assume only that users have a basic familiarity with molecular biology. Thorough coverage of useful data, theory, and applications ensures that this book is also a lasting resource for more adv

  6. High background radiation areas of Ram sar in Iran: evaluation of DNA damage by alkaline single cell gel electrophoresis (SCE)

    Energy Technology Data Exchange (ETDEWEB)

    Masoomi, J.R. [Biophysics Department, College of Sciences, Tarbiat Modarres University, Tehran (Iran, Islamic Republic of); Mohammadi, Sh. [Radiation Molecular Genetic Laboratory, National Radiation Protection Department (NRPD), Iranian Nuclear Regulatory Authority (INRA), P.O. Box 14155-4494, Tehran (Iran, Islamic Republic of); Amini, M. [Faculty of Pharmacy, Azad University of Tehran (Iran, Islamic Republic of); Ghiassi-Nejad, M. [Biophysics Department, College of Sciences, Tarbiat Modarres University, Tehran (Iran, Islamic Republic of)]. E-mail: ghiassi@mailcity.com

    2006-07-01

    The hot springs in special areas in Ram sar, a northern coastal town in Iran, contain {sup 226}Ra and {sup 222}Rn. The natural radiation effects, radiosensitivity or adaptive responses, on the inhabitants of high natural radiation in Ram sar were studied. The single cell gel electrophoresis was used to monitor DNA damages. Three groups of volunteers were selected, one from high natural background radiation areas as the case group and two from normal background radiation areas as controls (control 1 and control 2). The latter one had the similar living situation to case group while the other (control 2) had different living situation from the other groups. Peripheral blood mononuclear cells (PMNCs) were separated and irradiated by {sup 6}Co source at five different gamma doses. It was found that the spontaneous level of DNA damage and the induced DNA damage in all challenging doses in case group was considerably higher than control groups (p < 0.05). On the other hand, the repair rate in those volunteers, who received less than 10.2 mSv/y was significantly more than the control groups. In the contrary, individuals who live in homes with more than 10.2 mSv/y had incomplete repair. Additionally the plasma and urinary levels of vitamin C were measured spectrophotometrically. Although the concentration of vitamin C of plasma was equal in case and control 1 groups, the urinary level of vitamin C was found to be lower in the case group.

  7. Detection of Sperm DNA Damage in Workers Exposed to Benzene by Modified Single Cell Gel Electrophoresis

    Institute of Scientific and Technical Information of China (English)

    Bo SONG; Zhi-ming CAI; Xin LI; Li-xia DENG; Qiao ZHANG; Lu-kang ZHENG

    2005-01-01

    Objective To assess the effect of benzene on sperm DNA damageMethods Twenty-seven benzene-exposed workers were selected as exposed groupand 35 normal sperm donors as control group. Air concentration of benzene series inworkshop was determined by gas chromatography. As an internal exposure dose ofbenzene, the concentration of trans, trans-muconic acid (ttMA) was determined byhigh performance liquid chromatography. DNA was detected by modified single cellgel electrophoresis (SCGE).Results The air concentrations of benzene, toluene and xylene at the workplace were86.49 ± 2.83 mg/m3, 97.20 ±3.52 mg/m3 and 97.45 ±2.10 mg/m3, respectively.Urinary ttMA in exposed group (1.040 ± 0.617 mg/L) was significantly higher thanthat of control group (0.819 ± 0.157 mg/L). The percentage of head DNA, determinedby modified SCGE method, significantly decreased in the exposed group (n=13, 70.18%± 7.36%) compared with the control (n=16, 90.62% ± 2.94%)(P<0.001).Conclusion The modified SCGE method can be used to investigate the damage ofsperm DNA. As genotoxin and reprotoxins, benzene had direct effect on the germ cellsduring the spermatogenesiss.

  8. Comparative proteomics and difference gel electrophoresis.

    Science.gov (United States)

    Minden, Jonathan

    2007-12-01

    The goal of comparative proteomics is to analyze proteome changes in response to development, disease, or environment. This is a two-step process in which proteins within cellular extracts are first fractionated to reduce sample complexity, and then the proteins are identified by mass spectrometry. Two-dimensional electrophoresis (2DE) is the long-time standard for protein separation, but it has suffered from poor reproducibility and limited sensitivity. Difference gel electrophoresis (DIGE), in which two protein samples are separately labeled with different fluorescent dyes and then co-electrophoresed on the same 2DE gel, was developed to overcome the reproducibility and sensitivity limitations. In this essay, I discuss the principles of comparative proteomics and the development of DIGE. PMID:18251249

  9. Two-dimensional gel electrophoresis analysis of the proteomes expressed in the human hepatoma cell line BEL-7404 and normal liver cell line L-02

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Proteome analysis technology has been used extensively in conducting discovery research of biology and has become one of the most essential technologies in functional genomics. The proteomes of the human hepatoma cell line BEL-7404 and the normal human liver cell line L-02 have been separated by high resolution two-dimensional gel electrophoresis (2-DE) with immobilized pH gradient isoelectric focusing (IPG-IEF) in the first dimension and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) in the second dimension (IPG-DALT). The resulting images have been analyzed using 2-D analysis software. Quantitative analysis reveals that 7 protein spots are detected only in hepatoma BEL-7404 cells, 14 only in L-02 cells, and 78 protein spots show significant fluctuation in quantity in both cell lines (P<0.01).These protein spots have been displayed on a proteome differential expression map. Analysis for the reproducibility of 2-DE indicates that the positional variability in the IEF dimension is 0.73 mm, while the variability in the SDS-PAGE dimension is 0.44 mm, and the quantitative variability is 17.6%-19.2%. These results suggest that the reproducibility of 2-DE has been suitable for the study of differential expression of proteomes. Proteome differential expression maps can be useful tools for disease diagnosis, drug-target validation analysis and biological process elucidation.

  10. A high sensitivity, high throughput, automated single-cell gel electrophoresis ('Comet') DNA damage assay

    International Nuclear Information System (INIS)

    A fully automated microscopy machine vision image capture and analysis system for the collection of data from slides of 'comets' has been developed. The novel image processing algorithms employed in delineating the 'comet head' from the 'comet tail' allow us to determine accurately very low levels of damage. In conjunction with calibrated and automated image capture methods, we are able to eliminate operator subjectivity and analyse large numbers of cells (>2500) in a short time (<1 hour). The image processing algorithm is designed to handle particularly difficult nuclei containing a high degree of structure, due to DNA clumping. We also present techniques used to extend the assay's dynamic range by removing interfering background fluorescence and to define a region of interest. If subtle biological variations are to be quantified (e.g. cell cycle dependant damage), then the use of large cell populations is dictated. Under those circumstances, the use of a fully automated system is particularly advantageous providing that the manner in which data is extracted does not introduce any inadvertent bias. In practice, it is essential that the image processing steps are geared towards the correct recognition of an acceptable cell nucleus, i.e. comet 'head'. We acknowledge the financial support of CRUK, Programme Grant C133/A1812 - SP 2195-01/02 and the US Department of Energy Low Dose Radiation Research Program grant DE-FG07-99ER62878

  11. Gel Electrophoresis of Gold-DNA Nanoconjugates

    Directory of Open Access Journals (Sweden)

    T. Pellegrino

    2007-01-01

    Full Text Available Gold-DNA conjugates were investigated in detail by a comprehensive gel electrophoresis study based on 1200 gels. A controlled number of single-stranded DNA of different length was attached specifically via thiol-Au bonds to phosphine-stabilized colloidal gold nanoparticles. Alternatively, the surface of the gold particles was saturated with single stranded DNA of different length either specifically via thiol-Au bonds or by nonspecific adsorption. From the experimentally determined electrophoretic mobilities, estimates for the effective diameters of the gold-DNA conjugates were derived by applying two different data treatment approaches. The first method is based on making a calibration curve for the relation between effective diameters and mobilities with gold nanoparticles of known diameter. The second method is based on Ferguson analysis which uses gold nanoparticles of known diameter as reference database. Our study shows that effective diameters derived from gel electrophoresis measurements are affected with a high error bar as the determined values strongly depend on the method of evaluation, though relative changes in size upon binding of molecules can be detected with high precision. Furthermore, in this study, the specific attachment of DNA via gold-thiol bonds to Au nanoparticles is compared to nonspecific adsorption of DNA. Also, the maximum number of DNA molecules that can be bound per particle was determined.

  12. Exploitation of the Dose/Time-Response Relationship for a New Measure of DNA Repari in the Single-Cell Gel Electrophoresis (Comet) Assay

    International Nuclear Information System (INIS)

    The comet assay (also called the single-cell gel electrophoresis assay) has been widely used for detecting DNA damage and repair in individual cells. Since the conventional methods of evaluating comet assay data using frequency statistics are unsatisfactory we developed a new quantitative measure of DNA damage/repair that is based on all information residing in the dose/time-response curves of a comet experiment. Blood samples were taken from 25 breast cancer patients before undergoing radiotherapy. The comet assay was performed under alkaline conditions using isolated lymphocytes

  13. Proteins pattern alteration in AZT-treated K562 cells detected by two-dimensional gel electrophoresis and peptide mass fingerprinting

    Directory of Open Access Journals (Sweden)

    Mignogna Giuseppina

    2006-03-01

    Full Text Available Abstract In this study we report the effect of AZT on the whole protein expression profile both in the control and the AZT-treated K562 cells, evidenced by two-dimensional gel electrophoresis and peptide mass fingerprinting analysis. Two-dimensional gels computer digital image analysis showed two spots that appeared up-regulated in AZT-treated cells and one spot present only in the drug exposed samples. Upon extraction and analysis by peptide mass fingerprinting, the first two spots were identified as PDI-A3 and stathmin, while the third one was proved to be NDPK-A. Conversely, two protein spots were present only in the untreated K562 cells, and were identified as SOD1 and HSP-60, respectively.

  14. Two-dimensional gel electrophoresis for controlling and comparing culture supernatants of mammalian cell culture productions systems.

    Science.gov (United States)

    Wimmer, K; Harant, H; Reiter, M; Blüml, G; Gaida, T; Katinger, H

    1994-01-01

    A recombinant Chinese hamster ovary cell line, producing human erythropoietin, was cultivated in a continuous mode in a stirred tank reactor applying different dilution rates. In order to monitor the stability of this expression system, product and non-product proteins of the cell culture supernatant were analyzed by two-dimensional electrophoresis. The consistency of the isoforms of the recombinant product was determined by western blot combined with specific staining. The same cell line was propagated in a high cell density cultivation system based on macro-cell-aggregates. The patterns of secreted proteins of the cell line cultivated in the different systems were compared in order to detect modifications in protein expression of the product and of non product proteins relevant for cell culture supernatant. Hardly any alterations in two-dimensional pattern were detectable. The isoforms of erythropoietin, as well as the overall pattern of secreted proteins, detectable with the two-dimensional electrophoresis method were remarkably stable under different cultivation conditions.

  15. Inexpensive and Safe DNA Gel Electrophoresis Using Household Materials

    Science.gov (United States)

    Ens, S.; Olson, A. B.; Dudley, C.; Ross, N. D., III; Siddiqi, A. A.; Umoh, K. M.; Schneegurt, M. A.

    2012-01-01

    Gel electrophoresis is the single most important molecular biology technique and it is central to life sciences research, but it is often too expensive for the secondary science classroom or homeschoolers. A simple safe low-cost procedure is described here that uses household materials to construct and run DNA gel electrophoresis. Plastic…

  16. The application of single cell gel electrophoresis or comet assay to human monitoring studies Aplicacion de la electroforesis unicelular o ensayo cometa en estudios de monitoreo humano

    Directory of Open Access Journals (Sweden)

    Mahara Valverde

    1999-11-01

    Full Text Available Objective. In the search of new human genotoxic biomarkers, the single cell gel electrophoresis assay has been proposed as a sensible alternative. Material and methods. This technique detects principally single strand breaks as well as alkali-labile and repair-retarded sites. Results. Herein we present our experience using the single cell gel electrophoresis assay in human population studies, both occupationally and environmentally exposed. Conclusions. We discuss the assay feasibility as a genotoxic biomarker.Objetivo. En la búsqueda de nuevos marcadores genotóxicos aplicables a estudios de poblaciones humanas expuestos a xenobióticos, la utilización del ensayo de electroforesis en una sola célula se ha propuesto como un método sensible y una buena alternativa. Material y métodos. Esta técnica detecta rompimientos en el ADN de cadena sencilla, así como sitios álcali lábiles y sitios retardados de reparación. Resultados. En este trabajo, presentamos nuestra experiencia utilizando este ensayo en poblaciones humanas expuestas ocupacionalmente o ambientalmente a diferentes xenobióticos. Conclusiones. Se discute la posible utilidad de este ensayo como un biomarcador de efecto genotóxico.

  17. Feasibility of measuring radiation-induced DNA double strand breaks and their repair by pulsed field gel electrophoresis in freshly isolated cells from the mouse RIF-1 tumor

    International Nuclear Information System (INIS)

    Purpose: To examine the technical feasibility of pulsed field gel electrophoresis (PFGE) as a predictive assay for the radio responsiveness of tumors. Induction and repair of DNA double strand breaks (DSBs) in a freshly prepared cell suspension from a RIF-1 tumor (irradiated ex vivo) was compared with DSB induction and repair in exponentially growing RIF-1 cells in culture (irradiated in vitro). Methods and Materials: A murine RIF-1 tumor grown in vivo was digested, and cells were exposed to x-rays (ex vivo) at doses of 1 to 75 Gy. DNA damage was measured using CHEF (clamped homogeneous electric fields) electrophoresis. Repair kinetics were studied at 37 deg. C for 4 h after irradiation. Radiosensitivity was determined by clonogenic assay, and cell cycle distributions by flow cytometry. For comparison, a trypsinized suspension of exponentially growing RIF-1 cells in vitro was run parallel with each ex vivo experiment. Results: Induction of DSBs, expressed as % DNA extracted from the plug, was similar in the in vitro and ex vivo irradiated cells. Compared to repair rates in in vitro cultured RIF-1 cells, repair kinetics in a freshly prepared cell suspension from the tumor were decreased, unrelated to differences in radiosensitivity. Differences in repair could not be explained by endogenous DNA degradation, nor by influences of enzymes used for digestion of the tumor. A lower plating efficiency and differences in ploidy (as revealed by flow cytometry) were the only reproducible differences between in vivo and in vitro grown cells that may explain the differences in repair kinetics. Conclusions: The current results do not support the idea that PFGE is a technique robust enough to be a predictive assay for the radiosensitivity of tumor cells

  18. Further characterization of filarial antigens by SDS polyacrylamide gel electrophoresis

    OpenAIRE

    Dissanayake, S.; Galahitiyawa, S. C.; Ismail, M. M.

    1983-01-01

    SDS (sodium dodecyl sulfate)-polyacrylamide gel electrophoresis of an antigen isolated from sera of Wuchereria bancrofti-infected patients and Setaria digitata antigen SD2-4 is reported. Both antigens showed carbohydrate (glycoprotein) staining. The W. bancrofti antigen had an apparent relative molecular mass of 35 000 while the S. digitata antigen SD2-4 migrated at the marker dye position on SDS-polyacrylamide gel electrophoresis. SDS treatment of these antigens did not abolish the precipita...

  19. Diced electrophoresis gel assay for screening enzymes with specified activities.

    Science.gov (United States)

    Komatsu, Toru; Hanaoka, Kenjiro; Adibekian, Alexander; Yoshioka, Kentaro; Terai, Takuya; Ueno, Tasuku; Kawaguchi, Mitsuyasu; Cravatt, Benjamin F; Nagano, Tetsuo

    2013-04-24

    We have established the diced electrophoresis gel (DEG) assay as a proteome-wide screening tool to identify enzymes with activities of interest using turnover-based fluorescent substrates. The method utilizes the combination of native polyacrylamide gel electrophoresis (PAGE) with a multiwell-plate-based fluorometric assay to find protein spots with the specified activity. By developing fluorescent substrates that mimic the structure of neutrophil chemoattractants, we could identify enzymes involved in metabolic inactivation of the chemoattractants.

  20. Strategic analysis for a novel gel electrophoresis technology

    OpenAIRE

    Yu, Jeff

    2007-01-01

    A novel gel electrophoresis technology for separating protein and nucleic acid is under development by a research team at Simon Fraser University (SFU. Compared with the conventional gel electrophoresis technology, the new technology is easier to use, has higher throughput, and lower use cost. The purpose of this project is to help the researchers to commercialize the new technology. This report begins with introduction of the project, followed by an industry analysis. Then it develops and di...

  1. Evaluation of DNA damage in oral precancerous and squamous cell carcinoma patients by single cell gel electrophoresis

    Directory of Open Access Journals (Sweden)

    Sanjit Mukherjee

    2011-01-01

    Materials and Methods: Peripheral blood was collected by venepuncture and comet assay was performed using SCGE. Mean tail length was compared between diagnostic groups and between different oral habit groups using t-tests and analysis of variance (ANOVA. Pearson′s product moment correlation was used to examine the linear association between the extent of DNA damage and oral habit pack-years. Scheffe′s pair-wise test was employed to adjust for multiple comparisons. Results: None of the controls were associated with any oral habits. Mean (±SD tail lengths (in mm for cancer (24.95 ± 5.09 and leukoplakia (12.96 ± 2.68 were significantly greater than in controls (8.54 ± 2.55, P<0.05. After adjustment, well-, moderately, and poorly differentiated carcinomas had significantly greater tail length than controls. Whereas the extent of DNA damage in cancer cases was significantly greater in leukoplakia than in compared to OSMF (11.03 ± 5.92, the DNA damage in latter was not different from controls. DNA damage for people with any oral habit (19.78 ± 7.77 was significantly greater than those with no habits (8.54 ± 2.55; P<0.0001. Conclusions: DNA damage measured by SCGE is greater in leukoplakia and squamous cell carcinoma, but not in OSMF. Deleterious oral habits are also associated with greater DNA damage.

  2. Strain identification in Rhizobium by starch gel electrophoresis of isoenzymes

    DEFF Research Database (Denmark)

    Engvild, Kjeld Christensen; Nielsen, G.

    1985-01-01

    Sonieated extracts of rhizobia, especiaUy Rhizobium leguminosarum from pea and vetch, were run in horizontal starch gel electrophoresis in the cold. The rhizobia were grown on agar on a slime suppressing substrate of tryptone-yeast extract-CaCl2 with small amounts of mannitol, sorbitol and arabin......Sonieated extracts of rhizobia, especiaUy Rhizobium leguminosarum from pea and vetch, were run in horizontal starch gel electrophoresis in the cold. The rhizobia were grown on agar on a slime suppressing substrate of tryptone-yeast extract-CaCl2 with small amounts of mannitol, sorbitol...... and arabinose and other sugars as enzyme inducers. After electrophoresis the gels were separated into several slabs by a gel cutter. Each slab was stained for a particular enzyme. Among numerous enzyme systems tested we found useful variation in esterases (EC 3.1.1.1, EC 3.1.1.2), 3-hydroxybutyrate...

  3. Synchrotron radiation for direct analysis of metalloproteins on electrophoresis gels.

    Science.gov (United States)

    Ortega, Richard

    2009-03-01

    Metalloproteomics requires analytical techniques able to assess and quantify the inorganic species in metalloproteins. The most widely used methods are hyphenated techniques, based on the coupling of a high resolution chromatographic method with a high sensitivity method for metal analysis in solution. An alternative approach is the use of methods for solid sample analysis, combining metalloprotein separation by gel electrophoresis and direct analysis of the gels. Direct methods are based on beam analysis, such as lasers, ion beams or synchrotron radiation beams. The aim of this review article is to present the main features of synchrotron radiation based methods and their applications for metalloprotein analysis directly on electrophoresis gels. Synchrotron radiation X-ray fluorescence has been successfully employed for sensitive metal identification, and X-ray absorption spectroscopy for metal local structure speciation in proteins. Synchrotron based methods will be compared to ion beam and mass spectrometry for direct analysis of metalloproteins in electrophoresis gels.

  4. Evaluation of radio-induced DNA damage and their repair in human lymphocytes by comet assay or single cell gel electrophoresis

    International Nuclear Information System (INIS)

    The comet assay, also called single cell gel electrophoresis technique, permits to evaluate quantitatively DNA breakage induced by chemical and physical agents at the level of the single cell. The present paper refers to the construction of dose-response curves to DNA damage and repair studies in human peripheral lymphocytes, utilizing the comet assay for the radiosensitivity analysis. So, the blood samples were obtained from healthy donors (40-50 year old), irradiated in a 60 Co source (GAMMACEL 220) with doses of 0.17, 0.25, 0.57, 1.10, 2.12 and 4.22 Gy (0.59 Gy/min.) and processed 1 and 24 hours after the exposition. Results obtained showed a increase in the total lenght of comet (DNA migration) as a function of radiation dose in samples processed 1 and 24 hours after the treatment. The DNA lesion in irradiated lymphocytes with 4.22 Gy (means value of 101.4 μm) were 3.4 times higher than in the untreated lymphocytes (mean value of 30 μm) instead of 24 hours after the irradiation were 1.5 times higher (mean value of 46.3 μm). This reduction on DNA repair occurred in these cells. It was also possible visualized the presence of subpopulations of the cells with different sensitivity and repair capacity to ionizing radiation in these donors. (author). 8 refs., 3 figs

  5. Detection of DNA damage by alkaline single cell gel electrophoresis in 2,4-dichlorophenoxyacetic-acid- and butachlor-exposed erythrocytes of Clarias batrachus.

    Science.gov (United States)

    Ateeq, Bushra; Abul Farah, M; Ahmad, Waseem

    2005-11-01

    The alkaline single cell gel electrophoresis, also known as comet assay, is a rapid, simple and sensitive technique for measuring DNA strand breaks in individual cells. The present study was undertaken to evaluate the genotoxic potential of two widely used herbicides; 2,4-dichlorophenoxyacetic acid (2,4-D) and 2-chloro-2,6-diethyl-N-(butoxymethyl) acetanilide (butachlor) in erythrocytes of freshwater catfish, Clarias batrachus. Fish were exposed by medium treatment with three sub-lethal concentrations of 2,4-D (25, 50, and 75ppm) and butachlor (1, 2, and 2.5ppm) and alkaline comet assay was performed on nucleated erythrocytes after 48, 72, and 96h. The amount of DNA damage in cells was estimated from comet tail length as the extent of migration of the genetic material. A significant increase in comet tail length indicating DNA damage was observed at all concentrations of both the herbicides compared with control (Pbutachlor (9.28microm). This study confirmed that the comet assay applied on the fish erythrocyte is a useful tool in determining potential genotoxicity of water pollutants and might be appropriate as a part of a monitoring program.

  6. Purification of coated vesicles by agarose gel electrophoresis

    OpenAIRE

    1981-01-01

    We have applied agarose gel electrophoresis as a novel step in the purification of clathrin-coated vesicles. Preparations of coated vesicles obtained by sedimentation velocity and isopycnic centrifugation are resolved into two distinct fractions upon electrophoresis. The slower migrating fraction contains smooth vesicles, whereas the faster contains only coated vesicles and empty clathrin coats. The faster mobility of the coated vesicles is primarily caused by the acidic nature of clathrin. C...

  7. Biochemical Identification of the Two Races of Radopholus similis by Polyacrylamide Gel Electrophoresis

    OpenAIRE

    Huettel, R. N.; Dickson, D. W.; Kaplan, D. T.

    1983-01-01

    Analysis of proteins of the banana and citrus race of Radopholus similis was carried out by several different types of polyacrylamide gel electrophoresis. These included standard slab gel, SDS slab gel, gradient slab gel, and two-ditnensional slab gel electrophoresis. A major band difference was detected between the two races by slab gel electrophoresis. However, several other poorly resolved but consistent hands of high molecular weight proteins near the gel origin also were considered as di...

  8. Explorative data analysis of two-dimensional electrophoresis gels

    DEFF Research Database (Denmark)

    Schultz, J.; Gottlieb, D.M.; Petersen, Marianne Kjerstine;

    2004-01-01

    Methods for classification of two-dimensional (2-DE) electrophoresis gels based on multivariate data analysis are demonstrated. Two-dimensional gels of ten wheat varieties are analyzed and it is demonstrated how to classify the wheat varieties in two qualities and a method for initial screening...... of gels is presented. First, an approach is demonstrated in which no prior knowledge of the separated proteins is used. Alignment of the gels followed by a simple transformation of data makes it possible to analyze the gels in an automated explorative manner by principal component analysis, to determine...... if the gels should be further analyzed. A more detailed approach is done by analyzing spot volume lists by principal components analysis and partial least square regression. The use of spot volume data offers a mean to investigate the spot pattern and link the classified protein patterns to distinct spots...

  9. Genotoxicity assessment of antidiabetic formulation (ADPHF6 in human lymphocytes by single cell gel electrophoresis (comet assay - an in vitro study

    Directory of Open Access Journals (Sweden)

    Devanand Shanmugasundaram

    2015-06-01

    Full Text Available Levels of Reactive Oxygen Species (ROS molecules during aerobic metabolism are often regulated by unique endogenous antioxidant system. During hyperglycaemic condition, accumulation of excess fatty acids & glucose in adipose tissue (Wright Jr E., 2006 results in increased levels of ROS. When ROS molecules overwhelms the cells antioxidant defence system, it ends up in cellular oxidative stress; which in turn is reported to cause oxidative DNA damage & intervene damage to macromolecules & cellular membranes (Ahmad et al., 2013. Our novel anti-hyperglycaemic polyherbal formulation (ADPHF6 had already illustrated significant inhibitory activity against α-amylase & α-glucosidase enzymes and also scavenging free radicals (in vitro models. The present study demonstrates the protective effect of formulation against H2O2 induced DNA damage in human lymphocytes by Single Cell Gel Electrophoresis (SCGE assay. Experimental procedures were approved by Institutional Human Ethics Committee of Frontier Lifeline Hospital, Chennai, India (FLL/IEC/02/2014. Peripheral human lymphocytes were isolated (Duthie et.al, 2002 and subjected for Cell viability by Trypan blue exclusion method. The alkaline SCGE assay was carried out to determine the level of DNA damage in ADPHF6 treated cells with minor modifications from Singh et al., 1988. Frosted microscopic slides were pre-coated with 1% NMA followed by 1% LMA and incubated for 15 min at 15-20o C. 100 μL of freshly prepared cell suspension (2 x 104 cells was mixed with 0.5% LMA & casted on microscopic slide. The cells were immersed in lysing solution for 2 hours at 4O C and washed in TBE buffer for 5 min at RT. All the slides were treated with fresh alkaline solution for 20 minutes for expression of alkali-labile damage. Electrophoresis was performed at 24 V for 20 min at RT. Slides were washed in neutralizing buffer for 5 min at RT. All the groups were stained with Acridine Orange (20µg/ml & Propidium Iodide (20µg

  10. Characterisation of ribosomal proteins from HeLa and Krebs II mouse ascites tumor cells by different two-dimensional polyacrylamide gel electrophoresis techniques

    DEFF Research Database (Denmark)

    Issinger, O G; Beier, H

    1978-01-01

    Electrophoresis of ribosomal proteins according to Kaltschmidt and Wittmann, 1970a, b (pH 8.6/pH 4.5 urea system) yielded 29 proteins for the small subunits and 35 and 37 proteins for the large subunits of Krebs II ascites and HeLa ribosomes, respectively. Analysis of the proteins according...... to a modified technique by Mets and Bogorad (1974) (pH 4.5/pH 8.6 SDS system) revealed 28 and 29 proteins in the small subunits and 37 and 38 proteins in the large subunits of Krebs II ascites and HeLa ribosomes. The molecular weights of the individual proteins were determined by: 1. "three-dimensional" gel...... electrophoresis; 2. two-dimensional gel electrophoresis at pH 4.K/pH 8.6 in SDS. The molecular weights for 40S proteins ranged from 10,000 to 39,000 dalton (number average molecular weight: 21,000). The molecular weights for the 60S proteins ranged from 14,000 to 44,000 dalton (number average molecular weight: 23...

  11. DNA double-strand breaks in mammalian cells exposed to gamma-rays and very heavy ions. Fragment-size distributions determined by pulsed-field gel electrophoresis.

    Science.gov (United States)

    Kraxenberger, F; Weber, K J; Friedl, A A; Eckardt-Schupp, F; Flentje, M; Quicken, P; Kellerer, A M

    1998-07-01

    The spatial distribution of DNA double-strand breaks (DSB) was assessed after treatment of mammalian cells (V79) with densely ionizing radiation. Cells were exposed to beams of heavy charged particles (calcium ions: 6.9 MeV/u, 2.1.10(3) keV/microm; uranium ions: 9.0 MeV/u, 1.4.10(4) keV/microm) at the linear accelerator UNILAC of GSI, Darmstadt. DNA was isolated in agarose plugs and subjected to pulsed-field gel electrophoresis under conditions that separated DNA fragments of size 50 kbp to 5 Mbp. The measured fragment distributions were compared to those obtained after gamma-irradiation and were analyzed by means of a convolution and a deconvolution technique. In contrast to the finding for gamma-radiation, the distributions produced by heavy ions do not correspond to the random breakage model. Their marked overdispersion and the observed excess of short fragments reflect spatial clustering of DSB that extends over large regions of the DNA, up to several mega base pairs (Mbp). At fluences of 0.75 and 1.5/microm2, calcium ions produce nearly the same shape of fragment spectrum, merely with a difference in the amount of DNA entering the gel; this suggests that the DNA is fragmented by individual calcium ions. At a fluence of 0.8/microm2 uranium ions produce a profile that is shifted to smaller fragment sizes in comparison to the profile obtained at a fluence of 0.4/microm2; this suggests cumulative action of two separate ions in the formation of fragments. These observations are not consistent with the expectation that the uranium ions, with their much larger LET, should be more likely to produce single particle action than the calcium ions. However, a consideration of the greater lateral extension of the tracks of the faster uranium ions explains the observed differences; it suggests that the DNA is closely coiled so that even DNA locations several Mbp apart are usually not separated by less than 0. 1 or 0.2 microm. PMID:9728743

  12. Images of gel electrophoresis - RGP caps | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us RGP caps Images... of gel electrophoresis Data detail Data name Images of gel electrophoresis Description of da...pdate History of This Database Site Policy | Contact Us Images of gel electrophoresis - RGP caps | LSDB Archive ...

  13. Evaluation of DNA damage in agricultural workers exposed to pesticides using single cell gel electrophoresis (comet assay

    Directory of Open Access Journals (Sweden)

    Raminderjeet Kaur

    2011-01-01

    Full Text Available Background : Pesticides are used in agriculture to protect crops, but they pose a potential risk to farmers and environment. The aim of the present study is to investigate the relation between the occupational exposure to various pesticides and the presence of DNA damage. Materials and Methods : Blood samples of 210 exposed workers (after a day of intense spraying and 50 control subjects belonging to various districts of Punjab (India were evaluated using Comet assay. Sixty workers who showed DNA damage were selected for follow up at 5-6 months after the first sampling during a low or null spraying period. Results : Significant differences were found in DNA damage between freshly exposed workers and controls and freshly exposed and followed up cases. There was significant increase in the comet parameters viz. mean comet tail length and frequency of cells showing migration in exposed workers as compared to controls (72.22 ± 20.76 vs. 46.92 ± 8.17, P<0.001; 31.79 vs. 5.77, P<0.001. In the second samples, followed up cases showed significant decrease in frequency of damaged cells as compared to freshly exposed workers of first sampling (P<0.05. The confounding factors such as variable duration of pesticide exposure, age, smoking, drinking and dietary habits etc which were expected to modulate the damage, were instead found to have no significant effect on DNA fragmentation. Conclusion : The evidence of a genetic hazard related to exposure resulting from the intensive use of pesticides stresses the need for educational programs for agricultural workers to reduce the use of chemicals in agriculture.

  14. Aligning Goals, Assessments, and Activities: An Approach to Teaching PCR and Gel Electrophoresis

    Science.gov (United States)

    Phillips, Allison R.; Robertson, Amber L.; Batzli, Janet; Harris, Michelle; Miller, Sarah

    2008-01-01

    Polymerase chain reaction (PCR) and gel electrophoresis have become common techniques used in undergraduate molecular and cell biology labs. Although students enjoy learning these techniques, they often cannot fully comprehend and analyze the outcomes of their experiments because of a disconnect between concepts taught in lecture and experiments…

  15. Thermally reversible gels in electrophoresis. I - Matrix characterization

    Science.gov (United States)

    Righetti, Pier Giorgio; Snyder, Robert S.

    1988-01-01

    Two series of thermally reversible hydrogen-bonded gels have been characterized: (5 pct) PVA-(4 pct) PEG and (5 pct) PVA-(0.04 pct) borate gels. They both have extremely low melting points (16-17 C) and could be of potential interest for recovery of proteins after preparative electrophoresis. The PVA-borate gels can be exploited in the pH range 7-11 by progressively increasing the borate content in the pH interval 8 to 7 and concomitantly decreasing the borate levels in the pH zone 8 to 11. It is hypothesized that the low melting point of these gels is due to the fact that they are sparingly and sparsely hydrogen bonded along the PVA chain: on the average, 1 OH group out of 3 or 4 OH groups in the PVA polymer should be engaged in H-bond formation.

  16. Repair of γ-irradiation-induced DNA single-strand breaks in human bone marrow cells. Analysis of unfractionated and CD34+ cells using single-cell gel electrophoresis

    International Nuclear Information System (INIS)

    Human bone marrow mononuclear cells (BMMNCs) were separated by density gradient centrifugation, and a subpopulation of progenitor cells was further isolated using anti-CD34-coated magnetic beads. The cells were irradiated with γ-rays (0.93-5.43 Gy) from a 137Cs source. The extent of DNA damage, i.e., single-strand breaks (SSBs) and alkali-labile lesions of individual cells, was investigated using the alkaline single-cell gel electrophoresis technique. The irradiation resulted in a dose-dependent increase in DNA migration, reflecting the number of detectable DNA lesions. An approximately similar extent of SSB formation was observed in BMMNCs and CD34+ cells. Damage was repaired when the cells were incubated at 37C: a fast initial repair phase was followed by a slower rejoining of SSBs in both BMMNC and CD34+ cell populations. A significantly longer time was required to repair the lesions caused by 5.43 Gy than those caused by 0.93 Gy. In the present work we report, for the first time, the induction and repair of DNA SSBs at the level of single human bone marrow cells when exposed to ionizing radiation at clinically relevant doses. These data, together with our previous results with human blood granulocytes and lymphocytes, indicate an approximately similar extent of formation and repair of γ-irradiation-induced DNA SSBs in immature and mature human hematopoietic cells

  17. Insight of Saffron Proteome by Gel-Electrophoresis

    OpenAIRE

    Gianluca Paredi; Samanta Raboni; Francesco Marchesani; ORDOUDI, Stella A; TSIMIDOU, Maria Z; Andrea Mozzarelli

    2016-01-01

    Saffron is a spice comprised of the dried stigmas and styles of Crocus sativus L. flowers and, since it is very expensive, it is frequently adulterated. So far, proteomic tools have never been applied to characterize the proteome of saffron or identify possible cases of fraud. In this study, 1D-Gel Electrophoresis was carried out to characterize the protein profile of (i) fresh stigmas and styles of the plant; (ii) dried stigmas and styles from different geographical origins (Spanish, Italian...

  18. How to use 2D gel electrophoresis in plant proteomics.

    OpenAIRE

    Rabilloud, Thierry

    2014-01-01

    International audience Two-dimensional electrophoresis has nurtured the birth of proteomics. It is however no longer the exclusive setup used in proteomics, with the development of shotgun proteomics techniques that appear more fancy and fashionable nowadays.Nevertheless, 2D gel-based proteomics still has valuable features, and sometimes unique ones, which make it often an attractive choice when a proteomics strategy must be selected. These features are detailed in this chapter, as is the ...

  19. Statistical Analyses of Complex Denaturing Gradient Gel Electrophoresis Profiles

    OpenAIRE

    Gafan, Gavin P.; Lucas, Victoria S.; Roberts, Graham J.; Petrie, Aviva; Wilson, Michael; David A. Spratt

    2005-01-01

    Studies using molecular techniques have demonstrated that a culture-based approach can severely underestimate the bacterial diversity in most environments. One of the molecular techniques that has been applied in microbial ecology is denaturing gradient gel electrophoresis (DGGE). The purpose of this study was to investigate differences in the microbiota of plaque, using a number of analysis techniques, from children without gingivitis (n = 30) and from those with gingivitis (n = 30). Extract...

  20. Statistical analyses of complex denaturing gradient gel electrophoresis profiles

    OpenAIRE

    Gafan, G. P.; Lucas, V S; Roberts, G J; Petrie, A; Wilson, M; Spratt, D. A.

    2005-01-01

    Studies using molecular techniques have demonstrated that a culture-based approach can severely underestimate the bacterial diversity in most environments. One of the molecular techniques that has been applied in microbial ecology is denaturing gradient gel electrophoresis (DGGE). The purpose of this study was to investigate differences in the microbiota of plaque, using a number of analysis techniques, from children without gingivitis (n = 30) and from those with gingivitis (n = 30). Extract...

  1. Mapping and identification of HeLa cell proteins separated by immobilized pH-gradient two-dimensional gel electrophoresis and construction of a two-dimensional polyacrylamide gel electrophoresis database

    DEFF Research Database (Denmark)

    Shaw, AC; Rossel Larsen, M; Roepstorff, P;

    1999-01-01

    The HeLa cell line, a human adenocarcinoma, is used in many research fields, since it can be infected with a wide range of viruses and intracellular bacteria. Therefore, the mapping of HeLa cell proteins is useful for the investigation of parasite host cell interactions. Because of the recent...

  2. Demonstration of a third structurally distinct human Ia beta chain by two-dimensional gel electrophoresis

    OpenAIRE

    1982-01-01

    Previous studies have indicated that HLA-DR homozygous cell lines express two Ia alpha and Ia beta chains that combine to form at least two Ia molecules. This report demonstrates by two-dimensional gel electrophoresis the existence of a third structurally distinct human Ia beta chain on DR2 and DR5 cell lines. This suggests that at least five separate genes control the expression of Ia molecules on HLA-DR homozygous cell lines.

  3. Down-regulation of triose phosphate isomerase in Vineristine-resistant gastric cancer SGC7901 cell line identified by immobilized pH gradient two-dimensional gel electrophoresis and mierosequencing

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Objective:To exkplore new multidrug-resistance-related proteins in gastric SC7901 cells and clarify their mechanisms.Methods:Two-dimensional(2-D) polyacrylamide gel electrophoresis with immobilized pH gradients(IPG) was applied to compare the differential expression of multidrug-resistance-related proteins in gastric cancer SGC7901 cells and Vineristine-resistant SGC7901 cells (SGC7901/VCR) induced by vincristine sulfate.The 2-D gels were silver-stained.Then,preparative 2-D PAGE was performed.The differential proteins of PVDF membranes were cxcised and identified by N-terminal microsequencing.The mRNA expressions of differential proteins were detected in SGC 7901 cells and SGC7901/VCR cells by RT-PCR.Results:Approximatedly 680 protein sports were resolved on each 2-D gel by silver staining.Most protein spots showed no difference in composition,shape or density.25 proteins differed in abundance (6 higher in SGC7901/VCR cells;19 higher in 7901 cells);5 proteins were unique to one kind of cell or the othe(3 in SGC7901/VRC cells,2 in 7901 cells).One drug-resistance-related protein,which was down-regulated in SGC7901/VCR cells,was identified as trisephosphate isomerase(TPI),a glycolytic pathway enzyme.Conclusions:the results suggest that these differential proteins including TPI may be related to the Vincristine-resistant mechanism in human gastric cancer SGC7901/VCR cell line.

  4. Analysis of branched DNA replication and recombination intermediates from prokaryotic cells by two-dimensional (2D) native-native agarose gel electrophoresis.

    Science.gov (United States)

    Robinson, Nicholas P

    2013-01-01

    Branched DNA molecules are generated by the essential processes of replication and recombination. Owing to their distinctive extended shapes, these intermediates migrate differently from linear double-stranded DNA under certain electrophoretic conditions. However, these branched species exist in the cell at much low abundance than the bulk linear DNA. Consequently, branched molecules cannot be visualized by conventional electrophoresis and ethidium bromide staining. Two-dimensional native-native agarose electrophoresis has therefore been developed as a method to facilitate the separation and visualization of branched replication and recombination intermediates. A wide variety of studies have employed this technique to examine branched molecules in eukaryotic, archaeal, and bacterial cells, providing valuable insights into how DNA is duplicated and repaired in all three domains of life.

  5. Optimizing Human Bile Preparation for Two-Dimensional Gel Electrophoresis

    Directory of Open Access Journals (Sweden)

    Hao-Tsai Cheng

    2016-01-01

    Full Text Available Aims. Bile is an important body fluid which assists in the digestion of fat and excretion of endogenous and exogenous compounds. In the present study, an improved sample preparation for human bile was established. Methods and Material. The method involved acetone precipitation followed by protein extraction using commercially available 2D Clean-Up kit. The effectiveness was evaluated by 2-dimensional electrophoresis (2DE profiling quality, including number of protein spots and spot distribution. Results. The total protein of bile fluid in benign biliary disorders was 0.797 ± 0.465 μg/μL. The sample preparation method using acetone precipitation first followed by 2D Clean-Up kit protein extraction resulted in better quality of 2DE gel images in terms of resolution as compared with other sample preparation methods. Using this protocol, we obtained approximately 558 protein spots on the gel images and with better protein spots presentation of haptoglobin, serum albumin, serotransferrin, and transthyretin. Conclusions. Protein samples of bile prepared using acetone precipitation followed by 2D Clean-Up kit exhibited high protein resolution and significant protein profile. This optimized protein preparation protocol can effectively concentrate bile proteins, remove abundant proteins and debris, and yield clear presentation of nonabundant proteins and its isoforms on 2-dimensional electrophoresis gel images.

  6. System for loading slab-gel holders for electrophoresis separation

    Science.gov (United States)

    Anderson, Norman G.; Anderson, Norman L.

    1979-01-01

    A slab-gel loading system includes a prismatic chamber for filling a plurality of slab-gel holders simultaneously. Each slab-gel holder comprises a pair of spaced apart plates defining an intermediate volume for gel containment. The holders are vertically positioned in the chamber with their major surfaces parallel to the chamber end walls. A liquid inlet is provided at the corner between the bottom and a side wall of the chamber for distributing a polymerizable monomer solution or a coagulable colloidal solution into each of the holders. The chamber is rotatably supported so that filling can begin with the corner having the liquid inlet directed downwardly such that the solution is gently funneled upwardly, without mixing, along the diverging side and bottom surfaces. As filling proceeds, the chamber is gradually rotated to position the bottom wall in a horizontal mode. The liquid filling means includes a plastic envelope with a septum dividing it into two compartments for intermixing two solutions of different density and thereby providing a liquid flow having a density gradient. The resulting gels have a density gradient between opposite edges for subsequent use in electrophoresis separations.

  7. INDIRECT SAFETY ASSESSMENT OF ECTODERMAL MERCURY EXPOSURE BY TRADITIONAL MEDICAL FORMULATIONS ON FRESHWATER CAT FISH CLARIAS BATRACHUS USING MICRONUCLEUS ASSAY AND ALKALINE SINGLE-CELL GEL ELECTROPHORESIS (COMET ASSAY

    Directory of Open Access Journals (Sweden)

    Anand Prem Rajan

    2012-02-01

    Full Text Available Mercury and its salts are the major constituents of Ayurvedic, Chinese and Tibetan traditional formulations. The mercury is extensively reported to accumulate in food chain and cause many neurological disorders in environment. The safety assessment of mercury on the ectodermal application on animal model is rarely reported. The void in the scientific study on external exposure of mercury and its genotoxic inside the body lead to the necessity for the present study. The freshwater cat fish Clarias batrachus was used for broad specificity genotoxic indicators micronucleus assay and alkaline single-cell gel electrophoresis (comet assays. The fish was exposed to 0.03 ppm of mercuric chloride for a period of 7, 14, 28 and 35 days ectodermally. The blood sample was assayed for the genotoxicity. The results revealed undoubted DNA damage through the micronuclei and alkaline single-cell gel electrophoresis (comet assays. Hence it is concluded the usage of traditional medicines containing the mercury may be toxic at genetic level in prolonged usage.

  8. Optimal processing for gel electrophoresis images: Applying Monte Carlo Tree Search in GelApp.

    Science.gov (United States)

    Nguyen, Phi-Vu; Ghezal, Ali; Hsueh, Ya-Chih; Boudier, Thomas; Gan, Samuel Ken-En; Lee, Hwee Kuan

    2016-08-01

    In biomedical research, gel band size estimation in electrophoresis analysis is a routine process. To facilitate and automate this process, numerous software have been released, notably the GelApp mobile app. However, the band detection accuracy is limited due to a band detection algorithm that cannot adapt to the variations in input images. To address this, we used the Monte Carlo Tree Search with Upper Confidence Bound (MCTS-UCB) method to efficiently search for optimal image processing pipelines for the band detection task, thereby improving the segmentation algorithm. Incorporating this into GelApp, we report a significant enhancement of gel band detection accuracy by 55.9 ± 2.0% for protein polyacrylamide gels, and 35.9 ± 2.5% for DNA SYBR green agarose gels. This implementation is a proof-of-concept in demonstrating MCTS-UCB as a strategy to optimize general image segmentation. The improved version of GelApp-GelApp 2.0-is freely available on both Google Play Store (for Android platform), and Apple App Store (for iOS platform).

  9. Emerging applications of the single cell gel electrophoresis (Comet) assay. I. Management of invasive transitional cell human bladder carcinoma. II. Fluorescent in situ hybridization Comets for the identification of damaged and repaired DNA sequences in individual cells.

    Science.gov (United States)

    McKelvey-Martin, V J; Ho, E T; McKeown, S R; Johnston, S R; McCarthy, P J; Rajab, N F; Downes, C S

    1998-01-01

    ABSTRACT I: Management of invasive transitional cell human bladder carcinoma. The two main treatment options for invasive transitional cell bladder carcinoma are radiotherapy or primary cystectomy with urinary diversion or bladder substitution. Approximately 50% of patients fail to respond to radiotherapy and such patients so treated are disadvantaged by the absence of predictive information regarding their radiosensitivity, since the tumour gains additional time for metastatic spread before cystectomy is performed. The SF2 clonogenic assay, which measures the surviving fraction of tumour cells after 2 Gy X-ray irradiation, is regarded as a good measure of radiosensitivity. However, the assay is time consuming and provides results for only approximately 70% of human tumours. In this paper three bladder transitional cell carcinoma cell lines (HT1376, UMUC-3 and RT112) were exposed to X-irradiation (0-10 Gy). We have compared the responses obtained using a clonogenic assay and a more clinically feasible alkaline single cell gel electrophoresis (Comet) assay. A very good inverse correlation was obtained between cell survival (clonogenic assay) and mean tail moment (Comet assay) for the three cell lines, indicating that the Comet assay can be used to predict the radio-responsiveness of individual cell lines. The clinical usefulness of the assay for predicting response to radiotherapy in bladder cancer patients is currently being investigated. ABSTRACT II: Fluorescent in situ hybridization (FISH) Comets for the identification of damaged and repaired DNA sequences in individual cells. In mammalian cells the extent of DNA damage is partly and the rate of DNA repair very considerably dependent on DNA position and transcription. This has been established by biochemical techniques which are labour intensive and require large numbers of cells. The Comet assay for overall DNA damage and repair is relatively simple and allows individual cells to be examined. Here we present a

  10. Preparation of Barley Storage Protein, Hordein, for Analytical Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis

    DEFF Research Database (Denmark)

    Doll, Hans; Andersen, Bente

    1981-01-01

    The extraction, reduction, and alkylation of barley hordein for routine electrophoresis in sodium dodecyl sulfate-polyacrylamide gels were studied to set up a simple preparation procedure giving well-resolved bands in the electrophoresis gel. Hordein was extracted from single crushed seeds or flour...... in a buffer without propan-2-ol but containing sodium dodecyl sulfate....

  11. Proteomic Profiling Of Two-Dimensional Gel Electrophoresis Protein Expression Data

    Science.gov (United States)

    Ahmad, Norhaiza; Zhang, J.; Brown, P. J.; James, D. C.; Birch, J. R.; Racher, A. J.; Smales, C. M.

    2008-01-01

    We have undertaken two-dimensional gel electrophoresis (2-DE) proteomic profiling on a series of cell lines with different recombinant antibody production rates. Due to the nature of 2-DE proteomic investigations there will always be `process variability' factors in any data set collected in this way. Some of this variation will arise during sample preparation, gel running and staining, while further variation will arise from the gel analysis procedure. Therefore, in order to identify all significant changes in protein expression between biological samples when analysed by 2-DE, the system precision or `error', and how this correlates to protein abundance, must be known. Only then can the system be considered robust and investigators accurately and confidently report all observable statistically significant changes in protein expression. We introduce an expression variability test to identify protein spots whose expression correlates with increased antibody production. The results have highlighted a small number of candidate proteins for further investigation.

  12. 2-D gel electrophoresis-based proteomic analysis reveals that ormeloxifen induces G0-G1 growth arrest and ERK-mediated apoptosis in chronic myeloid leukemia cells K562.

    Science.gov (United States)

    Pal, Pooja; Kanaujiya, Jitendra K; Lochab, Savita; Tripathi, Shashi B; Bhatt, Madan L B; Singh, Pradhyumna K; Sanyal, Sabyasachi; Trivedi, Arun K

    2011-04-01

    Ormeloxifen is a nonsteroidal selective estrogen receptor modulator (SERM) and has been shown to possess anticancer activities in breast and uterine cancer. Here, we show that ormeloxifen induces apoptosis in dose-dependent manner in a variety of leukemia cells, more strikingly in K562. 2-DE-gel electrophoresis of K562 cells induced with ormeloxifen showed that 57 and 30% of proteins belong to apoptosis and cell-cycle pathways, respectively. Our data demonstrate that ormeloxifen-induced apoptosis in K562 cells involves activation of extracellular signal-regulated kinases (ERKs) and subsequent cytochrome c release, leading to mitochondria-mediated caspase-3 activation. Ormeloxifen-induced apoptosis via ERK activation was drastically inhibited by prior treatment of K562 cells with ERK inhibitor PD98059. Ormeloxifen also inhibits proliferation of K562 cells by blocking them in G0-G1 phase by inhibiting c-myc promoter via ormeloxifen-induced MBP-1 (c-myc promoter-binding protein) and upregulation of p21 expression. We further show that ormeloxifen-induced apoptosis in K562 is translatable to mononuclear cells isolated from chronic myeloid leukemia (CML) patients. Thus, ormeloxifen induces apoptosis in K562 cells via phosphorylation of ERK and arrests them in G0-G1 phase by reciprocal regulation of p21 and c-myc. Therefore, inclusion of ormeloxifen in the therapy of chronic myeloid leukemia can be of potential utility. PMID:21360677

  13. Epidemiological Typing of Moraxella Catarrhalis by Pulsed Field Gel Electrophoresis

    Directory of Open Access Journals (Sweden)

    Susan M Davison

    1995-01-01

    Full Text Available Pulsed field gel electrophoresis (pfge was used to compare 59 strains of Moraxella catarrhalis to evaluate pfge for the epidemiological typing of this organism. pfge-generated patterns were compared with those obtained by small fragment restriction enzyme analysis (rea and species-specific probe hybridization. The strains used in the study were isolated from various geographic locations and included proven epidemiologically related strains. pfge yielded more unique patterns than dna-dna hybridization – 30 versus 18, respectively – but fewer than rea, which generated 45 unique patterns. Strains that demonstrated the same rea pattern or dna-dna hybridization pattern did not always demonstrate the same pfge pattern. For example, in 23 epidemiologically unrelated strains that shared six rea patterns, pfge differentiated the isolates into 12 patterns. Conversely, strains that demonstrated the same pfge pattern did not always demonstrate the same rea pattern or hybridization pattern. For example, in 42 strains that shared 13 pfge patterns, rea differentiated the isolates into 31 patterns and dna-dna hybridization differentiated them into 16 patterns. However, compared with rea, pfge yielded less complex patterns that were more easily comparable, and compared with dna-dna hybridization, pfge was technically easier.

  14. Comparison of protein patterns of xrs-5, a radiosensitive Chinese hamster ovary cell line, and CHO-K1, its radioresistant parent, using two-dimensional gel-electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Kramer, J.M. (Miami Univ., Oxford, OH (USA). Dept. of Zoology)

    1991-01-01

    X-ray sensitive strains of Chinese hamster ovary cell lines have been used to analyze radiation repair mechanisms. One cell line, xrs-5, has been shown to be very sensitive to ionizing radiation and radical forming chemical mutagens. This sensitivity is thought to be a result a mutation in the DNA double strand break (DSB) repair mechanism, and its characterization has been a goal of several repair mechanism studies. Using two-dimensional gel electrophoresis, we have detected a protein (MW approximately 55KD) in the DNA/Nuclear Matrix (nucleoid) cell fraction of CHO-Kl cells that is absent in the nucleoid fraction of xrs-5. This protein is present, however, in both CHO-Kl and xrs-5 whole cell protein maps. To determine whether the 55KD protein is responsible for the radiosensitive and defective DSB repair phenotype of xrs-5 cells, studies are now underway to analyze revertants of xrs-5 that are proficient in DSB repair. Furthermore, an effort to sequence the protein in question is planned. 23 refs., 2 figs.

  15. Comparison of protein patterns of xrs-5, a radiosensitive Chinese hamster ovary cell line, and CHO-K1, its radioresistant parent, using two-dimensional gel-electrophoresis

    International Nuclear Information System (INIS)

    X-ray sensitive strains of Chinese hamster ovary cell lines have been used to analyze radiation repair mechanisms. One cell line, xrs-5, has been shown to be very sensitive to ionizing radiation and radical forming chemical mutagens. This sensitivity is thought to be a result a mutation in the DNA double strand break (DSB) repair mechanism, and its characterization has been a goal of several repair mechanism studies. Using two-dimensional gel electrophoresis, we have detected a protein (MW approximately 55KD) in the DNA/Nuclear Matrix (nucleoid) cell fraction of CHO-Kl cells that is absent in the nucleoid fraction of xrs-5. This protein is present, however, in both CHO-Kl and xrs-5 whole cell protein maps. To determine whether the 55KD protein is responsible for the radiosensitive and defective DSB repair phenotype of xrs-5 cells, studies are now underway to analyze revertants of xrs-5 that are proficient in DSB repair. Furthermore, an effort to sequence the protein in question is planned. 23 refs., 2 figs

  16. Insight of Saffron Proteome by Gel-Electrophoresis

    Directory of Open Access Journals (Sweden)

    Gianluca Paredi

    2016-01-01

    Full Text Available Saffron is a spice comprised of the dried stigmas and styles of Crocus sativus L. flowers and, since it is very expensive, it is frequently adulterated. So far, proteomic tools have never been applied to characterize the proteome of saffron or identify possible cases of fraud. In this study, 1D-Gel Electrophoresis was carried out to characterize the protein profile of (i fresh stigmas and styles of the plant; (ii dried stigmas and styles from different geographical origins (Spanish, Italian, Greek and Iranian that had been stored for various periods of time after their processing; and (iii two common plant adulterants, dried petals of Carthamus tinctorius L. and dried fruits of Gardenia jasminoides Ellis. A selective protein extraction protocol was applied to avoid interference from colored saffron metabolites, such as crocins, during electrophoretic analyses of saffron. We succeeded in separating and assigning the molecular weights to more than 20 proteins. In spite of the unavailability of the genome of saffron, we were able to identify five proteins by Peptide Mass Fingerprinting: phosphoenolpyruvate carboxylase 3, heat shock cognate 70 KDa protein, crocetin glucosyltransferase 2, α-1,4-glucan-protein synthase and glyceraldehydes-3-phosphate dehydrogenase-2. Our findings indicate that (i few bands are present in all saffron samples independently of origin and storage time, with amounts that significantly vary among samples and (ii aging during saffron storage is associated with a reduction in the number of detectable bands, suggesting that proteases are still active. The protein pattern of saffron was quite distinct from those of two common adulterants, such as the dried petals of Carthamus tinctorius and the dried fruits of Gardenia jasminoides indicating that proteomic analyses could be exploited for detecting possible frauds.

  17. Insight of Saffron Proteome by Gel-Electrophoresis.

    Science.gov (United States)

    Paredi, Gianluca; Raboni, Samanta; Marchesani, Francesco; Ordoudi, Stella A; Tsimidou, Maria Z; Mozzarelli, Andrea

    2016-01-01

    Saffron is a spice comprised of the dried stigmas and styles of Crocus sativus L. flowers and, since it is very expensive, it is frequently adulterated. So far, proteomic tools have never been applied to characterize the proteome of saffron or identify possible cases of fraud. In this study, 1D-Gel Electrophoresis was carried out to characterize the protein profile of (i) fresh stigmas and styles of the plant; (ii) dried stigmas and styles from different geographical origins (Spanish, Italian, Greek and Iranian) that had been stored for various periods of time after their processing; and (iii) two common plant adulterants, dried petals of Carthamus tinctorius L. and dried fruits of Gardenia jasminoides Ellis. A selective protein extraction protocol was applied to avoid interference from colored saffron metabolites, such as crocins, during electrophoretic analyses of saffron. We succeeded in separating and assigning the molecular weights to more than 20 proteins. In spite of the unavailability of the genome of saffron, we were able to identify five proteins by Peptide Mass Fingerprinting: phosphoenolpyruvate carboxylase 3, heat shock cognate 70 KDa protein, crocetin glucosyltransferase 2, α-1,4-glucan-protein synthase and glyceraldehydes-3-phosphate dehydrogenase-2. Our findings indicate that (i) few bands are present in all saffron samples independently of origin and storage time, with amounts that significantly vary among samples and (ii) aging during saffron storage is associated with a reduction in the number of detectable bands, suggesting that proteases are still active. The protein pattern of saffron was quite distinct from those of two common adulterants, such as the dried petals of Carthamus tinctorius and the dried fruits of Gardenia jasminoides indicating that proteomic analyses could be exploited for detecting possible frauds. PMID:26840283

  18. Denaturing gradient gel electrophoresis profiling of bacterial communities composition in Arabian Sea

    Digital Repository Service at National Institute of Oceanography (India)

    Singh, S.K.; Ramaiah, N.

    Denaturing gradient gel electrophoresis (DGGE) was used to elucidate spatial and temporal variations in bacterial community composition (BCC) from four locations along the central west coast of India. DNA extracts from 36 water samples collected...

  19. Proteomic characterization of harvested pseudopodia with differential gel electrophoresis and specific antibodies.

    Science.gov (United States)

    Beckner, Marie E; Chen, Xuan; An, Jiyan; Day, Billy W; Pollack, Ian F

    2005-03-01

    Malignant gliomas (astrocytomas) are lethal tumors that invade the brain. Invasive cell migration is initiated by extension of pseudopodia into interstitial spaces. In this study, U87 glioma cells formed pseudopodia in vitro as cells pushed through 3 microm pores of polycarbonate membranes. Harvesting pseudopodia in a novel two-step method provided material for proteomic analysis. Differences in the protein profiles of pseudopodia and whole cells were found using differential gel electrophoresis (DIGE) and immunoblotting. Proteins from two-dimensional (2D) gels with M(R)'s of 20-100 kDa and pI's of 3.0-10.0 were identified by peptide mass fingerprinting analysis using mass spectrometry. For DIGE, lysates of pseudopodia and whole cells were each labeled with electrophilic forms of fluorescent dyes, Cy3 or Cy5, and analyzed as mixtures. Analysis was repeated with reciprocal labeling. Differences in protein distributions were detected by manual inspection and computer analysis. Topographical digital maps of the scanned gels were used for algorithmic spot matching, normalization of background, quantifying spot differences, and elimination of artifacts. Pseudopodial proteins in Coomassie-stained 2D gels included isoforms of glycolytic enzymes as the largest group, seven of 24 proteins. Peptide mass fingerprint analysis of DIGE gels demonstrated increased isoforms of annexin (Anx) I, AnxII, enolase, pyruvate kinase, and aldolase, and decreased mitochondrial manganese superoxide dismutase and transketolase in pseudopodia. Specific antibodies showed restricted immunoreactivity of the hepatocyte growth factor (HGF) alpha chain to pseudopodia, indicating localization of its active form. Met (the HGF receptor), actin, and total AnxI were increased in pseudopodial lysates on immunoblots. Increased constituents of the pseudopodial proteome in glioma cells, identified in this study as actin, HGF, Met, and isoforms of AnxI, AnxII, and several glycolytic enzymes, represent

  20. Inositol pyrophosphates and their unique metabolic complexity: analysis by gel electrophoresis.

    Directory of Open Access Journals (Sweden)

    Oriana Losito

    Full Text Available BACKGROUND: Inositol pyrophosphates are a recently characterized cell signalling molecules responsible for the pyrophosphorylation of protein substrates. Though likely involved in a wide range of cellular functions, the study of inositol pyrophosphates has suffered from a lack of readily available methods for their analysis. PRINCIPAL FINDING: We describe a novel, sensitive and rapid polyacrylamide gel electrophoresis (PAGE-based method for the analysis of inositol pyrophosphates. Using 4',6-diamidino-2-phenylindole (DAPI and Toluidine Blue we demonstrate the unequivocal detection of various inositol pyrophosphate species. CONCLUSION: The use of the PAGE-based method reveals the likely underestimation of inositol pyrophosphates and their signalling contribution in cells when measured via traditional HPLC-based techniques. PAGE-based analyses also reveals the existence of a number of additional, previously uncharacterised pyrophosphorylated inositol reaction products, defining a more complex metabolism associated with the catalytically flexible kinase class responsible for the production of these highly energetic cell signalling molecules.

  1. In-gel staining of proteins in native poly acryl amide gel electrophoresis using tetrakis(4-sulfonato phenyl)porphyrin.

    Science.gov (United States)

    Divakar, Kalivarathan; Sujatha, Vijayan; Barath, Sridhar; Srinath, Krishnamurthy; Gautam, Pennathur

    2011-01-01

    Protein identification in polyacrylamide gel electrophoresis (PAGE) requires post-electrophoretic steps like fixing, staining and destaining of the gel, which are time-consuming and cumbersome. We have developed a method for direct visualization of protein bands in PAGE using tetrakis(4-sulfonato phenyl)porphyrin (TPPS) as a dye without the need for any post electrophoretic steps, where separation and recovery of enzymes become much easier for further analysis. Activity staining was done to prove that the biochemical activity of the enzymes was preserved after electrophoresis. PMID:21233569

  2. In-gel staining of proteins in native polyacrylamide gel electrophoresis using meso-tetrakis(4-sulfonatophenyl) porphyrin.

    Science.gov (United States)

    Divakar, K; Devi, G Nandhini; Gautam, Pennathur

    2012-01-01

    Protein identification in polyacrylamide gel electrophoresis (PAGE) requires post-electrophoretic steps like fixing, staining, and destaining of the gel, which are time-consuming and cumbersome. A new method for direct visualization of protein bands in PAGE has been developed using meso-tetrakis(4-sulfonatophenyl)porphyrin (TPPS) as a dye without the need for any post-electrophoretic steps; thus, separation and recovery of enzymes become much easier for further analysis. Activity staining was carried out to show that the biochemical activity of the enzymes was preserved after electrophoresis. PMID:22585523

  3. Determination of damage and In vivo DNA repairing through the unicellular in gel electrophoresis technique

    International Nuclear Information System (INIS)

    The experimental conditions were standardized for the unicellular in gel electrophoresis technique setting up (EUG) at the Cellular Radiobiology laboratory. Preliminary experiments were realized with human cells and mouse which were exposed to ionizing radiation or hydroxide peroxide (H2O2) to induce DNA damage and to verify the technique performance. It was analysed the In vivo repairing kinetics of induced damage by gamma radiation in mouse leukocytes which were exposed to 137 Cs source and taking samples of peripheric blood of the tail of each mouse at different exposure times and processing them for EUG. In function of the cells proportion with damage in each time it was determined the existence of fast repairing mechanism at the first 15 minutes followed by a slight increase in the damage and a late repairing stage between 30 and 90 minutes. It was analysed this behavior and the potentiality of this In vivo system. (Author)

  4. Optimization of Pulsed-field Gel Electrophoresis Procedure for Bacillus cereus.

    Science.gov (United States)

    Zhang, Hui Juan; Pan, Zhuo; Wei, Jian Chun; Zhang, En Min; Cai, Hong; Liang, Xu Dong; Li, Wei

    2016-03-01

    In order to develop a rapid and reliable method for B. cereus genotyping, factors influencing PFGE results, including preparation of bacterial cells embedded in agarose, lysis of embedded cells, enzymatic digestion of intact genomic DNA, and electrophoresis parameters allowing for reproducible and meaningful DNA fragment separation, were controlled. Optimal cellular growth (Luria-Bertani agar plates for 12-18 h) and lysis conditions (4 h incubation with 500 µg/mL lysozyme) produced sharp bands on the gel. Restriction enzyme NotI was chosen as the most suitable. Twenty-two isolates were analyzed by NotI digestion, using three electrophoretic parameters (EPs). The EP-a was optimal for distinguishing between isolates. The optimized protocol could be completed within 40 h which is a significant improvement over the previous methods. PMID:27109136

  5. Genotoxicity of three food processing contaminants in transgenic mice expressing human sulfotransferases 1A1 and 1A2 as assessed by the in vivo alkaline single cell gel electrophoresis assay.

    Science.gov (United States)

    Høie, Anja Hortemo; Svendsen, Camilla; Brunborg, Gunnar; Glatt, Hansruedi; Alexander, Jan; Meinl, Walter; Husøy, Trine

    2015-10-01

    The food processing contaminants 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), 5-hydroxymethylfurfural (HMF) and 2,5 dimethylfuran (DMF) are potentially both mutagenic and carcinogenic in vitro and/or in vivo, although data on DMF is lacking. The PHIP metabolite N-hydroxy-PhIP and HMF are bioactivated by sulfotransferases (SULTs). The substrate specificity and tissue distribution of SULTs differs between species. A single oral dose of PhIP, HMF or DMF was administered to wild-type (wt) mice and mice expressing human SULT1A1/1A2 (hSULT mice). DNA damage was studied using the in vivo alkaline single cell gel electrophoresis (SCGE) assay. No effects were detected in wt mice. In the hSULT mice, PhIP and HMF exposure increased the levels of DNA damage in the liver and kidney, respectively. DMF was not found to be genotoxic. The observation of increased DNA damage in hSULT mice compared with wt mice supports the role of human SULTs in the bioactivation of N-hydroxy-PhIP and HMF in vivo. PMID:26270892

  6. Gel-eletroforese no diagnóstico da varíola Gel-electrophoresis in the smallpox diagnosis

    Directory of Open Access Journals (Sweden)

    Julio A. Mesquita

    1972-01-01

    Full Text Available O emprego de gel-eletroforese no diagnóstico da varíola, demonstrou ser ao menos trinta vezes (30X mais sensível que o teste de agar-gel, nas condições descritas (tabela I. Doze (12 espécimes, cujos testes convencionais de inoculação em ovos embrionados e de agar-gel resultaram positivos, foram testados em suas diluições originais congeladas por mais de um ano, sendo seis deles revelados por gel-eletroforese enquanto nenhum o foi por agar-gel (tabela II. Trinta e três (33 amostras isoladas no laboratório, foram testadas com material colhido de membrana cório-alantóica da primeira inoculação para o diagnóstico, conservado em glicerina 50%, resultando 15 positivas em gel-eletroforese e apenas 3 em agar-gel (tabela II. Os últimos 60 espécimes recebidos para diagnóstico, através a Campanha de Erradicação da Varíola, também resultaram negativos em gel-eletroforese, que não mostrou falsos-positivos nas condições descritas.The test of gel-electrophoresis applied to the pox virus group showed to be at least thirth times (30X more sensitive than agar-gel test on the described conditions (Table I. Twelve specimens, which were positives form Smallpox in the conventional tests of egg inoculation and agar-gel difusion test, have been screened in their original dilutions frozen for more than 1 year and six of them were still detectable by gel-eletrophoresis, while by agar-gel test any of them was positive (Table II. Thirty three Smallpox isolates have been tested with material from first egg inoculation (chorioallantoic membranes which have been stored in glycerin 50%, at - 15ºC. Fifteen of them were still positive by gel-electrophoresis and only 3 by agar-gel (Table II. The last 60 specimens received for diagnosis from Smallpox Erradication Campaign (CEV, were negatives by both tests. The gel-electrophoresis, did not show false-positives on described conditions.

  7. Application of pulsed field gel electrophoresis to determine γ-ray-induced double-strand breaks in yeast chromosomal molecules

    International Nuclear Information System (INIS)

    The frequency of DNA double-strand breaks (dsb) was determined in yeast cells exposed to γ-rays under anoxic conditions. Genomic DNA of treated cells was separated by pulsed field gel electrophoresis, and two different approaches for the evaluation of the gels were employed: (1) The DNA mass distribution profile obtained by electrophoresis was compared to computed profiles, and the number of DSB per unit length was then derived in terms of a fitting procedure; (2) hybridization of selected chromosomes was performed, and a comparison of the hybridization signals in treated and untreated samples was then used to derive the frequency of dsb. The two assays gave similar results for the frequency of dsb ((1.07 ± 0.06) x 10-9 Gy-1 bp-1 and (0.93 ± 0.09) x 10-9 Gy-1 bp-1, respectively). The dsb frequency was found to be linearly dependent on dose. (author)

  8. Titanium Dioxide Photocatalytic Polymerization of Acrylamide for Gel Electrophoresis (TIPPAGE) of Proteins and Structural Identification by Mass Spectrometry

    OpenAIRE

    Wenyang Zhang; Zhiwei Yuan; Lulu Huang; Jie Kang; Ruowei Jiang; Hongying Zhong

    2016-01-01

    Polyacrylamide gel electrophoresis (PAGE) coupled with mass spectrometry has been well established for separating, identifying and quantifying protein mixtures from cell lines, tissues or other biological samples. The copolymerization process of acrylamide and bis-acrylamide is the key to mastering this powerful technique. In general, this is a vinyl addition reaction initiated by free radical-generating reagents such as ammonium persulfate (APS) and tetramethylethylenediamine (TEMED) under b...

  9. Detection of the irradiation treatment of foods using micro gel electrophoresis of DNA

    International Nuclear Information System (INIS)

    Ionizing radiation has profound effects on nucleic acids, reflected by e.g. base damage and strandbreaks. These effects of radiation contribute to the aim of food irradiation: undesirable microorganisms are inactivated, insect infestation eliminated, sprouting inhibited or ripening delayed. It is, therefore, conceivable that methods of detection of a radiation treatment could be based on changes in DNA, either in microbes or insects or in the food itself. A promising method of detecting DNA fragments in irradiated food is the microelectrophoresis of single cells. Advantages of the method are its simplicity and its speed, the electrophoretic separation only requiring 2.5-5 minutes. The principle is based on migration of DNA in an agarose gel exposed to an electric field. Single cells or nuclei are embedded in the agarose and after lysis intact DNA will practically not move upon electrophoresis, due to the gel strains, whereas if DNA fragmentation has occurred, the DNA is able to migrate and ''comets'' following the cells or nuclei become visible after staining. This paper describes our experience obtained by analyzing chicken, beef and pork meat, shrimps and mushrooms. The method therefore has its limitations, although good results both from frozen and fresh meats, fresh fish, onions and potatoes have been reported. Also strawberries have been identified using this technique. Further experience may strengthen the evidence that this simple and cheap technique may have its place among the battery of tests to detect the radiation treatment of foods. (orig./vhe)

  10. Optimizing Human Bile Preparation for Two-Dimensional Gel Electrophoresis

    OpenAIRE

    Hao-Tsai Cheng; Sen-Yung Hsieh; Chang-Mu Sung; Betty Chien-Jung Pai; Nai-Jen Liu; Carl PC Chen

    2016-01-01

    Aims. Bile is an important body fluid which assists in the digestion of fat and excretion of endogenous and exogenous compounds. In the present study, an improved sample preparation for human bile was established. Methods and Material. The method involved acetone precipitation followed by protein extraction using commercially available 2D Clean-Up kit. The effectiveness was evaluated by 2-dimensional electrophoresis (2DE) profiling quality, including number of protein spots and spot distribut...

  11. Colonization of Bordetella pertussis clinical isolates that differ by pulsed field gel electrophoresis types in the lungs of naïve mice or mice immunized with the whole-cell pertussis vaccine used in Poland.

    Science.gov (United States)

    Polak, Maciej; Zawadka, Monika; Mosiej, Ewa; Rabczenko, Daniel; Augustynowicz, Ewa; Guiso, Nicole; Lutyńska, Anna

    2015-04-01

    The goal of our study was to compare the elimination of Bordetella pertussis clinical isolates that differ according to pulsed field gel electrophoresis (PFGE), serotypes and genes encoding virulence factors from the lungs of naïve mice or mice immunized with commercial diphtheria-tetanus-whole-cell pertussis vaccine used in Poland. When a mixture of four isolates, given in equal proportions and harboring different PFGE profiles, serotypes, and alleles encoding virulence factors, was used to infect non-immunized mice, a single isolate, characterized by PFGE type IVγ, Fim2 phenotype and ptxA1-prn2-tcfA2-fim2-1-ptxP1-ptxC1-fim3-1 alleles, was found to be significantly predominant compared to the others. This PFGE profile is commonly found in B. pertussis isolates circulating in some European countries since the late 1990s, confirming its high fitness. The Polish commercial whole-cell pertussis vaccine induced an immunity effective at eliminating the B. pertussis isolates from the lungs. However, the elimination of the isolate harboring PFGE type C profile, Fim2,3 phenotype and ptxA1-prn1-tcfA2-fim2-1-ptxP1-ptxC1-fim3-1 alleles was delayed as compared to the others, suggesting phenotypic differences with the other isolates and vaccine strains. Nevertheless, the same isolate, when challenged into mice in the defined mixture of strains, lost the competition with the others, as measured by lung colonization efficiency. This PFGE profile represents 15 % of the isolates circulating in Poland between 2001 and 2012.

  12. Comparative proteome analysis of three mouse lung adenocarcinoma CMT cell lines with different metastatic potential by two-dimensional gel electrophoresis and mass spectrometry

    DEFF Research Database (Denmark)

    Zhang, Kelan; Wrzesinski, Krzysztof; Stephen, J Fey;

    2008-01-01

    Metastasis is a lethal attribute of a cancer and presents a continuing therapeutic challenge. Metastasis is a highly complex process and more knowledge about the mechanisms behind metastasis is highly desirable. Isogenic CMT cell lines were selected from a spontaneous mouse lung adenocarcinoma...

  13. Single cell gel electrophoresis as a tool to assess genetic damage in Heleobia cf. australis (Mollusca: Gastropoda as sentinel for industrial and domestic pollution in Montevideo bay (Uruguay

    Directory of Open Access Journals (Sweden)

    Silvia Villar

    2015-09-01

    Full Text Available AbstractThe knowledge of the extent of DNA damage in aquatic organisms in polluted areas is an important issue because contamination may alter their health at sublethal levels. Although molluscs have been widely used to monitor water pollution, there are no records of in vivo genotoxicity studies. Heleobia cf. australis, is distributed in almost all Uruguayan coastal ecosystems, including highly polluted sites. The comet assay is a damage genetic biomarker based on the migration of negatively charged DNA fragments produced by mutagenic agents in individual cells. Live individuals were collected in the Montevideo Bay (impacted area and Laguna Garzón (control to analyze the presence of mutagenic agents in the former site through comet assay. Cells from organisms of the impacted area showed significantly higher levels of genetic damage than those obtained in the control population, measured by percentage of DNA in the tail. Although preliminary, this approach supports the idea that H. cf. australis could be used as a sentinel to evaluate the presence of mutagenic agents in estuarine environments, alerting to the impact of contamination in its early stages.

  14. Evaluation of the radioprotective effect of Carissa carandas Linn. fruit extract in cultured human peripheral blood lymphocytes exposed to electron beam radiation by Single Cell Gel Electrophoresis (Comet Assay)

    International Nuclear Information System (INIS)

    Radiation is a well-known inducer of free radicals and compounds that can scavenge free radicals may reduce radiation-induced DNA damage. Carissa carandas commonly known as Karanda belongs to family Apocynaceae. Traditionally, whole plant and its parts were used in the treatment of various ailments. The aim of the present study was to assess the radioprotective effect of ethanolic extract of Carissa carandas fruit (ECF) in cultured human peripheral blood lymphocytes (HPBLs) by comet assay. The optimum protective dose of the extract was selected by treating HPBLs with 50 and 100 μg/ml ECF after exposure to 2 Gy electron beam radiation and then evaluating the frequency of DNA damage in HPBLs using Single cell gel electrophoresis (Comet Assay). To understand the mechanism of action of ECF separate experiments were conducted to evaluate the free radical scavenging of DPPH, and Fe3+ in vitro. ECF was found to inhibit free radicals in a dose dependent manner up to a dose of 1000 μg/ml for the majority of radicals as observed by the in vitro free radical scavenging assays. The irradiation of HPBLs with 2 Gy dose of electron beam radiation caused an increase in the frequency of DNA damage while treatment of HPBLs with different concentrations of ECF reduced the frequency of DNA damage significantly with the greatest reduction being observed for 100 μg/ml when compared with the irradiated control. Our study demonstrates the potential of ECF as an effective agent against radiation induced DNA damage. (author)

  15. Introducing Proteomics in the Undergraduate Curriculum: A Simple 2D Gel Electrophoresis Exercise with Serum Proteins

    Science.gov (United States)

    Kim, Thomas D.; Craig, Paul A.

    2010-01-01

    Two-dimensional gel electrophoresis (2DGE) remains an important tool in the study of biological systems by proteomics. While the use of 2DGE is commonplace in research publications, there are few instructional laboratories that address the use of 2DGE for analyzing complex protein samples. One reason for this lack is the fact that the preparation…

  16. Analysis of soybean embryonic axis proteins by two-dimensional gel electrophoresis and mass spectrometry

    Science.gov (United States)

    A proteomic approach based on two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) for protein separation and subsequent mass spectrometry (MS) for protein identification was applied to establish a proteomic reference map for the soybean embryonic axis. Proteins were extracted from dissecte...

  17. Disposable pen-shaped capillary gel electrophoresis cartridge for fluorescence detection of bio-molecules

    Science.gov (United States)

    Amirkhanian, Varoujan; Tsai, Shou-Kuan

    2014-03-01

    We introduce a novel and cost-effective capillary gel electrophoresis (CGE) system utilizing disposable pen-shaped gelcartridges for highly efficient, high speed, high throughput fluorescence detection of bio-molecules. The CGE system has been integrated with dual excitation and emission optical-fibers with micro-ball end design for fluorescence detection of bio-molecules separated and detected in a disposable pen-shaped capillary gel electrophoresis cartridge. The high-performance capillary gel electrophoresis (CGE) analyzer has been optimized for glycoprotein analysis type applications. Using commercially available labeling agent such as ANTS (8-aminonapthalene-1,3,6- trisulfonate) as an indicator, the capillary gel electrophoresis-based glycan analyzer provides high detection sensitivity and high resolving power in 2-5 minutes of separations. The system can hold total of 96 samples, which can be automatically analyzed within 4-5 hours. This affordable fiber optic based fluorescence detection system provides fast run times (4 minutes vs. 20 minutes with other CE systems), provides improved peak resolution, good linear dynamic range and reproducible migration times, that can be used in laboratories for high speed glycan (N-glycan) profiling applications. The CGE-based glycan analyzer will significantly increase the pace at which glycoprotein research is performed in the labs, saving hours of preparation time and assuring accurate, consistent and economical results.

  18. An electrophoretic karyotype for Schizosaccharomyces pombe by pulsed field gel electrophoresis.

    OpenAIRE

    Smith, C.L.; Matsumoto, T.; Niwa, O; Klco, S; Fan, J B; Yanagida, M.; Cantor, C R

    1987-01-01

    The three chromosomal DNAs of S. pombe have been fractionated by pulsed field gel electrophoresis. The resulting molecular karyotype will greatly speed gene mapping in this organism, and it indicates that the separation range of the technique extends to DNA molecules as large as 9,000,000 base pairs.

  19. Proteome analysis of vaccinia virus IHD-W-infected HEK 293 cells with 2-dimensional gel electrophoresis and MALDI-PSD-TOF MS of on solid phase support N-terminally sulfonated peptides

    Directory of Open Access Journals (Sweden)

    Bartel Sebastian

    2011-08-01

    Full Text Available Abstract Background Despite the successful eradication of smallpox by the WHO-led vaccination programme, pox virus infections remain a considerable health threat. The possible use of smallpox as a bioterrorism agent as well as the continuous occurrence of zoonotic pox virus infections document the relevance to deepen the understanding for virus host interactions. Since the permissiveness of pox infections is independent of hosts surface receptors, but correlates with the ability of the virus to infiltrate the antiviral host response, it directly depends on the hosts proteome set. In this report the proteome of HEK293 cells infected with Vaccinia Virus strain IHD-W was analyzed by 2-dimensional gel electrophoresis and MALDI-PSD-TOF MS in a bottom-up approach. Results The cellular and viral proteomes of VACV IHD-W infected HEK293 cells, UV-inactivated VACV IHD-W-treated as well as non-infected cells were compared. Derivatization of peptides with 4-sulfophenyl isothiocyanate (SPITC carried out on ZipTipμ-C18 columns enabled protein identification via the peptides' primary sequence, providing improved s/n ratios as well as signal intensities of the PSD spectra. The expression of more than 24 human proteins was modulated by the viral infection. Effects of UV-inactivated and infectious viruses on the hosts' proteome concerning energy metabolism and proteins associated with gene expression and protein-biosynthesis were quite similar. These effects might therefore be attributed to virus entry and virion proteins. However, the modulation of proteins involved in apoptosis was clearly correlated to infectious viruses. Conclusions The proteome analysis of infected cells provides insight into apoptosis modulation, regulation of cellular gene expression and the regulation of energy metabolism. The confidence of protein identifications was clearly improved by the peptides' derivatization with SPITC on a solid phase support. Some of the identified proteins

  20. Rapid Detection of Glycogen Synthase Kinase-3 Activity in Mouse Sperm Using Fluorescent Gel Shift Electrophoresis

    Directory of Open Access Journals (Sweden)

    Hoseok Choi

    2016-04-01

    Full Text Available Assaying the glycogen synthase kinase-3 (GSK3 activity in sperm is of great importance because it is closely implicated in sperm motility and male infertility. While a number of studies on GSK3 activity have relied on labor-intensive immunoblotting to identify phosphorylated GSK3, here we report the simple and rapid detection of GSK3 activity in mouse sperm using conventional agarose gel electrophoresis and a fluorescent peptide substrate. When a dye-tethered and prephosphorylated (primed peptide substrate for GSK3 was employed, a distinct mobility shift in the fluorescent bands on the agarose was observed by GSK3-induced phosphorylation of the primed peptides. The GSK3 activity in mouse testes and sperm were quantifiable by gel shift assay with low sample consumption and were significantly correlated with the expression levels of GSK3 and p-GSK3. We suggest that our assay can be used for reliable and rapid detection of GSK3 activity in cells and tissue extracts.

  1. Ag-nanoparticle fractionation by low melting point agarose gel electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Guarrotxena, Nekane, E-mail: nekane@ictp.csic.es [Consejo Superior de Investigaciones Cientificas (CSIC), Instituto de Ciencia y Tecnologia de Polimeros (ICTP) (Spain); Braun, Gary [University of California, Santa Barbara, Department of Chemistry and Biochemistry (United States)

    2012-10-15

    The separation of surface-enhanced raman scattering (SERS)-active Ag-multi-nanoparticle (NP) assemblies by low melting point agarose gel electrophoresis was accomplished here by controlling surface charge using NP capping agents, and the pore size of agarose gel matrix. Detailed transmission electron microscopy analysis of excised gel fractions showed dimers and small clusters to have the greatest SERS activity and a mobility in between the monomers and large aggregates. This strategy enables one to: (1) stabilize small multispherical Ag clusters against further aggregation during purification; (2) fractionate and recover spherical assemblies by nuclearity; and (3) analyze SERS-enhancements for each fraction to optimize purification conditions.

  2. CHARACTERIZATION OF PATHOGENIC FUNGI GENOMES USING PULSED FIELD GEL ELECTROPHORESIS

    Institute of Scientific and Technical Information of China (English)

    吴绍熙; 郭宁如; 殷正男; 柴建华

    1996-01-01

    Pulsed field gel eleetrophoresis (PFGE) has been firstly introdueed in characterization of the pathogenic fungi Pericillium marneffei and Exophiata dermatitidis genomes. The numbers and sizes of their chromosomes have been detected. Polymorphism was identified on the smallest chromosome of E.derntatitidis. The result shows that PFGE for characterization of large molecular DNA pathogenic fungi is very suitable, it is more simple and more efficacy. The result also shows the diversity of pathogenic fungi is relative common even in rare occurred pathogeafie fungi such as E. dermatitidis.

  3. Enhanced Resolution of DNA Separation Using Agarose Gel Electrophoresis Doped with Graphene Oxide.

    Science.gov (United States)

    Li, Jialiang; Yang, Yushi; Mao, Zhou; Huang, Wenjie; Qiu, Tong; Wu, Qingzhi

    2016-12-01

    In this work, a novel agarose gel electrophoresis strategy has been developed for separation of DNA fragments by doping graphene oxide (GO) into agarose gel. The results show that the addition of GO into agarose gel significantly improved the separation resolution of DNA fragments by increasing the shift distances of both the single DNA fragments and the adjacent DNA fragments and completely eliminating the background noise derived from the diffusion of the excessive ethidium bromide (EB) dye in the gel after electrophoresis. The improved resolution of DNA fragments in GO-doped agarose gel could be attributed to the successive adsorption-desorption processes between DNA fragments and GO sheets, while the elimination of the background noise could be attributed to the adsorption of the excessive EB dye on the surface of GO sheets and high fluorescence quenching efficiency of GO. These results provide promising potential for graphene and its derivate utilized in various electrophoresis techniques for separation and detection of DAN fragments and other biomolecules. PMID:27637896

  4. Enhanced Resolution of DNA Separation Using Agarose Gel Electrophoresis Doped with Graphene Oxide

    Science.gov (United States)

    Li, Jialiang; Yang, Yushi; Mao, Zhou; Huang, Wenjie; Qiu, Tong; Wu, Qingzhi

    2016-09-01

    In this work, a novel agarose gel electrophoresis strategy has been developed for separation of DNA fragments by doping graphene oxide (GO) into agarose gel. The results show that the addition of GO into agarose gel significantly improved the separation resolution of DNA fragments by increasing the shift distances of both the single DNA fragments and the adjacent DNA fragments and completely eliminating the background noise derived from the diffusion of the excessive ethidium bromide (EB) dye in the gel after electrophoresis. The improved resolution of DNA fragments in GO-doped agarose gel could be attributed to the successive adsorption-desorption processes between DNA fragments and GO sheets, while the elimination of the background noise could be attributed to the adsorption of the excessive EB dye on the surface of GO sheets and high fluorescence quenching efficiency of GO. These results provide promising potential for graphene and its derivate utilized in various electrophoresis techniques for separation and detection of DAN fragments and other biomolecules.

  5. The relationship of agarose gel structure to the sieving of spheres during agarose gel electrophoresis.

    OpenAIRE

    Griess, G A; Guiseley, K B; Serwer, P

    1993-01-01

    To understand the organization of fibers in an agarose gel, digitized electron micrographs are used here to determine the frequency distribution of interfiber distance (2Pc) in thin sections of agarose gels. For a preparation of underivatized agarose, a 1.5% gel has a Pc distribution that is indistinguishable from the Pc distribution of a computer-generated, random-fiber gel; the log of the occurrence frequency (F) decreases linearly as a function of Pc. As the agarose concentration decreases...

  6. Nitroproteins in Human Astrocytomas Discovered by Gel Electrophoresis and Tandem Mass Spectrometry

    Science.gov (United States)

    Peng, Fang; Li, Jianglin; Guo, Tianyao; Yang, Haiyan; Li, Maoyu; Sang, Shushan; Li, Xuejun; Desiderio, Dominic M.; Zhan, Xianquan

    2015-12-01

    Protein tyrosine nitration is involved in the pathogenesis of highly fatal astrocytomas, a type of brain cancer. To understand the molecular mechanisms of astrocytomas and to discover new biomarkers/therapeutic targets, we sought to identify nitroproteins in human astrocytoma tissue. Anti-nitrotyrosine immunoreaction-positive proteins from a high-grade astrocytoma tissue were detected with two-dimensional gel electrophoresis (2DGE)-based nitrotyrosine immunoblots, and identified with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Fifty-seven nitrotyrosine immunopositive protein spots were detected. A total of 870 proteins (nitrated and non-nitrated) in nitrotyrosine-immunopositive 2D gel spots were identified, and 18 nitroproteins and their 20 nitrotyrosine sites were identified with MS/MS analysis. These nitroproteins participate in multiple processes, including drug-resistance, signal transduction, cytoskeleton, transcription and translation, cell proliferation and apoptosis, immune response, phenotypic dedifferentiation, cell migration, and metastasis. Among those nitroproteins that might play a role in astrocytomas was nitro-sorcin, which is involved in drug resistance and metastasis and might play a role in the spread and treatment of an astrocytoma. Semiquantitative immune-based measurements of different sorcin expressions were found among different grades of astrocytomas relative to controls, and a semiquantitative increased nitration level in high-grade astrocytoma relative to control. Nitro-β-tubulin functions in cytoskeleton and cell migration. Semiquantitative immunoreactivity of β-tubulin showed increased expression among different grades of astrocytomas relative to controls and semiquantitatively increased nitration level in high-grade astrocytoma relative to control. Each nitroprotein was rationalized and related to the corresponding functional system to provide new insights into tyrosine nitration and its potential role in the

  7. Gel versus capillary electrophoresis genotyping for categorizing treatment outcomes in two anti-malarial trials in Uganda

    Directory of Open Access Journals (Sweden)

    Hubbard Alan E

    2010-01-01

    Full Text Available Abstract Background Molecular genotyping is performed in anti-malarial trials to determine whether recurrent parasitaemia after therapy represents a recrudescence (treatment failure or new infection. The use of capillary instead of agarose gel electrophoresis for genotyping offers technical advantages, but it is unclear whether capillary electrophoresis will result in improved classification of anti-malarial treatment outcomes. Methods Samples were genotyped using both gel and capillary electrophoresis from randomized trials of artemether-lumefantrine (AL vs. dihydroartemisinin-piperaquine (DP performed in two areas of Uganda: Kanungu, where transmission is moderate, and Apac, where transmission is very high. Both gel and capillary methods evaluated polymorphic regions of the merozoite surface protein 1 and 2 and glutamine rich protein genes. Results Capillary electrophoresis detected more alleles and provided higher discriminatory power than agarose gel electrophoresis at both study sites. There was only moderate agreement between classification of outcomes with the two methods in Kanungu (kappa = 0.66 and poor agreement in Apac (kappa = 0.24. Overall efficacy results were similar when using gel vs. capillary methods in Kanungu (42-day risk of treatment failure for AL: 6.9% vs. 5.5%, p = 0.4; DP 2.4% vs. 2.9%, p = 0.5. However, the measured risk of recrudescence was significantly higher when using gel vs. capillary electrophoresis in Apac (risk of treatment failure for AL: 17.0% vs. 10.7%, p = 0.02; DP: 8.5% vs. 3.4%, p = 0.03. Risk differences between AL and DP were not significantly different whether gel or capillary methods were used. Conclusions Genotyping with gel electrophoresis overestimates the risk of recrudescence in anti-malarial trials performed in areas of high transmission intensity. Capillary electrophoresis provides more accurate outcomes for such trials and should be performed when possible. In areas of moderate transmission

  8. DNA sequencing with capillary electrophoresis and single cell analysis with mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Fung, N.

    1998-03-27

    Since the first demonstration of the laser in the 1960`s, lasers have found numerous applications in analytical chemistry. In this work, two different applications are described, namely, DNA sequencing with capillary gel electrophoresis and single cell analysis with mass spectrometry. Two projects are described in which high-speed DNA separations with capillary gel electrophoresis were demonstrated. In the third project, flow cytometry and mass spectrometry were coupled via a laser vaporization/ionization interface and individual mammalian cells were analyzed. First, DNA Sanger fragments were separated by capillary gel electrophoresis. A separation speed of 20 basepairs per minute was demonstrated with a mixed poly(ethylene oxide) (PEO) sieving solution. In addition, a new capillary wall treatment protocol was developed in which bare (or uncoated) capillaries can be used in DNA sequencing. Second, a temperature programming scheme was used to separate DNA Sanger fragments. Third, flow cytometry and mass spectrometry were coupled with a laser vaporization/ionization interface.

  9. Extracting information from two-dimensional electrophoresis gels by partial least squares regression

    DEFF Research Database (Denmark)

    Jessen, Flemming; Lametsch, R.; Bendixen, E.;

    2002-01-01

    Two-dimensional gel electrophoresis (2-DE) produces large amounts of data and extraction of relevant information from these data demands a cautious and time consuming process of spot pattern matching between gels. The classical approach of data analysis is to detect protein markers that appear...... or disappear depending on the experimental conditions. Such biomarkers are found by comparing the relative volumes of individual spots in the individual gels. Multivariate statistical analysis and modelling of 2-DE data for comparison and classification is an alternative approach utilising the combination...... of all proteins/spots in the gels. In the present study it is demonstrated how information can be extracted by multivariate data analysis. The strategy is based on partial least squares regression followed by variable selection to find proteins that individually or in combination with other proteins vary...

  10. Optimisation of the two-dimensional gel electrophoresis protocol using the Taguchi approach

    Directory of Open Access Journals (Sweden)

    Blow J Julian

    2004-09-01

    Full Text Available Abstract Background Quantitative proteomic analyses have traditionally used two-dimensional gel electrophoresis (2DE for separation and characterisation of complex protein mixtures. Among the difficulties associated with this approach is the solubilisation of protein mixtures for isoelectric focusing (IEF. To find the optimal formulation of the multi-component IEF rehydration buffer (RB we applied the Taguchi method, a widely used approach for the robust optimisation of complex industrial processes, to determine optimal concentrations for the detergents, carrier ampholytes and reducing agents in RB for 2DE using commercially supplied immobilised pH gradient (IPG gel strips. Results Our optimisation resulted in increased protein solubility, improved resolution and reproducibility of 2D gels, using a wide variety of samples. With the updated protocol we routinely detected approximately 4-fold more polypeptides on samples containing complex protein mixtures resolved on small format 2D gels. In addition the pI and size ranges over which proteins could be resolved was substantially improved. Moreover, with improved sample loading and resolution, analysis of individual spots by immunoblotting and mass spectrometry revealed previously uncharacterised posttranscriptional modifications in a variety of chromatin proteins. Conclusions While the optimised RB (oRB is specific to the gels and analysis approach we use, our use of the Taguchi method should be generally applicable to a broad range of electrophoresis and analysis systems.

  11. Microplate array diagonal gel electrophoresis for cohort studies of microsatellite loci.

    Science.gov (United States)

    Chen, Xiao-he; O'Dell, Sandra D; Day, Ian N M

    2002-05-01

    After PCR amplification, we have achieved precise sizing of trinucleotide and tetranucleotide microsatellite alleles on 96-well open-faced polyacrylamide microplate array diagonal gel electrophoresis (MADGE) gels: two tetranucleotide repeats, HUMTHOI (five alleles 248-263 bp) and DYS390 (eight alleles 200-228 bp), and DYS392, a trinucleotide repeat (eight alleles 210-231 bp). A gel matrix of Duracryl, a high mechanical strength polyacrylamide derivative, and appropriate ionic conditions provide the 1.3%-1.5% band resolution required. No end-labeling of primers is needed, as the sensitive Vistra Green intercalating dye is used for the visualization of bands. Co-run markers bracketing the PCR fragments ensure accurate sizing without inter-lane variability. Electrophoresis of multiple gels in a thermostatically controlled tank allows up to 1000 samples to be run in 90 min. Gel images were analyzed using a Fluorlmager 595 fluorescent scanning system, and alleles were identified using Phoretix software for band migration measurement and Microsoft Excel to compute fragment sizes. Estimated sizes were interpolated precisely to achieve accurate binning. Microsatellite-MADGE represents a utilitarian methodfor high-throughput genotyping in cohort studies, using standard laboratory equipment.

  12. New Microsatellite Markers for Anthyllis vulneraria (Fabaceae, Analyzed with Spreadex Gel Electrophoresis

    Directory of Open Access Journals (Sweden)

    Halil Kesselring

    2013-12-01

    Full Text Available Premise of the study: New microsatellite primers were developed for the diploid herb Anthyllis vulneraria. These primers will be used in upcoming studies focusing on random genetic variation, local adaptation, and phenotypic plasticity in alpine plants. Methods and Results: The new primers were adjusted to separate PCR amplicons (70 to 170 bp on precast Spreadex gels using horizontal gel electrophoresis. No capillary sequencer was needed. Three to twelve alleles were found per locus depending on the population studied. Conclusions: Our preliminary results showed that the three studied alpine populations are predominantly outcrossing, but include variable levels of self-fertilization.

  13. Molecular Analysis of Mycobacterium avium Isolates by Using Pulsed-Field Gel Electrophoresis and PCR

    OpenAIRE

    Pestel-Caron, Martine; Graff, Gabriel; Berthelot, Gilles; Pons, Jean-Louis; Lemeland, Jean-François

    1999-01-01

    Genetic relationships among 46 isolates of Mycobacterium avium recovered from 37 patients in a 2,500-bed hospital from 1993 to 1998 were assessed by pulsed-field gel electrophoresis (PFGE) and PCR amplification of genomic sequences located between the repetitive elements IS1245 and IS1311. Each technique enabled the identification of 27 to 32 different patterns among the 46 isolates, confirming that the genetic heterogeneity of M. avium strains is high in a given community. Furthermore, this ...

  14. Detection of Rifampin Resistance in Mycobacterium tuberculosis by Double Gradient-Denaturing Gradient Gel Electrophoresis

    Science.gov (United States)

    Scarpellini, Paolo; Braglia, Sergio; Carrera, Paola; Cedri, Maura; Cichero, Paola; Colombo, Alessia; Crucianelli, Rosella; Gori, Andrea; Ferrari, Maurizio; Lazzarin, Adriano

    1999-01-01

    We applied double gradient-denaturing gradient gel electrophoresis (DG-DGGE) for the rapid detection of rifampin (RMP) resistance from rpoB PCR products of Mycobacterium tuberculosis isolates and clinical samples. The results of this method were fully concordant with those of DNA sequencing and susceptibility testing analyses. DG-DGGE is a valid alternative to the other methods of detecting mutations for predicting RMP resistance. PMID:10508043

  15. Genomic fingerprinting of Borrelia burgdorferi sensu lato by pulsed-field gel electrophoresis.

    OpenAIRE

    1993-01-01

    A total of 46 Borrelia burgdorferi sensu lato isolates that were isolated from patients with Lyme borreliosis and infected animals or were extracted from ticks of the genus Ixodes were analyzed. Large restriction fragment patterns obtained after cleavage of genomic DNAs with MluI were analyzed by pulsed-field gel electrophoresis (PFGE). To eliminate the contribution of plasmid DNA, only fragments greater than 70 kb were used for the analysis. The results indicated that each of the 14 B. burgd...

  16. Identification of the Bacterial Microflora in Dairy Products by Temporal Temperature Gradient Gel Electrophoresis

    OpenAIRE

    Ogier, Jean-Claude; Son, Olivier; Gruss, Alexandra; Tailliez, Patrick; Delacroix-Buchet, Agnes

    2002-01-01

    Numerous microorganisms, including bacteria, yeasts, and molds, are present in cheeses, forming a complex ecosystem. Among these organisms, bacteria are responsible for most of the physicochemical and aromatic transformations that are intrinsic to the cheesemaking process. Identification of the bacteria that constitute the cheese ecosystem is essential for understanding their individual contributions to cheese production. We used temporal temperature gradient gel electrophoresis (TTGE) to ide...

  17. Rubella virion polypeptides. Characterization by polyacrylamide gel electrophoresis, isoelectric focusing and peptide mapping

    Energy Technology Data Exchange (ETDEWEB)

    Ho-Terry, L.; Cohen, A. (University Coll. Hospital Medical School, London (UK))

    1982-01-01

    Four polypeptides with molecular weights of 55K, 47K, 45K, and 33K have been resolved by polyacrylamide gel electrophoresis of immune precipitated rubella virus. The 47K and 45K components have similar peptide maps but different isoelectric points so that the same polypeptide may exist in more than one charged form. The 55K and 45K components have similar isoelectric points but different peptide maps showing that similarity of isoelectric point is not evidence of identity.

  18. Molecular Typing by Pulsed-Field Gel Electrophoresis of Spanish Animal and Human Listeria monocytogenes Isolates

    OpenAIRE

    Vela, A. I.; Fernandez-Garayzabal, J F; Vazquez, J. A.; Latre, M. V.; Blanco, M. M.; Moreno, M. A.; de la Fuente, L.; Marco, J.; C. Franco; Cepeda, A.; Rodriguez Moure, A. A.; Suarez, G; Dominguez, L

    2001-01-01

    A total of 153 strains of Listeria monocytogenes isolated from different sources (72 from sheep, 12 from cattle, 18 from feedstuffs, and 51 from humans) in Spain from 1989 to 2000 were characterized by pulsed-field gel electrophoresis. The strains of L. monocytogenes displayed 55 pulsotypes. The 84 animal, 51 human, and 18 feedstuff strains displayed 31, 29, and 7 different pulsotypes, respectively, indicating a great genetic diversity among the Spanish L. monocytogenes isolates studied. L. m...

  19. Pulsed-Field Gel Electrophoresis (PFGE) Technique and its use in Molecular Biology

    OpenAIRE

    BASIM, Esin (HACIOĞLU)

    2001-01-01

    In recent years, the use of pulsed-field gel electrophoresis (PFGE) in the molecular biology area has been subject to much research. PFGE is a powerful tool for characterizing various strains at the DNA level, obtaining relevant information on genome size and constructing the physical and genetic map of the chromosome of bacteria that are poorly understood at the genetic level as well as in separating chromosomes in microorganisms, and in the long-range mapping of mammalian genes. PFGE also h...

  20. Streptococcus agalactiae pulsed-field gel electrophoresis patterns cross capsular types

    OpenAIRE

    Pillai, P.; Srinivasan, U; ZHANG, L.; BORCHARDT, S.M.; Debusscher, J; Marrs, C F; Foxman, B.

    2009-01-01

    Streptococcus agalactiae is a genetically diverse organism; when typed by pulsed-field gel electrophoresis (PFGE), multiple types appear within a single serotype. We tested whether S. agalactiae PFGE types correspond to a specific serotype within individuals, and different individuals from the same geographic area. A total of 872 S. agalactiae isolates from 152 healthy individuals were classified by PFGE and capsular serotype. Serotype V was the most homogeneous (Simpson’s diversity index 0.5...

  1. Identification of Methanococcus Jannaschii Proteins in 2-D Gel Electrophoresis Patterns by Mass Spectrometry

    Science.gov (United States)

    Liang, X.

    1998-06-10

    The genome of Methanococcus jannaschii has been sequenced completely and has been found to contain approximately 1,770 predicted protein-coding regions. When these coding regions are expressed and how their expression is regulated, however, remain open questions. In this work, mass spectrometry was combined with two-dimensional gel electrophoresis to identify which proteins the genes produce under different growth conditions, and thus investigate the regulation of genes responsible for functions characteristic of this thermophilic representative of the methanogenic Archaea.

  2. Pulsed-field Gel Electrophoresis for Salmonella Infection Surveillance, Texas, USA, 2007

    Centers for Disease Control (CDC) Podcasts

    2010-06-14

    This podcast describes monitoring of the use of pulsed-field gel electrophoresis for Salmonella surveillance in Houston, Texas. CDC microbiologist Peter Gerner-Smidt discusses the importance of the PulseNet national database in surveillance of food-borne infections.  Created: 6/14/2010 by National Center for Emerging and Zoonotic Infectious Diseases (NCEZID).   Date Released: 6/14/2010.

  3. Purification of Peptide Components including Melittin from Bee Venom using gel filtration chromatography and propionic acid/urea polyacrylamide gel electrophoresis

    OpenAIRE

    Young Chon Choi; Ki Rok, Kwon; Suk Ho, Choi

    2006-01-01

    Objectives : This study was conducted to carry out Purification of Melittin and other peptide components from Bee Venom using gel filtration chromatography and propionic acid/urea polyacrylamide gel electrophoresis Methods : Melittin and other peptide components were separated from bee venom by using gel filtration chromatography on Sephadex G-50 column in 0.05M ammonium acetate buffer. Results : Melittin and other peptide components were separated from bee venom by using gel filtration...

  4. Effects of Reusing Gel Electrophoresis and Electrotransfer Buffers on Western Blotting.

    Science.gov (United States)

    Heda, Ghanshyam D; Omotola, Oluwabukola B; Heda, Rajiv P; Avery, Jamie

    2016-09-01

    SDS-PAGE and Western blotting are 2 of the most commonly used biochemical methods for protein analysis. Proteins are electrophoretically separated based on their MWs by SDS-PAGE and then electrotransferred to a solid membrane surface for subsequent protein-specific analysis by immunoblotting, a procedure commonly known as Western blotting. Both of these procedures use a salt-based buffer, with the latter procedure consisting of methanol as an additive known for its toxicity. Previous reports present a contradictory view in favor or against reusing electrotransfer buffer, also known as Towbin's transfer buffer (TTB), with an aim to reduce the toxic waste. In this report, we present a detailed analysis of not only reusing TTB but also gel electrophoresis buffer (EB) on proteins of low to high MW range. Our results suggest that EB can be reused for at least 5 times without compromising the electrophoretic separation of mixture of proteins in an MW standard, BSA, and crude cell lysates. Additionally, reuse of EB did not affect the quality of subsequent Western blots. Successive reuse of TTB, on the other hand, diminished the signal of proteins of different MWs in a protein standard and a high MW membrane protein cystic fibrosis transmembrane-conductance regulator (CFTR) in Western blotting. PMID:27582639

  5. Application of preparative disk gel electrophoresis for antigen purification from inclusion bodies.

    Science.gov (United States)

    Okegawa, Yuki; Koshino, Masanori; Okushima, Teruya; Motohashi, Ken

    2016-02-01

    Specific antibodies are a reliable tool to examine protein expression patterns and to determine the protein localizations within cells. Generally, recombinant proteins are used as antigens for specific antibody production. However, recombinant proteins from mammals and plants are often overexpressed as insoluble inclusion bodies in Escherichia coli. Solubilization of these inclusion bodies is desirable because soluble antigens are more suitable for injection into animals to be immunized. Furthermore, highly purified proteins are also required for specific antibody production. Plastidic acetyl-CoA carboxylase (ACCase: EC 6.4.1.2) from Arabidopsis thaliana, which catalyzes the formation of malonyl-CoA from acetyl-CoA in chloroplasts, formed inclusion bodies when the recombinant protein was overexpressed in E. coli. To obtain the purified protein to use as an antigen, we applied preparative disk gel electrophoresis for protein purification from inclusion bodies. This method is suitable for antigen preparation from inclusion bodies because the purified protein is recovered as a soluble fraction in electrode running buffer containing 0.1% sodium dodecyl sulfate that can be directly injected into immune animals, and it can be used for large-scale antigen preparation (several tens of milligrams).

  6. Titanium Dioxide Photocatalytic Polymerization of Acrylamide for Gel Electrophoresis (TIPPAGE) of Proteins and Structural Identification by Mass Spectrometry.

    Science.gov (United States)

    Zhang, Wenyang; Yuan, Zhiwei; Huang, Lulu; Kang, Jie; Jiang, Ruowei; Zhong, Hongying

    2016-02-11

    Polyacrylamide gel electrophoresis (PAGE) coupled with mass spectrometry has been well established for separating, identifying and quantifying protein mixtures from cell lines, tissues or other biological samples. The copolymerization process of acrylamide and bis-acrylamide is the key to mastering this powerful technique. In general, this is a vinyl addition reaction initiated by free radical-generating reagents such as ammonium persulfate (APS) and tetramethylethylenediamine (TEMED) under basic pH and degassing experimental condition. We report herein a photocatalytic polymerization approach that is based on photo-generated hydroxyl radicals with nanoparticles of titanium dioxide. It was shown that the polymerization process is greatly accelerated in acidic condition when ultraviolet light shots on the gel solution containing TiO2 nanoparticles without degassing. This feature makes it very useful in preparing Triton X-100 acid urea (TAU) gel that has been developed for separating basic proteins such as histones and variants in acidic experimental condition. Additionally, the presence of titanium dioxide in the gel not only improves mechanistic property of gels but also changes the migration pattern of different proteins that have different affinities to titanium dioxide.

  7. Titanium Dioxide Photocatalytic Polymerization of Acrylamide for Gel Electrophoresis (TIPPAGE) of Proteins and Structural Identification by Mass Spectrometry

    Science.gov (United States)

    Zhang, Wenyang; Yuan, Zhiwei; Huang, Lulu; Kang, Jie; Jiang, Ruowei; Zhong, Hongying

    2016-02-01

    Polyacrylamide gel electrophoresis (PAGE) coupled with mass spectrometry has been well established for separating, identifying and quantifying protein mixtures from cell lines, tissues or other biological samples. The copolymerization process of acrylamide and bis-acrylamide is the key to mastering this powerful technique. In general, this is a vinyl addition reaction initiated by free radical-generating reagents such as ammonium persulfate (APS) and tetramethylethylenediamine (TEMED) under basic pH and degassing experimental condition. We report herein a photocatalytic polymerization approach that is based on photo-generated hydroxyl radicals with nanoparticles of titanium dioxide. It was shown that the polymerization process is greatly accelerated in acidic condition when ultraviolet light shots on the gel solution containing TiO2 nanoparticles without degassing. This feature makes it very useful in preparing Triton X-100 acid urea (TAU) gel that has been developed for separating basic proteins such as histones and variants in acidic experimental condition. Additionally, the presence of titanium dioxide in the gel not only improves mechanistic property of gels but also changes the migration pattern of different proteins that have different affinities to titanium dioxide.

  8. Local Pixel Value Collection Algorithm for Spot Segmentation in Two-Dimensional Gel Electrophoresis Research

    Directory of Open Access Journals (Sweden)

    Peter Peer

    2007-01-01

    Full Text Available Two-dimensional gel-electrophoresis (2-DE images show the expression levels of several hundreds of proteins where each protein is represented as a blob-shaped spot of grey level values. The spot detection, that is, the segmentation process has to be efficient as it is the first step in the gel processing. Such extraction of information is a very complex task. In this paper, we propose a novel spot detector that is basically a morphology-based method with the use of a seeded region growing as a central paradigm and which relies on the spot correlation information. The method is tested on our synthetic as well as on real gels with human samples from SWISS-2DPAGE (two-dimensional polyacrylamide gel electrophoresis database. A comparison of results is done with a method called pixel value collection (PVC. Since our algorithm efficiently uses local spot information, segments the spot by collecting pixel values and its affinity with PVC, we named it local pixel value collection (LPVC. The results show that LPVC achieves similar segmentation results as PVC, but is much faster than PVC.

  9. Cytoplasmic polyhedrosis virus classification by electropherotype; validation by serological analyses and agarose gel electrophoresis.

    Science.gov (United States)

    Mertens, P P; Crook, N E; Rubinstein, R; Pedley, S; Payne, C C

    1989-01-01

    Serological analyses of several different cytoplasmic polyhedrosis viruses (CPVs), including two type 1 CPVs from Bombyx mori, type 1 CPV from Dendrolimus spectabilis, type 12 CPV from Autographa gamma, type 2 CPV from Inachis io, type 5 CPV from Orgyia pseudotsugata and type 5 CPV from Heliothis armigera, demonstrated a close correlation between the antigenic properties of the polyhedrin or virus particle structural proteins and the genomic dsRNA electropherotypes. The dsRNAs of these viruses were analysed by electrophoresis in 3% and 10% polyacrylamide gels with a discontinuous Tris-HCl/Tris-glycine buffer system or by 1% agarose gel electrophoresis using a continuous Tris-acetate-EDTA buffer system. Electrophoretic analysis in agarose gels was found to be the most suitable for the classification of CPV isolates into electropherotypes, and the results obtained showed a close correlation with the observed antigenic relationships between different virus isolates. However, electrophoretic analysis in 10% polyacrylamide gels was most sensitive for the detection of intra-type variation and the presence of mixed virus isolates. PMID:2499658

  10. Quantifying clustered DNA damage induction and repair by gel electrophoresis, electronic imaging and number average length analysis

    Science.gov (United States)

    Sutherland, Betsy M.; Georgakilas, Alexandros G.; Bennett, Paula V.; Laval, Jacques; Sutherland, John C.; Gewirtz, A. M. (Principal Investigator)

    2003-01-01

    Assessing DNA damage induction, repair and consequences of such damages requires measurement of specific DNA lesions by methods that are independent of biological responses to such lesions. Lesions affecting one DNA strand (altered bases, abasic sites, single strand breaks (SSB)) as well as damages affecting both strands (clustered damages, double strand breaks) can be quantified by direct measurement of DNA using gel electrophoresis, gel imaging and number average length analysis. Damage frequencies as low as a few sites per gigabase pair (10(9)bp) can be quantified by this approach in about 50ng of non-radioactive DNA, and single molecule methods may allow such measurements in DNA from single cells. This review presents the theoretical basis, biochemical requirements and practical aspects of this approach, and shows examples of their applications in identification and quantitation of complex clustered damages.

  11. Quantifying clustered DNA damage induction and repair by gel electrophoresis, electronic imaging and number average length analysis

    Energy Technology Data Exchange (ETDEWEB)

    Sutherland, Betsy M.; Georgakilas, Alexandros G.; Bennett, Paula V.; Laval, Jacques; Sutherland, John C

    2003-10-29

    Assessing DNA damage induction, repair and consequences of such damages requires measurement of specific DNA lesions by methods that are independent of biological responses to such lesions. Lesions affecting one DNA strand (altered bases, abasic sites, single strand breaks (SSB)) as well as damages affecting both strands (clustered damages, double strand breaks) can be quantified by direct measurement of DNA using gel electrophoresis, gel imaging and number average length analysis. Damage frequencies as low as a few sites per gigabase pair (10{sup 9} bp) can be quantified by this approach in about 50 ng of non-radioactive DNA, and single molecule methods may allow such measurements in DNA from single cells. This review presents the theoretical basis, biochemical requirements and practical aspects of this approach, and shows examples of their applications in identification and quantitation of complex clustered damages.

  12. High—Speed Analyzing PCR Products of M.tuberculosis Genome Stained by Ethidium Bromide on Microchip Gel Electrophoresis

    Institute of Scientific and Technical Information of China (English)

    金庆辉; 陈继锋; 等

    2002-01-01

    The technique of microchip gel electrophoresis(MCGE) was used to analyze the polymerase chain reaction (PCR) products of M.tuberculosis Genome stained by ethidium bromide,The electrophoretic Process was completed within 3-4 min and the results show that the technique of microchip electrophoresis is a high-speed and high-sensitivity analyzing method.

  13. Multivariate data analysis of two-dimensional gel electrophoresis protein patterns from few samples

    DEFF Research Database (Denmark)

    Jensen, Kristina Nedenskov; Jessen, Flemming; Jørgensen, Bo

    2008-01-01

    One application of 2D gel electrophoresis is to reveal differences in protein pattern between two or more groups of individuals, attributable to their group membership. Multivariate data analytical methods are useful in pinpointing the spots relevant for discrimination by focusing not only...... on single spot differences, but on the covariance structure between proteins. However, their outcome is dependent on data scaling, and they may fail in producing valid multivariate models due to the much higher number of "irrelevant" spots present in the gels. The case where only few gels are available...... 'autoscaling' of the full data set based on within-group standard deviations is introduced and shown to be advantageous in revealing potential group-dependent proteins additional to those found by prefiltering....

  14. Purification of Peptide Components including Melittin from Bee Venom using gel filtration chromatography and propionic acid/urea polyacrylamide gel electrophoresis

    Directory of Open Access Journals (Sweden)

    Young Chon Choi

    2006-06-01

    Full Text Available Objectives : This study was conducted to carry out Purification of Melittin and other peptide components from Bee Venom using gel filtration chromatography and propionic acid/urea polyacrylamide gel electrophoresis Methods : Melittin and other peptide components were separated from bee venom by using gel filtration chromatography on Sephadex G-50 column in 0.05M ammonium acetate buffer. Results : Melittin and other peptide components were separated from bee venom by using gel filtration chromatography on Sephadex G-50 column in 0.05M ammonium acetate buffer. The fractions obtained from gel filtration chromatography was analyzed by using SDS-PAGE and propionic acid/urea polyacrylamide gel electrophoresis. The melittin obtained from the gel filtration contained residual amount of phospholipase A2 and a protein with molecular weight of 6,000. The contaminating proteins were removed by the second gel filtration chromatography. Conclusion : Gel filtration chromatography and propionic acid/urea polyacrylamide gel electrophoresis are useful to separate peptide components including melittin from bee venom.

  15. DNA electrophoresis in tri-block copolymer gels--experiments and Brownian dynamics simulation

    Science.gov (United States)

    Wei, Ling; van Winkle, David H.

    2015-03-01

    The mobility of double-stranded DNA ladders in Pluronics®P105, P123 and F127, was measured by two-dimensional gel electrophoresis. Pluronics®are triblock copolymers which form gel-like phases of micelles arranged with cubic order at room temperature. A 10 base pair and a 25 base pair DNA ladder were used as samples in gel electrophoresis. The monotonically decreasing mobility with increasing length observed in the agarose separations is not observed in separations in Pluronics®. Rather, a complicated dependence of mobility on DNA length is observed, where mobility vs. length increases for short DNA molecules then decreases for longer molecules. There is also a variation of mobility with length correlated to the micelle diameter. Brownian dynamics simulations of a discrete wormlike chain model were performed to simulate short DNA molecules migrating in free solution and in a face-centered cubic matrix. By incorporating hydrodynamic interactions, the trend of simulated length-dependent mobility qualitatively agrees with experimental measurements.

  16. Genomic DNA detection using cycling probe technology and capillary gel electrophoresis with laser-induced fluorescence.

    Science.gov (United States)

    Dickinson Laing, Terrina; Mah, David C W; Poirier, Robert T; Bekkaoui, Faouzi; Lee, William E; Bader, Douglas E

    2004-10-01

    Cycling probe technology (CPT) is an isothermal DNA analysis method that has been shown to be useful for identifying genetic markers of antibiotic-resistant bacteria in clinical settings. CPT assays have previously employed several assay methods that include polyacrylamide gel electrophoresis and magnetic beads for separations and radioisotopic and colorimetric detection for detection. Capillary gel electrophoresis with laser-induced fluorescence (CGE-LIF) is an alternative separation and detection method that offers attributes such as low sample consumption, short analysis times, no radiation hazards and potential for high throughput. We report on the development of a CGE-LIF CPT assay for genomic DNA from Erwinia herbicola and the comparison of this assay with a conventional 32p radioisotopic PAGE CPT assay. Separation and detection of intact and cleaved fluorescein-labeled CPT probe molecules by CGE-LIF was achieved in under 4 min through a gel-filled capillary (7 cm separation length to detector). Total time, from setup to detection, was about 1 h for the complete assay versus several hours (3-12 h) for the radioisotopic PAGE CPT assay. Similar detection limits of 10(5)-10(6) copies of genomic target DNA were observed with each assay method. This study demonstrated that CGE-LIF CPT is a suitable analysis method for the detection of genomic DNA sequences. PMID:15356906

  17. High Resolution Quantitative Proteomics of HeLa Cells Protein Species Using Stable Isotope Labeling with Amino Acids in Cell Culture(SILAC), Two-Dimensional Gel Electrophoresis(2DE) and Nano-Liquid Chromatograpohy Coupled to an LTQ-OrbitrapMass Spectrometer*

    Science.gov (United States)

    Thiede, Bernd; Koehler, Christian J.; Strozynski, Margarita; Treumann, Achim; Stein, Robert; Zimny-Arndt, Ursula; Schmid, Monika; Jungblut, Peter R.

    2013-01-01

    The proteomics field has shifted over recent years from two-dimensional gel electrophoresis (2-DE)-based approaches to SDS-PAGE or gel-free workflows because of the tremendous developments in isotopic labeling techniques, nano-liquid chromatography, and high-resolution mass spectrometry. However, 2-DE still offers the highest resolution in protein separation. Therefore, we combined stable isotope labeling with amino acids in cell culture of controls and apoptotic HeLa cells with 2-DE and the subsequent analysis of tryptic peptides via nano-liquid chromatography coupled to an LTQ-Orbitrap mass spectrometer to obtain quantitative data using the methods with the highest resolving power on all levels of the proteomics workflow. More than 1,200 proteins with more than 2,700 protein species were identified and quantified from 816 Coomassie Brilliant Blue G-250 stained 2-DE spots. About half of the proteins were identified and quantified only in single 2-DE spots. The majority of spots revealed one to five proteins; however, in one 2-DE spot, up to 23 proteins were identified. Only half of the 2-DE spots represented a dominant protein with more than 90% of the whole protein amount. Consequently, quantification based on staining intensities in 2-DE gels would in approximately half of the spots be imprecise, and minor components could not be quantified. These problems are circumvented by quantification using stable isotope labeling with amino acids in cell culture. Despite challenges, as shown in detail for lamin A/C and vimentin, the quantitative changes of protein species can be detected. The combination of 2-DE with high-resolution nano-liquid chromatography-mass spectrometry allowed us to identify proteomic changes in apoptotic cells that would be unobservable using any of the other previously employed proteomic workflows. PMID:23033477

  18. Proteomic analysis of human saliva from lung cancer patients using two-dimensional difference gel electrophoresis and mass spectrometry.

    Science.gov (United States)

    Xiao, Hua; Zhang, Lei; Zhou, Hui; Lee, Jay M; Garon, Edward B; Wong, David T W

    2012-02-01

    Lung cancer is often asymptomatic or causes only nonspecific symptoms in its early stages. Early detection represents one of the most promising approaches to reduce the growing lung cancer burden. Human saliva is an attractive diagnostic fluid because its collection is less invasive than that of tissue or blood. Profiling of proteins in saliva over the course of disease progression could reveal potential biomarkers indicative of oral or systematic diseases, which may be used extensively in future medical diagnostics. There were 72 subjects enrolled in this study for saliva sample collection according to the approved protocol. Two-dimensional difference gel electrophoresis combined with MS was the platform for salivary proteome separation, quantification, and identification from two pooled samples. Candidate proteomic biomarkers were verified and prevalidated by using immunoassay methods. There were 16 candidate protein biomarkers discovered by two-dimensional difference gel electrophoresis and MS. Three proteins were further verified in the discovery sample set, prevalidation sample set, and lung cancer cell lines. The discriminatory power of these candidate biomarkers in lung cancer patients and healthy control subjects can reach 88.5% sensitivity and 92.3% specificity with AUC = 0.90. This preliminary data report demonstrates that proteomic biomarkers are present in human saliva when people develop lung cancer. The discriminatory power of these candidate biomarkers indicate that a simple saliva test might be established for lung cancer clinical screening and detection.

  19. Polyacrylamide gel electrophoresis-SDS as a tool to study myofibrillar proteins. A review.

    Directory of Open Access Journals (Sweden)

    Perez-Chabela, M. Lourdes

    2015-12-01

    Full Text Available Miofibrillar proteins are part of land and sea animals’ muscle. Nonetheless, even when muscle proteins are the same type of proteins, their structure, rigor mortis time, and biochemical process associated to muscle to meat conversion, are different among animal species. This review has the aim to describe the advantages of SDS-polyacrylamide gel electrophoresis (SDS-PAGE in the study of myofibrillar proteins structure, besides the influence of many parameters on this technique to obtain an electrophoretic profile. Applications of this technique as a diagnostic tool in the food science, ecology and health are described as well.

  20. Genome size of human oral Treponema species by pulsed-field gel electrophoresis.

    Science.gov (United States)

    Correia, F F; Plummer, A R; Paster, B J; Dewhirst, F E

    2004-04-01

    The genome sizes of seven strains of oral treponemes were determined using pulsed-field gel electrophoresis (PFGE). These strains represent members from six of the currently known cultivable oral treponeme groups. The PFGE fragments were digitally recorded and then quantitated using GIMP v 1.2, an image manipulation program. The results show that the six oral treponeme genomes are comparable in size, ranging from approximately 2.2 to 2.5 Mbp. The genome sizes of these strains are 20-25% smaller than Treponema denticola strains, which have genome sizes of approximately 2.8-3.0 Mbp. PMID:14871355

  1. A Novel Strategy for Characterization of Glycosylated Proteins Separated by Gel Electrophoresis

    DEFF Research Database (Denmark)

    Larsen, Martin; Skottrup, Peter; Enghild, Jan Johannes;

    Protein glycosylation can be vital for changing the function or physiochemical properties of a protein. Abnormal glycosylation can lead to protein malfunction, resulting in severe diseases. Therefore, it is important to develop techniques for characterization of such modifications in proteins...... at a sensitivity level comparable with state-of-the-art proteomics. Whereas techniques exist for characterization of high abundant glycoproteins, no single method is presently capable of providing information on both site occupancy and glycan structure on a single band or spot excised from an electrophoretic gel....... We present a new technique, which allows full characterization of low amounts of glycoproteins separated by gel electrophoresis. The method takes advantage of sequential specific and non-specific enzymatic treatment, followed by selective purification and characterization of the glycopeptides using...

  2. Agarose gel purification of PCR products for denaturing gradient gel electrophoresis results in GC-clamp deletion.

    Science.gov (United States)

    Sun, Guowei; Xiao, Jinzhou; Lu, Man; Wang, Hongming; Chen, Xiaobing; Yu, Yongxin; Pan, Yingjie; Wang, Yongjie

    2015-01-01

    The 16S ribosomal RNA (rRNA) gene of marine archaeal samples was amplified using a nested PCR approach, and the V3 region of 16S rRNA gene of crab gut microbiota (CGM) was amplified using the V3 universal primer pair with a guanine and cytosine (GC)-clamp. Unpurified PCR products (UPPs), products purified from reaction solution (PPFSs), and products purified from gel (PPFGs) of above two DNA samples were used for denaturing gradient gel electrophoresis (DGGE) analysis, respectively. In contrast to almost identical band patterns shared by both the UPP and PPFS, the PPFGs were barely observed on the DGGE gel for both the marine archaea and CGM samples. Both PPFS and PPFG of CGM V3 regions were subjected to cloning. A small amount of positive clones was obtained for PPFS, but no positive clones were observed for PPFG. The melt curve and direct sequencing analysis of PPFS and PPFG of E. coli V3 region indicated that the Tm value of PPFG (82.35 ± 0.19 °C) was less than that of PPFS (83.81 ± 0.11 °C), and the number of shorter GC-clamps was significant higher in PPFG than in PPFS. The ultraviolet exposure experiment indicated that the ultraviolet was not responsible for the deletion of the GC-clamps. We conclude that the gel purification method is not suitable for DGGE PCR products or even other GC-rich DNA samples. PMID:25300603

  3. Comparative analyses of amplicon migration behavior in differing denaturing gradient gel electrophoresis (DGGE) systems

    Science.gov (United States)

    Thornhill, D. J.; Kemp, D. W.; Sampayo, E. M.; Schmidt, G. W.

    2010-03-01

    Denaturing gradient gel electrophoresis (DGGE) is commonly utilized to identify and quantify microbial diversity, but the conditions required for different electrophoretic systems to yield equivalent results and optimal resolution have not been assessed. Herein, the influence of different DGGE system configuration parameters on microbial diversity estimates was tested using Symbiodinium, a group of marine eukaryotic microbes that are important constituents of coral reef ecosystems. To accomplish this, bacterial clone libraries were constructed and sequenced from cultured isolates of Symbiodinium for the ribosomal DNA internal transcribed spacer 2 (ITS2) region. From these, 15 clones were subjected to PCR with a GC clamped primer set for DGGE analyses. Migration behaviors of the resulting amplicons were analyzed using a range of conditions, including variation in the composition of the denaturing gradient, electrophoresis time, and applied voltage. All tests were conducted in parallel on two commercial DGGE systems, a C.B.S. Scientific DGGE-2001, and the Bio-Rad DCode system. In this context, identical nucleotide fragments exhibited differing migration behaviors depending on the model of apparatus utilized, with fragments denaturing at a lower gradient concentration and applied voltage on the Bio-Rad DCode system than on the C.B.S. Scientific DGGE-2001 system. Although equivalent PCR-DGGE profiles could be achieved with both brands of DGGE system, the composition of the denaturing gradient and application of electrophoresis time × voltage must be appropriately optimized to achieve congruent results across platforms.

  4. Comparison of Pseudomonas aeruginosa isolates from mink by serotyping and pulsed-field gel electrophoresis

    DEFF Research Database (Denmark)

    Hammer, Anne Sofie; Pedersen, Karl; Andersen, Thomas Holmen;

    2003-01-01

    Isolates of Pseudomonas aeruginosa from clinical infections in mink were subjected to serotyping and pulsed-field gel electrophoresis (PFGE) using SpeI. A total of 212 isolates of P aeruginosa from the year 1998 to 2001 were included in this study: 168 isolates from mink obtained from 74 farm out...... by pathogenic strains of R aeruginosa spread between farms and animals either mechanically, or through feed or water from a common source, rather than by random nosocomial infections with strains from the farm environment.......Isolates of Pseudomonas aeruginosa from clinical infections in mink were subjected to serotyping and pulsed-field gel electrophoresis (PFGE) using SpeI. A total of 212 isolates of P aeruginosa from the year 1998 to 2001 were included in this study: 168 isolates from mink obtained from 74 farm...... outbreaks of haemorrhagic pneumonia. Isolates from mink were separated into 34 distinct clones by PFGE subtyping. All isolates from mink infected during the same farm outbreak were identical, except in one case where two different strains were isolated from mink obtained from the same farm outbreak. R...

  5. A control method to inspect the compositional authenticity of Minas Frescal cheese by gel electrophoresis.

    Science.gov (United States)

    Magenis, Renata B; Prudêncio, Elane S; Molognoni, Luciano; Daguer, Heitor

    2014-08-20

    This study introduces a qualitative method to inspect the compositional authenticity of white nonripened cheeses like Minas Frescal, a typical Brazilian cheese, especially when irregular replacement of milk by whey is suspected. A sodium dodecyl sulfate gel electrophoresis (SDS-PAGE) method, followed by image densitometry, was validated. Cheeses were freeze-dried to electrophoresis, and β-lactoglobulin (β-LG) was chosen as the adulteration marker. In gel trypsin digestion followed by matrix assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry provided its identification. Cheeses with a minimum of 14 mg·g(-1) of β-LG are considered to be adulterated. The method shows satisfactory precision with a detection limit of 7 mg·g(-1). Forty-two commercial samples from inspected establishments were then assessed and subjected to cluster analysis. Compliant and noncompliant groups were set with 24 (57%) authentic samples and 18 (43%) adulterated samples, respectively, showing that proper analytical monitoring is required to inhibit this practice.

  6. Optimization of a pulsed-field gel electrophoresis for molecular typing of Proteus mirabilis

    Directory of Open Access Journals (Sweden)

    Alper Karagöz

    2013-09-01

    Full Text Available Objective: For the detection of outbreaks caused byProteus mirabilis, strains clonal relations are determinedmethods as “pulsed-field gel electrophoresis (PFGE”.The aim of this study was optimization of a pulsed-fieldgel electrophoresis for molecular typing of P. mirabilis.Methods: In this study, PFGE’ protocol is optimized foruse in molecular typing of P. mirabilis. Phylogenetic analyzesof strains were evaluated with Bionumerics softwaresystem (version 6.01; Applied Maths, Sint-Martens-Latem, Belgium.Results: This protocol compared with Gram-negativebacteria PFGE protocols, NotI enzyme is suitable for thisbacterium. Electrophoresis conditions should be revealedas; - block 1: initial pulse duration 1 sec, ending pulseduration 30 sec, striking angle 120°, the current 6 V/cm2,temperature 14°C, time 8 hours; - block 2: initial pulseduration 30 sec, ending pulse duration 70 sec, strikingangle 120°, the current 6 V/cm2, temperature 14°C, time16 hours; - TBE, pH=8.4.Conclusion: P. mirabilis strains were typed by PFGE andBionumerics analysis program were determined clonal relationships.The procedure was simple, reproducible andsuitable for these bacteria. Also it was evaluated, becauseof reducing time, the solution volumes and enzymes canbe economically. Outbreaks of nosocomial infections dueto bacteria studied assessment and the potential to provideuseful information about the degree of prevalence.This optimized protocol is allowed different centers’ PFGEresults to compare with other laboratories results. J ClinExp Invest 2013; 4 (3: 306-312Key words: Proteus mirabilis, molecular typing, pulsedfieldgel electrophoresis.

  7. ISOLATION OF EGG DROP SYNDROME VIRUS AND ITS MOLECULAR CHARACTERIZATION USING SODIUM DODECYL SULPHATE POLYACRYLAMIDE GEL ELECTROPHORESIS

    Directory of Open Access Journals (Sweden)

    M. H. Rasool, S. U. Rahman and M. K. Mansoor

    2005-10-01

    Full Text Available Six isolates of egg drop syndrome (EDS virus were recovered from five different outbreaks of EDS in commercial laying hens in and around Faisalabad. The aberrant eggs were fed to the susceptible laying hens for experimental induction of infection. The samples from infected birds (egg washing, cloacal swabs, oviducts and spleens were collected, processed and inoculated into 11-day old duck embryos. The presence of virus in harvested allanto-amniotic fluid was monitored by spot and microhaemagglutination tests and confirmed by haemagglutination inhibition and agar gel precipitation tests. The EDS virus grew well in duck embryos and agglutinated only avian but not mammalian red blood cells. These isolates were purified through velocity density gradient centrifugation. Protein concentration was determined through Lowry method and sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE was conducted by loading 300 µg protein concentration on 12.5% gel using discontinuous buffer system. All the six isolates showed 13 polypeptides, which were identical to those described in the referral EDS-76 virus (strain-127. The molecular weights of the polypeptides ranged from 6.5 KDa to 126 KDa.

  8. PHProteomicDB: A Module for Two-dimensional Gel Electrophoresis Database Creation on Personal Web Sites

    Institute of Scientific and Technical Information of China (English)

    Pascal Pernet; Arnaud Bruneel; Bruno Baudin; Michel Vaubourdolle

    2006-01-01

    PHProteomicDB is a PHP-written module to help researchers in proteomics to share two-dimensional gel electrophoresis data using personal web sites. No technical or PHP knowledge is necessary except a few basics about web site management. PHProteomicDB has a user-friendly administration interface to enter and update data. It creates web pages on the fly displaying gel characteristics,gel pictures, and numbered gel spots with their related identifications pointing to their reference pages in protein databanks. The module is freely available at http://www.huvec.com/index.php3?rub=Download.

  9. Silky gels for cells

    NARCIS (Netherlands)

    Wlodarczyk, M.K.

    2016-01-01

    Tissue engineering is a relatively new, but actively developing field of biomedical science. It aims at organ or tissue regeneration by use of scaffolds, which are usually seeded with cells prior to implantation, and stimulated by bioactive cues or growth factors. It is a promising and valuable alte

  10. Population dynamics of two antilisterial cheese surface consortia revealed by temporal temperature gradient gel electrophoresis

    Directory of Open Access Journals (Sweden)

    Hasler Madlen

    2010-03-01

    Full Text Available Abstract Background Surface contamination of smear cheese by Listeria spp. is of major concern for the industry. Complex smear ecosystems have been shown to harbor antilisterial potential but the microorganisms and mechanisms involved in the inhibition mostly remain unclear, and are likely related to complex interactions than to production of single antimicrobial compounds. Bacterial biodiversity and population dynamics of complex smear ecosystems exhibiting antilisterial properties in situ were investigated by Temporal temperature gradient gel electrophoresis (TTGE, a culture independent technique, for two microbial consortia isolated from commercial Raclette type cheeses inoculated with defined commercial ripening cultures (F or produced with an old-young smearing process (M. Results TTGE revealed nine bacterial species common to both F and M consortia, but consortium F exhibited a higher diversity than consortium M, with thirteen and ten species, respectively. Population dynamics were studied after application of the consortia on fresh-produced Raclette cheeses. TTGE analyses revealed a similar sequential development of the nine species common to both consortia. Beside common cheese surface bacteria (Staphylococcus equorum, Corynebacterium spp., Brevibacterium linens, Microbacterium gubbeenense, Agrococcus casei, the two consortia contained marine lactic acid bacteria (Alkalibacterium kapii, Marinilactibacillus psychrotolerans that developed early in ripening (day 14 to 20, shortly after the growth of staphylococci (day 7. A decrease of Listeria counts was observed on cheese surface inoculated at day 7 with 0.1-1 × 102 CFU cm-2, when cheeses were smeared with consortium F or M. Listeria counts went below the detection limit of the method between day 14 and 28 and no subsequent regrowth was detected over 60 to 80 ripening days. In contrast, Listeria grew to high counts (105 CFU cm-2 on cheeses smeared with a defined surface culture

  11. Genetic heterogeneity of Campylobacter concisus determined by pulsed field gel electrophoresis-based macrorestriction profiling

    DEFF Research Database (Denmark)

    Matsheka, M.I.; Elisha, B.G.; Lastovica, A.L.;

    2002-01-01

    In order to investigate the genetic diversity of Campylobacter concisus to assist molecular typing studies, the use of macrorestriction profiling was examined. A suitable protocol was developed that included the use of formaldehyde pretreatment to prevent DNA degradation, and restriction enzyme Not......1 for pulsed field gel electrophoresis-based genotyping. Subsequently, 53 strains of C concisus, principally from cases of diarrhoea in children, were examined. Fifty-one distinct patterns were obtained, indicating the high discriminatory potential of the method. Patterns comprised between one...... and 14 restriction fragments, with type and reference strains of two well-defined genomospecies of oral and faecal origin containing six and 12 fragments respectively. Our results show that C concisus is genetically diverse and suggest the species as currently defined to be a taxonomic continuum...

  12. New Primers for Denaturing Gradient Gel Electrophoresis Analysis of Nitrate-Reducing Bacterial Community in Soil

    Institute of Scientific and Technical Information of China (English)

    R.PASTORELLI; R.PICCOLO; S.SIMONCINI; S.LANDI

    2013-01-01

    The narG gene is frequently used as a molecular marker for bacterial nitrate-reducing community analysis.In this study,a new set of primers targeting the narG gene was designed and applied to semi-nested polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) assay.The potential of the new primers was verified on DNA directly extracted from soils from five different experimental sites distributed in Central and Southern Italy.Specificity of the primers was determined by excision,amplification,and sequencing of bands resolved by DGGE.A phylogenetic analysis showed the correlation between the sequences retrieved from the soils studied and the narG sequences from β and γ-Proteobacteria.These primers expanded the existing molecular tools for ecological study on the size and diversity of nitrate-reducing bacterial community in soil.

  13. Typing dinucleotide repeat loci using microplate array diagonal gel electrophoresis: proof of principle.

    Science.gov (United States)

    Rodríguez, Santiago; Chen, Xiao-He; Day, Ian N M

    2004-04-01

    Polymorphic dinucleotide repeat loci ('microsatellite markers') are found in varying abundance throughout the genomes of most organisms. They have been extensively used for genetic studies, but conventional techniques used for their genotyping require sophisticated equipment. Microplate array diagonal gel electrophoresis (MADGE) has previously been extended to economical high-throughput genotyping of trinucleotide and tetranucleotide microsatellite amplicons. However, the capability of this technique to resolve the alleles of dinucleotide repeat loci has not been explored previously. Here we show that a modified microsatellite-MADGE approach can provide sufficient resolution for dinucleotide repeat typing. This enables economical and convenient set up for analysis of single markers in many samples in parallel, suitable, for example, for population association studies.

  14. Rapid pulsed-field gel electrophoresis protocol for Legionella pneumophila typing

    Directory of Open Access Journals (Sweden)

    Massimiliano Orsini

    2008-06-01

    Full Text Available

    Background: Genomic DNA patterns generated by pulsed-field gel electrophoresis (PGFE are highly specific for different strains of an organism and have significant value in epidemiologic investigations of infectious disease outbreaks. A disadvantage of PFGE is that the procedure requires up to 6 days to complete.

    Methods: We developed a rapid PFGE protocol for subtyping Legionella pneumophila isolates based on the standardized protocol currently used. Various combinations of reaction conditions (e.g., lysis time and temperature, restriction enzyme concentration and electrophoresis parameters were applied to devise a simple and rapid PFGE protocol that could also be used for frozen bacteria.

    Results: PFGE analysis of Legionella pneumophila isolates can be completed in 26 hours using this protocol compared to 6 days for the conventional one.

    Conclusions: We successfully applied a rapid PFGE protocol for Legionella pneumophila typing and comparison of the patterns obtained from the rapid compared with the conventional method showed that the rapid protocol gave identical and highly reproducible results.

  15. Protein profile analysis of Malaysian snake venoms by two-dimensional gel electrophoresis

    Directory of Open Access Journals (Sweden)

    J Vejayan

    2010-01-01

    Full Text Available Snake venoms comprise a highly complex mixture of proteins, which requires for their characterization the use of versatile two-dimensional electrophoresis techniques. In the present study, venoms obtained from eight snakes (Ophiophagus hannah, Naja kaouthia, Naja sumatrana, Bungarus fasciatus, Trimeresurus sumatranus, Tropidolaemus wagleri, Enhydrina schistosa and Calloselasma rhodostoma commonly found in Malaysia were separated based on two independent properties, isoelectric point (pI and molecular weight (MW. Many differences in snake venoms at the inter-family, inter-subfamily, inter-genus and inter-species levels were revealed. Notably, proteins from individuals of the Viperidae family - Trimeresurus sumatranus, Tropidolaemus wagleri and Calloselasma rhodostoma - were found to be numerous and scattered by the two-dimensional gel electrophoresis (2DE specifically in regions between 37 and 100 kDa compared to the Elapidae venom proteins. The latter were clustered at the basic and lower molecular mass region (less than 20 kDa. Trains of spots were commonly observed, indicating that these proteins may be derived from post-translational modifications. Ophiophagus hannah (Elapidae revealed a great amount of protein spots in the higher molecular mass range when compared to Enhydrina schistosa, Naja kaouthia, Naja sumatrana and Bungarus fasciatus. Overall 2DE showed large differences in the venom profile of each species, which might be employed as an ancillary tool to the identification of venomous snake species.

  16. Comparative Studies on Preparation of Large Plant DNA Fragments by Pulse Field Gel Electrophoresis

    Institute of Scientific and Technical Information of China (English)

    Yang Jiliang(杨继良); Wang Qinghua(王庆华); Deng Daiyong; Yang Dianer; Jin Demin; Weng Manli; Zhang Juren; Wang Bin

    2004-01-01

    The preparation of large plant DNA fragments is extremely important to the construction of large insert DNA libraries (YAC, BAC, PAC and TAC). Although several techniques have been developed in each step of large plant DNA fragments preparation, the whole processing remains complicated and difficult. Based on authors research experience and the recent worldwide development in this field, the following aspects are discussed in this paper: techniques of plant high molecular weight (HMW) DNA purification by pre-electrophoresis, the optimal conditions for the partial digestion of the HMW DNA by HindIII, the isolation effects of of large plant DNA fragments (100~400 kb) with different parameters of pulse field gel electrophoresis (PFGE), and the recovery of large DNA fragments. Through comparative studies, the advantages and disadvantages of each technique are discussed and some recommendations are proposed for preparing high quality large plant DNA fragments. The suggested techniques have been used in preparing the large DNA fragments of maize, rice, moss, laver, sea tangle and peach,and similar results are obtained among all the materials. This paper only reports the results using maize as material.

  17. Determination of the enantiomeric purity of (-) terbutaline by capillary electrophoresis using cyclodextrins as chiral selectors in a polyethylene glycol gel

    NARCIS (Netherlands)

    de Boer, T; Ensing, K

    1998-01-01

    A method was developed for determination of the enantiomeric purity of the therapeutic-pharmacological active (-)-enantiomer of terbutaline using cyclodextrins as a chiral selector dissolved in a removable liquid polyethylene glycol gel by use of capillary electrophoresis. The effect of temperature,

  18. Triton X-114 cloud point extraction to subfractionate blood plasma proteins for two-dimensional gel electrophoresis

    DEFF Research Database (Denmark)

    Jessen, Flemming; Wulff, Tune

    2015-01-01

    A simple and reproducible procedure for enrichment of a plasma protein subfraction suitable for two-dimensional polyacrylamide gel electrophoresis (2DE) was developed, using a Triton X-114-based cloud point extraction (CPE). Appropriate conditions for such a CPE procedure were found by SDS...

  19. Evaluation of repetitive extragenic palindromic-PCR and denatured gradient gel electrophoresis in identifying Salmonella serotypes isolated from processed turkeys

    Science.gov (United States)

    Salmonella has been reported as the leading foodborne pathogen in the US. A study was conducted to compare the use of automated repetitive extragenic palindromic (REP-PCR) and denaturing gradient gel electrophoresis (DGGE) as diagnostic tools for identifying Salmonella serotypes. The interspersed ...

  20. Differentiation of Neisseria gonorrhoeae isolates requiring proline, citrulline, and uracil by plasmid content, serotyping, and pulsed-field gel electrophoresis.

    OpenAIRE

    Ng, L K; Carballo, M.; Dillon, J A

    1995-01-01

    A combination of DNA macrorestriction analysis using pulsed-field gel electrophoresis and a serotyping method using three panels of monoclonal antibody was used to discriminate 43 epidemiologically unrelated Neisseria gonorrhoeae isolates requiring proline, citrulline, and uracil (PCU-) into 35 groups. This indicates that PCU- isolates of N. gonorrhoeae are not clonal.

  1. Construction of physical and genetic maps of Chlamydia trachomatis serovar L2 by pulsed-field gel electrophoresis

    DEFF Research Database (Denmark)

    Birkelund, Svend; Stephens, RS

    1992-01-01

    We constructed the physical map of Chlamydia trachomatis serovar L2 by using three restriction endonucleases, NotI (GC[GGCCGC), SgrAI (C(A/G)[CCGG(T/G)G), and Sse8387I (CCTGCA[GG), and we analyzed the fragments by pulsed-field gel electrophoresis. A total of 25 restriction endonuclease sites and 13...

  2. Characterization and identification of early proteins in Chlamydia trachomatis serovar L2 by two-dimensional gel electrophoresis

    DEFF Research Database (Denmark)

    Lundemose, AG; Birkelund, Svend; Larsen, PM;

    1990-01-01

    The synthesis of early proteins from Chlamydia trachomatis serovar L2 was analyzed by two-dimensional gel electrophoresis. By pulse-label experiments, the synthesis of seven proteins was observed at 2 to 8 h postinfection before the major outer membrane protein was detected at 8 to 10 h after...

  3. Comprehensive TP53-denaturing gradient gel electrophoresis mutation detection assay also applicable to archival paraffin-embedded tissue

    NARCIS (Netherlands)

    Hayes, V M; Bleeker, W; Verlind, E; Timmer, T; Karrenbeld, A; Plukker, J T; Marx, M P; Hofstra, R M; Buys, C H

    1999-01-01

    A comprehensive mutation detection assay is described for the entire coding region and all splice site junctions of TP53. The assay is based on denaturing gradient gel electrophoresis, which follows either multiplex polymerase chain reaction (PCR) applied to DNA extracted from fresh or frozen tissue

  4. Implementation of Salmonella serotype determination using pulsed-field gel electrophoresis in a state public health laboratory.

    Science.gov (United States)

    Bopp, Dianna J; Baker, Deborah J; Thompson, Lisa; Saylors, Amy; Root, Timothy P; Armstrong, Leeanna; Mitchell, Kara; Dumas, Nellie B; Musser, Kimberlee Arruda

    2016-08-01

    We examined the use of pulsed-field gel electrophoresis (PFGE) to predict serotype for Salmonella isolates. Between 2012 and 2014 we assessed 4481 isolates, resulting in >90% assigned serotypes. PFGE is efficient for determining serotype in the majority of cases and results in expedited serotype determination, as well as cost savings. PMID:27220605

  5. Theory of DNA electrophoresis in physical gels and entangled polymer solutions

    Science.gov (United States)

    Duke, Thomas; Viovy, Jean Louis

    1994-03-01

    A scaling theory is presented for the electrophoretic mobility of DNA in sieving media that form dynamically evolving meshworks, such as physical gels and solutions of entangled polymers. In such media, the topological constraints on the DNA's motion are perpetually changing as cross links break and rejoin or as the polymers diffuse. It is shown that if the rate of constraint release falls within a certain range (which depends on the field strength), fractionation can be extended to higher molecular weights than would be feasible using a permanent gel of equivalent pore size. This improvement is a consequence of the disruptive effect that constraint release has on the mechanism of molecular orientation. Numerical simulations support the predictions of the theory. The possibility of realizing such a system in practice, with the aim of improving on current electrophoresis methods, is commented upon. It is suggested that semidilute polymer solutions may be a versatile medium for the rapid separation of long single-stranded DNA molecules, and the particular quality of solution required is identified.

  6. A novel multi-scale Hessian based spot enhancement filter for two dimensional gel electrophoresis images.

    Science.gov (United States)

    Shamekhi, Sina; Miran Baygi, Mohammad Hossein; Azarian, Bahareh; Gooya, Ali

    2015-11-01

    Two dimensional gel electrophoresis (2DGE) is a useful method for studying proteins in a wide variety of applications including identifying post-translation modification (PTM), biomarker discovery, and protein purification. Computerized segmentation and detection of the proteins are the two main processes that are carried out on the scanned image of the gel. Due to the complexities of 2DGE images and the presence of artifacts, the segmentation and detection of protein spots in these images are non-trivial, and involve supervised and time consuming processes. This paper introduces a new spot filter for enhancing, and separating the closely overlapping spots of protein in 2DGE images based on the multi-scale eigenvalue analysis of the image Hessian. Using a Gaussian spot model, we have derived closed form equations to compute the eigen components of the image Hessian of two overlapping spots in a multi-scale fashion. Based on this analysis, we have proposed a novel filter that suppresses the overlapping area and results in a better spot separation. The performance of the proposed filter has been evaluated on the synthetic and real 2DGE images. The comparison with three conventional techniques and a commercial software package reveals the superiority and effectiveness of the proposed filter. PMID:26409228

  7. Application of single cell gel electrophoresis (SCGE) assay:comparative study of DNA damage induced by arsenic in human cells%应用单细胞凝胶电泳比较研究砷对人类细胞DNA的损伤

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Objective To study the different responses of cells to arsenic-induced genotoxicity and its possible mechanisms.Methods Single cell gel electrophoresis (SCGE) assay was used to study the arsenic-induced DNA damage in human promyelocytic HL60,DMSO-differentiated HL60 (DMSO-HL60),PMA-differentiated HL60 (PMA-HL60) and unstimulated human lymphocytes.Results Significant dose-effect relationship and time-course were found between arsenic exposure and DNA damage in the treated cells.The sequence for the sensitivity of cells to arsenic-induced genotoxicity was obtained as follows.PMA-HL60 > DMSO-HL60 > HL60 > human lymphocytes.A same result was obtained by counting the classes of the comet tail and by measuring the tail moment in human lymphocytes.The same significance was achieved using nonparametric Mann-Whitney multiple comparisons for visual classes of comet tail and parametric Tukey multiple comparisons for Tail moment.A higher correlation was shown between the comet tail of Class 5,than between total positive comet tail,and doses of arsenic.Conclusions Micromolar amount of arsenic induces DNA damage in human cells.Different populations of cells had different responses to arsenic-induced genotoxicity.SCGE assay is a economic,rapid,sensitive and economic method detecting genotoxicity.It could be applied in all levels of monitoring and study on environmental pollution and human diseases (arsenic pollution).%目的探讨不同细胞对砷的基因毒性反应及其机理;探讨快速、敏感及经济的细胞基因毒性检测方法。方法应用单细胞凝胶电泳 (Single cell gel electrophoresis,SCGE)或彗星试验(comet assay)比较研究。结果细胞DNA损伤与砷处理量间呈显著的剂量反应关系和时效关系。受试细胞对砷的基因毒性反应的敏感性强弱顺序为:PMA-HL60>DMSO-HL60>HL60>淋巴细胞。人工计数彗星尾分级频数与计算机自动测量彗星尾DNA泳动量的结果完全一致,用非参数Mann

  8. An improved method for detecting genetic variation in DNA using denaturing gradient gel electrophoresis

    International Nuclear Information System (INIS)

    We have examined the feasibility of denaturing gradient gel electrophoresis (DGGE) of RNA:DNA duplexes to detect variations in genomic and cloned DNAs. The result has demonstrated that use of RNA:DNA duplexes makes DGGE much more practical for screening a large number of samples than use of DNA:DNA heteroduplexes, because preparation of RNA probes is easier than that of DNA probes. Three different 32P-labeled RNA probes were produced. Genomic or cloned DNAs were digested with restriction enzymes and hybridized to labeled RNA probes, and resulting RNA:DNA duplexes were examined by DGGE. The presence of a mismatch(es) was detected as a difference in the mobility of bands on the gel. The experimental conditions were determined using DNA segments from cloned normal and three thalassemic human β-globin genes. The results from experiments on the cloned DNAs suggest that DGGE of RNA:DNA duplexes will detect nucleotide substitutions and deletions in DNA. In the course of these studies, a polymorphism due to a single-base substitution at position 666 of IVS2 (IVS2-666) of the human β-globin gene was directly identified using genomic DNA samples. A study of 59 unrelated Japanese from Hiroshima was undertaken in which the frequency of the allele with C at IVS2-666 was 0.48 and that of the allele with T was 0.52. This approach was found to be very effective for detecting heritable variation and should be a powerful tool for detecting fresh mutations in DNA, which occur outside the known restriction sites. (author)

  9. Microbial Community Structure of Korean Cabbage Kimchi and Ingredients with Denaturing Gradient Gel Electrophoresis.

    Science.gov (United States)

    Hong, Sung Wook; Choi, Yun-Jeong; Lee, Hae-Won; Yang, Ji-Hee; Lee, Mi-Ai

    2016-06-28

    Kimchi is a traditional Korean fermented vegetable food, the production of which involves brining of Korean cabbage, blending with various other ingredients (red pepper powder, garlic, ginger, salt-pickled seafood, etc.), and fermentation. Recently, kimchi has also become popular in the Western world because of its unique taste and beneficial properties such as antioxidant and antimutagenic activities, which are derived from the various raw materials and secondary metabolites of the fermentative microorganisms used during production. Despite these useful activities, analysis of the microbial community present in kimchi has received relatively little attention. The objective of this study was to evaluate the bacterial community structure from the raw materials, additives, and final kimchi product using the culture-independent method. Specifically, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) was used to analyze the 16S rRNA partial sequences of the microflora. One primer set for bacteria, 341F(GC)-518R, reliably produced amplicons from kimchi and its raw materials, and these bands were clearly separated on a 35-65% denaturing gradient gel. Overall, 117 16S rRNA fragments were identified by PCR-DGGE analysis. Pediococcus pentosaceus, Leuconostoc citreum, Leuconostoc gelidum, and Leuconostoc mesenteroides were the dominant bacteria in kimchi. The other strains identified were Tetragenococcus, Pseudomonas, Weissella, and uncultured bacterium. Comprehensive analysis of these microorganisms could provide a more detailed understanding of the biologically active components of kimchi and help improve its quality. PCR-DGGE analysis can be successfully applied to a fermented food to detect unculturable or other species. PMID:26907755

  10. A multi-channel gel electrophoresis and continuous fraction collection apparatus for high throughput protein separation and characterization

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Megan; Nordmeyer, Robert A.; Cornell, Earl; Dong, Ming; Biggin, Mark D.; Jin, Jian

    2009-10-02

    To facilitate a direct interface between protein separation by PAGE and protein identification by mass spectrometry, we developed a multichannel system that continuously collects fractions as protein bands migrate off the bottom of gel electrophoresis columns. The device was constructed using several short linear gel columns, each of a different percent acrylamide, to achieve a separation power similar to that of a long gradient gel. A Counter Free-Flow elution technique then allows continuous and simultaneous fraction collection from multiple channels at low cost. We demonstrate that rapid, high-resolution separation of a complex protein mixture can be achieved on this system using SDS-PAGE. In a 2.5 h electrophoresis run, for example, each sample was separated and eluted into 48-96 fractions over a mass range of 10-150 kDa; sample recovery rates were 50percent or higher; each channel was loaded with up to 0.3 mg of protein in 0.4 mL; and a purified band was eluted in two to three fractions (200 L/fraction). Similar results were obtained when running native gel electrophoresis, but protein aggregation limited the loading capacity to about 50 g per channel and reduced resolution.

  11. Suitability of PCR fingerprinting, infrequent-restriction-site PCR, and pulsed-field gel electrophoresis, combined with computerized gel analysis, in library typing of Salmonella enterica serovar enteritidis

    DEFF Research Database (Denmark)

    Garaizar, J.; Lopez-Molina, N.; Laconcha, I.;

    2000-01-01

    Strains of Salmonella enterica (n = 212) of different serovars and phage types were used to establish a library typing computerized system for serovar Enteritidis on the basis of PCR fingerprinting, infrequent-restriction-site PCR (IRS-PCR), or pulsed-field gel electrophoresis (PFGE). The rate...... showed an intercenter reproducibility value of 93.3%. The high reproducibility of PFGE combined with the previously determined high discrimination directed its use for library typing. The use of PFGE with enzymes XbaI, BlnI, and SpeI for library typing of serovar Enteritidis was assessed with GelCompar 4...

  12. Molecular Typing of Acinetobacter Baumannii Clinical Strains in Tehran by Pulsed-Field Gel Electrophoresis

    Directory of Open Access Journals (Sweden)

    Neda Farahani

    2013-03-01

    Full Text Available Background & Objective : Currently, Acinetobacter baumannii is an important nosocomial pathogen insofar as its hospital outbreaks have been described from various geographical areas. Since the discrimination of strains within a species is important for delineating nosocomial outbreaks, this study was conducted with the aim of genotyping the A. baumannii clinical strains in Tehran via the pulsed-field gel electrophoresis (PFGE method, which is the most accurate method used for the typing of bacterial species.   Materials & methods: This study was performed on 70 isolates of acinetobacter baumannii isolated from patients from Baqiyatallah, Rasoole Akram, and Milad hospitals in Tehran. Cultural and biochemical methods were used for the identification of the isolates in species level, and then susceptibility tests were carried out on 50 isolates of A. baumannii using the disk diffusion method. The PFGE method was performed on the isolates by Apa I restriction enzyme. Finally, the results of the PFGE were analyzed. Result: Acinetobacter baumannii strains isolated from hospitals in Tehran showed seven different genetic patterns, two of which were sporadic . Also, genotypic profiles were different in each hospital, and different patterns of genetic resistance to common antibiotics were observed. Conclusion: A lthough diversity was observed among the strains of A. baumannii by the PFGE method in Tehran, no epidemic strains were found among them.  

  13. Molecular Analysis of Mycobacterium avium Isolates by Using Pulsed-Field Gel Electrophoresis and PCR

    Science.gov (United States)

    Pestel-Caron, Martine; Graff, Gabriel; Berthelot, Gilles; Pons, Jean-Louis; Lemeland, Jean-François

    1999-01-01

    Genetic relationships among 46 isolates of Mycobacterium avium recovered from 37 patients in a 2,500-bed hospital from 1993 to 1998 were assessed by pulsed-field gel electrophoresis (PFGE) and PCR amplification of genomic sequences located between the repetitive elements IS1245 and IS1311. Each technique enabled the identification of 27 to 32 different patterns among the 46 isolates, confirming that the genetic heterogeneity of M. avium strains is high in a given community. Furthermore, this retrospective analysis of sporadic isolates allowed us (i) to suggest the existence of two remanent strains in our region, (ii) to raise the question of the possibility of nosocomial acquisition of M. avium strains, and (iii) to document laboratory contamination. The methods applied in the present study were found to be useful for the typing of M. avium isolates. In general, both methods yielded similar results for both related and unrelated isolates. However, the isolates in five of the six PCR clusters were distributed among two to three PFGE patterns, suggesting that this PCR-based method may have limitations for the analysis of strains with low insertion sequence copy numbers or for resolution of extended epidemiologic relationships. PMID:10405383

  14. Typing of Methicillin Resistant Staphylococcus Aureus Using DNA Fingerprints by Pulsed-field Gel Electrophoresis

    Science.gov (United States)

    Rebic, Velma; Budimir, Ana; Aljicevic, Mufida; Bektas, Sabaheta; Vranic, Sabina Mahmutovic; Rebic, Damir

    2016-01-01

    Background: Methicillin resistant Staphylococcus aureus (MRSA) is responsible for a wide spectrum of nosocomial and community associated infections worldwide. The aim of this study was to analyze MRSA strains from the general population in Canton Sarajevo, B&H. Methods: Our investigation including either phenotypic and genotypic markers such as antimicrobial resistance, pulsed-field gel electrophoresis (PFGE), SCC typing, and Panton-Valentine leukocidin (PVL) detection. Results: Antimicrobial susceptibility: all MRSA isolates were resistant to the β-lactam antibiotics tested, and all isolates were susceptible trimethoprim sulphamethoxazole, rifampicin, fusidic acid, linezolid and vancomycin. Sixty-eight per cent of the MRSA isolates were resistant to erythromycin, 5% to clindamycin, 5% to gentamicin and 4% to ciprofloxacin. After the PFGE analysis, the isolates were grouped into five similarity groups: A-E. The largest number of isolates belonged to one of two groups: C: 60 (60%) and D: 27 (27%). In both groups C and D, SCCmec type IV was predominant (60% and 88, 8%, respectively). A total of 24% of the isolates had positive expression of PVL genes, while 76% showed a statistically significantly greater negative expression of PVL genes. Conclusion: SCCmec type IV, together with the susceptibility profile and PFGE grouping, is considered to be typical of CA-MRSA PMID:27708486

  15. Identification of plant viruses using one-dimensional gel electrophoresis and peptide mass fingerprints.

    Science.gov (United States)

    Luo, H; Wylie, S J; Jones, M G K

    2010-05-01

    A generic assay to detect and partially characterize unknown viruses from plants was developed. Proteins extracted from virus-infected and uninfected plants were separated in one dimension by SDS polyacrylamide gel electrophoresis. Differentially expressed protein bands were eluted after trypsin digestion and resulting peptide fragments separated according to their mass by matrix-assisted laser-desorption ionization time-of-flight (MALDI-TOF) mass spectrometry. Resulting peptide mass fingerprints (PMF) were compared with those in protein databases. The assay was used to identify three known viruses: the potyviruses Zucchini yellow mosaic virus and Turnip mosaic virus, and an alfamovirus Alfalfa mosaic virus. It was also used to identify a virus that manifested symptoms in wild Cakile maritima plants, tentatively identified as Pelargonium zonate spot virus (PZSV) (genus Anulavirus) by its PMF, and then confirmed by nucleotide sequencing. The detection of PZSV constitutes a first record of this virus in Australia and in this host. It is proposed that this rapid and simple assay is a useful approach for analysis of plant samples known to harbor viruses that could not be identified using antisera or nucleic acid-based assays. PMID:20170682

  16. Assessment of microbial populations in methyl ethyl ketone degrading biofilters by denaturing gradient gel electrophoresis.

    Science.gov (United States)

    Li, C; Moe, W M

    2004-05-01

    Denaturing gradient gel electrophoresis (DGGE) analysis of polymerase chain reaction-amplified genes coding for 16S rRNA was used to assess differences in bacterial community structure as a function of spatial location along the height of two biofilters used to treat a model waste gas stream containing methyl ethyl ketone (MEK). One of the laboratory-scale biofilters was operated as a conventional continuous-flow biofilter (CFB) and the other was operated as a sequencing batch biofilter (SBB). Both biofilters, inoculated with an identical starting culture and operated over a period lasting more than 300 days, received the same influent MEK concentration and same mass of MEK on a daily basis. The systems differed, however, in terms of the fraction of time during which contaminated air was supplied and the overall operating strategy employed. DGGE analysis indicated that microbial community structures differed as a function of height in each of the biofilters. The DGGE banding patterns also differed between the two biofilters, suggesting that operating strategies imposed on the biofilters imparted a sufficiently large selective pressure to influence microbial community structures. This may explain, in part, the superior performance of the SBB over the CFB during model transient loading conditions, and it may open new possibilities for purposely manipulating the microbial populations in biofilters treating gas-phase contaminants in a manner that leads to more favorable treatment performance.

  17. Indirect fluorometric detection techniques on thin layer chromatography and effect of ultrasound on gel electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Yinfa, Ma.

    1990-12-10

    Thin-layer chromatography (TLC) is a broadly applicable separation technique. It offers many advantages over high performance liquid chromatography (HPLC), such as easily adapted for two-dimensional separation, for whole-column'' detection and for handling multiple samples, etc. However, due to its draggy development of detection techniques comparing with HPLC, TLC has not received the attention it deserves. Therefore, exploring new detection techniques is very important to the development of TLC. It is the principal of this dissertation to present a new detection method for TLC -- indirect fluorometric detection method. This detection technique is universal sensitive, nondestructive, and simple. This will be described in detail from Sections 1 through Section 5. Section 1 and 3 describe the indirect fluorometric detection of anions and nonelectrolytes in TLC. In Section 2, a detection method for cations based on fluorescence quenching of ethidium bromide is presented. In Section 4, a simple and interesting TLC experiment is designed, three different fluorescence detection principles are used for the determination of caffeine, saccharin and sodium benzoate in beverages. A laser-based indirect fluorometric detection technique in TLC is developed in Section 5. Section 6 is totally different from Sections 1 through 5. An ultrasonic effect on the separation of DNA fragments in agarose gel electrophoresis is investigated. 262 refs.

  18. Active Gel Model of Amoeboid Cell Motility

    CERN Document Server

    Callan-Jones, A C

    2013-01-01

    We develop a model of amoeboid cell motility based on active gel theory. Modeling the motile apparatus of a eukaryotic cell as a confined layer of finite length of poroelastic active gel permeated by a solvent, we first show that, due to active stress and gel turnover, an initially static and homogeneous layer can undergo a contractile-type instability to a polarized moving state in which the rear is enriched in gel polymer. This agrees qualitatively with motile cells containing an actomyosin-rich uropod at their rear. We find that the gel layer settles into a steadily moving, inhomogeneous state at long times, sustained by a balance between contractility and filament turnover. In addition, our model predicts an optimal value of the gel-susbstrate adhesion leading to maximum layer speed, in agreement with cell motility assays. The model may be relevant to motility of cells translocating in complex, confining environments that can be mimicked experimentally by cell migration through microchannels.

  19. New algorithmic approaches to protein spot detection and pattern matching in two-dimensional electrophoresis gel databases.

    Science.gov (United States)

    Pleissner, K P; Hoffmann, F; Kriegel, K; Wenk, C; Wegner, S; Sahlström, A; Oswald, H; Alt, H; Fleck, E

    1999-01-01

    Protein spot identification in two-dimensional electrophoresis gels can be supported by the comparison of gel images accessible in different World Wide Web two-dimensional electrophoresis (2-DE) gel protein databases. The comparison may be performed either by visual cross-matching between gel images or by automatic recognition of similar protein spot patterns. A prerequisite for the automatic point pattern matching approach is the detection of protein spots yielding the x(s),y(s) coordinates and integrated spot intensities i(s). For this purpose an algorithm is developed based on a combination of hierarchical watershed transformation and feature extraction methods. This approach reduces the strong over-segmentation of spot regions normally produced by watershed transformation. Measures for the ellipticity and curvature are determined as features of spot regions. The resulting spot lists containing x(s),y(s),i(s)-triplets are calculated for a source as well as for a target gel image accessible in 2-DE gel protein databases. After spot detection a matching procedure is applied. Both the matching of a local pattern vs. a full 2-DE gel image and the global matching between full images are discussed. Preset slope and length tolerances of pattern edges serve as matching criteria. The local matching algorithm relies on a data structure derived from the incremental Delaunay triangulation of a point set and a two-step hashing technique. For the incremental construction of triangles the spot intensities are considered in decreasing order. The algorithm needs neither landmarks nor an a priori image alignment. A graphical user interface for spot detection and gel matching is written in the Java programming language for the Internet. The software package called CAROL (http://gelmatching.inf.fu-berlin.de) is realized in a client-server architecture.

  20. Physical and genetic mapping of the genomes of five Mycoplasma hominis strains by pulsed-field gel electrophoresis

    DEFF Research Database (Denmark)

    Ladefoged, Søren; Christiansen, Gunna

    1992-01-01

    We present the complete maps of five Mycoplasma hominis genomes, including a detailed restriction map and the locations of a number of genetic loci. The restriction fragments were resolved by field inversion gel electrophoresis or by the contour-clamped homogeneous-electric-field system of pulsed......-field gel electrophoresis. All the ApaI, SmaI, BamHI, XhoI, and SalI restriction sites (total of 21 to 33 sites in each strain) were placed on the physical map, yielding an average resolution of 26 kb. The maps were constructed using three different approaches: (i) size determination of DNA fragments...... partially or completely cleaved with one or two restriction enzymes, (ii) hybridization analysis with purified restriction fragments and specific probes, and (iii) use of linking clones. A genetic map was constructed by hybridization with gene-specific probes for rpoA, rpoC, rrn, tuf, gyrB, hup, fts...

  1. EXAFS analysis of a human Cu,Zn SOD isoform focused using non-denaturing gel electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Chevreux, Sylviane; Roudeau, Stephane; Deves, Guillaume; Ortega, Richard [Laboratoire de Chimie Nucleaire Analytique et Bioenvironnementale, CNRS UMR5084, Universite Bordeaux 1, Chemin du Solarium, F-33175 Gradignan cedex (France); Solari, Pier Lorenzo [Synchrotron SOLEIL, L' Orme des Merisiers, BP 48, F-91192 Gif-sur-Yvette cedex, Saint-Aubin (France); Alliot, Isabelle; Testemale, Denis; Hazemann, Jean Louis, E-mail: ortega@cenbg.in2p3.f [FAME, ESRF, 6 rue Jules Horowitz, BP220, F-38043 Grenoble cedex (France)

    2009-11-15

    Isoelectric point isoforms of a metalloprotein, copper-zinc superoxide dismutase (CuZnSOD), separated on electrophoresis gels were analyzed using X-ray Absorption Spectroscopy. Mutations of this protein are involved in familial cases of amyotrophic lateral sclerosis. The toxicity of mutants could be relied to defects in the metallation state. Our purpose is to establish analytical protocols to study metallation state of protein isoforms such as those from CuZnSOD. We previously highlighted differences in the copper oxidation state between CuZnSOD isoforms using XANES. Here, we present the first results for EXAFS analyses performed at Cu and Zn K-edge on the majoritary expressed isoform of human CuZnSOD separated on electrophoresis gels.

  2. EXAFS analysis of a human Cu,Zn SOD isoform focused using non-denaturing gel electrophoresis

    Science.gov (United States)

    Chevreux, Sylviane; Solari, Pier Lorenzo; Roudeau, Stéphane; Deves, Guillaume; Alliot, Isabelle; Testemale, Denis; Hazemann, Jean Louis; Ortega, Richard

    2009-11-01

    Isoelectric point isoforms of a metalloprotein, copper-zinc superoxide dismutase (CuZnSOD), separated on electrophoresis gels were analyzed using X-ray Absorption Spectroscopy. Mutations of this protein are involved in familial cases of amyotrophic lateral sclerosis. The toxicity of mutants could be relied to defects in the metallation state. Our purpose is to establish analytical protocols to study metallation state of protein isoforms such as those from CuZnSOD. We previously highlighted differences in the copper oxidation state between CuZnSOD isoforms using XANES. Here, we present the first results for EXAFS analyses performed at Cu and Zn K-edge on the majoritary expressed isoform of human CuZnSOD separated on electrophoresis gels.

  3. Method for the typing of Clostridium difficile based on polyacrylamide gel electrophoresis of [35S]methionine-labeled proteins

    International Nuclear Information System (INIS)

    A typing method for Clostridium difficile based on the incorporation of [35S]methionine into cellular proteins, their separation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and their visualization by autoradiography is described. On analysis of the radiolabeled-protein profiles, nine distinct groups were observed (A to E and W to Z). The method, which is simple, reproducible, and readily expandable, has been applied in epidemiological studies to demonstrate cross-infection and hospital acquisition of C. difficile

  4. Multicolour hybrid nanoprobes of molecular beacon conjugated quantum dots: FRET and gel electrophoresis assisted target DNA detection

    International Nuclear Information System (INIS)

    We have developed multicolour hybrid DNA probes employing green, yellow and orange colour quantum dot conjugated molecular beacons with black hole quencher 2. Optical and electrophoretic characterization revealed fluorescent energy transfer that follows the FRET mechanism with single nucleotide discrimination. Target DNA identification was observed to be highly sensitive up to 8 ng in gel electrophoresis. Comparison with the conventional organic dye SYBR Gold(TM) showed that our hybrid nanoprobes exhibit more stable performance with less background signal

  5. Design and Evaluation of PCR Primers for Analysis of Bacterial Populations in Wine by Denaturing Gradient Gel Electrophoresis

    OpenAIRE

    Lopez, Isabel; Ruiz-Larrea, Fernanda; Cocolin, Luca; Orr, Erica; Phister, Trevor; Marshall, Megan; VanderGheynst, Jean; Mills, David A.

    2003-01-01

    Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified ribosomal DNA (rDNA) is routinely used to compare levels of diversity of microbial communities and to monitor population dynamics. While using PCR-DGGE to examine the bacteria in wine fermentations, we noted that several commonly used PCR primers for amplifying bacterial 16S rDNA also coamplified yeast, fungal, or plant DNA present in samples. Unfortunately, amplification of nonbacterial DNA can result in a masking of bacterial p...

  6. Method for the typing of Clostridium difficile based on polyacrylamide gel electrophoresis of (/sup 35/S)methionine-labeled proteins

    Energy Technology Data Exchange (ETDEWEB)

    Tabaqchali, S.; O' Farrell, S.; Holland, D.; Silman, R.

    1986-01-01

    A typing method for Clostridium difficile based on the incorporation of (/sup 35/S)methionine into cellular proteins, their separation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and their visualization by autoradiography is described. On analysis of the radiolabeled-protein profiles, nine distinct groups were observed (A to E and W to Z). The method, which is simple, reproducible, and readily expandable, has been applied in epidemiological studies to demonstrate cross-infection and hospital acquisition of C. difficile.

  7. Polyacrylamide gel electrophoresis of RNA compared with polyclonal- and monoclonal-antibody-based enzyme immunoassays for rotavirus.

    OpenAIRE

    Pacini, D L; Brady, M T; Budde, C T; Connell, M J; Hamparian, V V; Hughes, J. H.

    1988-01-01

    Polyacrylamide gel electrophoresis (PAGE) of rotaviral RNA, a sensitive and highly specific test for detecting rotavirus in stool, was compared with two commercially available enzyme immunoassays (EIAs), monoclonal (Pathfinder) and polyclonal (Rotazyme II). Stool samples from 204 children with nosocomial diarrhea were tested for rotavirus by both EIAs and by PAGE of RNA extracted from raw stools or 10% stool suspensions. Samples which tested positive by either EIA but were negative by PAGE we...

  8. Quality Control and Stability Studies with the Monoclonal Antibody, Trastuzumab: Application of 1D- vs. 2D-Gel Electrophoresis

    Directory of Open Access Journals (Sweden)

    Dashnor Nebija

    2014-04-01

    Full Text Available Recombinant monoclonal antibodies (rmAbs are medicinal products obtained by rDNA technology. Consequently, like other biopharmaceuticals, they require the extensive and rigorous characterization of the quality attributes, such as identity, structural integrity, purity and stability. The aim of this work was to study the suitability of gel electrophoresis for the assessment of charge heterogeneity, post-translational modifications and the stability of the therapeutic, recombinant monoclonal antibody, trastuzumab. One-dimensional, SDS-PAGE, under reducing and non-reducing conditions, and two-dimensional gel electrophoresis were used for the determination of molecular mass (Mr, the isoelectric point (pI, charge-related isoform patterns and the stability of trastuzumab, subjected to stressed degradation and long-term conditions. For the assessment of the influence of glycosylation in the charge heterogeneity pattern of trastuzumab, an enzymatic deglycosylation study has been performed using N-glycosidase F and sialidase, whereas carboxypeptidase B was used for the lysine truncation study. Experimental data documented that 1D and 2D gel electrophoresis represent fast and easy methods to evaluate the quality of biological medicinal products. Important stability parameters, such as the protein aggregation, can be assessed, as well.

  9. Proteomic Comparison of Two-Dimensional Gel Electrophoresis Pro files from Human Lung Squamous Carcinoma and Normal Bronchial Epithelial Tissues

    Institute of Scientific and Technical Information of China (English)

    Cui Li; Ping Chen; Jingyun Xie; Songping Liang; Xianquan Zhan; Maoyu Li; Xiaoying Wu; Feng Li; Jianling Li; Zhiqiang Xiao; Zhuchu Chen; Xueping Feng

    2003-01-01

    Differential proteome profiles of human lung squamous carcinoma tissue compared to paired tumor-adjacent normal bronchial epithelial tissue were established and analyzed by means of immobilized pH gradient-based two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS). The results showed that well-resolved, reproducible 2-DE patterns of human lung squamous carcinoma and adjacent normal bronchial epithelial tissues were obtained under the condition of 0.75-ug protein-load. The average deviation of spot position was 0.733+0.101 mm in IEF direction, and 0.925+0.207 mm in SDS-PAGE direction. For tumor tissue, a total of 1241±88 spots were detected, 987±65 spots were matched with an average matching rate of 79.5%. For control, a total of 1190+72 spots were detected, and 875±48 spots were matched with an average matching rate of 73.5%. A total of 864±34 spots were matched between tumors and controls.Forty-three differential proteins were characterized: some proteins were related to oncogenes, and others involved in the regulation of cell cycle and signal transduction. It is suggested that the differential proteomic approach is valuable for mass identification of differentially expressed proteins involved in lung carcinogenesis.These data will be used to establish human lung cancer proteome database to further study human lung squamous carcinoma.

  10. Detection of antimicrobial (poly)peptides with acid urea polyacrylamide gel electrophoresis followed by Western immunoblot.

    Science.gov (United States)

    Porter, Edith; Valore, Erika V; Anouseyan, Rabin; Salzman, Nita H

    2015-01-01

    Antimicrobial (poly)peptides (AMPs) are ancient key effector molecules of innate host defense and have been identified in mammals, insects, plants, and even fungi (Nakatsuji and Gallo, J Invest Dermatol, 132: 887-895, 2012). They exhibit a cationic net charge at physiological pH and are rich in hydrophobic amino acids (Dufourc et al., Curr Protein Pept Sci, 13: 620-631, 2012). Their mode of action has been best investigated in bacteria. When assuming secondary structure the cationic and hydrophobic amino acids are sequestered creating a bipartitioned molecule in which the cationic amino acids mediate initial electrostatic interaction with the negatively charged bacterial surface and the hydrophobic amino acids mediate embedding into the bacterial membranes followed by a multitude of effects interfering with bacterial viability (Nicolas, FEBS J, 276: 6483-6496, 2009; Padovan et al., Curr Protein Pept Sci, 11: 210-219, 2010). However, immunomodulatory, antitumor, and other effects have been added to the ever increasing list of AMP functions (Pushpanathan et al., Int J Pept, 2013: 675391, 2013). Several classes of AMPs have been distinguished based on structure, namely anti-parallel beta-sheet, alpha-helical, circular, as well as disulfide bridge connectivity (Bond and Khalid, Protein Pept Lett, 17: 1313-1327, 2010). Many of the AMPs undergo posttranslational modification including further proteolysis. Biochemical analysis at the protein level is of great interest for a wide range of scientists and important when studying host-pathogen interaction, for example Salmonella invasion of the small intestine. Acid-urea polyacrylamide gel electrophoresis (AU-PAGE) followed by Western immunoblotting is an important tool for the identification and quantification of cationic AMPs. The protocol for these procedures outlined here describes, in detail, the necessary steps; including pouring the AU-gels, preparing the test samples, performing the electrophoretic separation and

  11. Clonal evolution multi-drug resistant Acinetobacter baumannii by pulsed-field gel electrophoresis

    Directory of Open Access Journals (Sweden)

    P Mohajeri

    2015-01-01

    Full Text Available Background: Acinetobacter baumannii is usually multi-drug resistant (MDR, including third generation cephalosporins, amino glycosides and fluoroquinolone. Resistance to these antibiotics is mediated by multiple factors such as: lactamases, efflux pumps and other mechanisms of resistance. Pulsed-field gel electrophoresis (PFGE was then used to investigate the genetic relationships among the MDR isolates. Aim: The aim of this study was to determine MDR isolates and the existence of OXAs genes among MDR isolates of A. baumannii collected from Kermanshah hospitals in west of Iran. Materials and Methods: Forty-two MDR A. baumannii were collected from patients at Kermanshah hospitals. The isolates were identified by biochemical tests and API 20NE kit. The susceptibility to different antibiotics by disk diffusion method was determined. Polymerase chain reaction (PCR was performed for detection of blaOXA-23-like , blaOXA-24-like , blaOXA-51-like and blaOXA-58-like betalactamase genes in isolates and clonal relatedness was done by PFGE (with the restriction enzyme ApaI and patterns analyzed by Bionumeric software. Results: This study showed high resistant to ciprofloxacin, piperacillin, ceftazidime and also resistant to other anti-microbial agents and more spread blaOXA-23-like gene (93% in MDR isolate. The PFGE method obtained six clones: A (10, B (9, C (5, D (4, E (11 and F (3 that clone E was outbreak and dominant in different wards of hospitals studied. Conclusion: An isolate from the emergency ward of these hospitals had indistinguishable isolates PFGE profile and similar resistance profile to isolates from intensive care unit (ICU, suggesting likely transmission from ICU to emergency via patient or hospital staff contact.

  12. Meta-analysis of pulsed-field gel electrophoresis fingerprints based on a constructed Salmonella database.

    Directory of Open Access Journals (Sweden)

    Wen Zou

    Full Text Available A database was constructed consisting of 45,923 Salmonella pulsed-field gel electrophoresis (PFGE patterns. The patterns, randomly selected from all submissions to CDC PulseNet during 2005 to 2010, included the 20 most frequent serotypes and 12 less frequent serotypes. Meta-analysis was applied to all of the PFGE patterns in the database. In the range of 20 to 1100 kb, serotype Enteritidis averaged the fewest bands at 12 bands and Paratyphi A the most with 19, with most serotypes in the 13-15 range among the 32 serptypes. The 10 most frequent bands for each of the 32 serotypes were sorted and distinguished, and the results were in concordance with those from distance matrix and two-way hierarchical cluster analyses of the patterns in the database. The hierarchical cluster analysis divided the 32 serotypes into three major groups according to dissimilarity measures, and revealed for the first time the similarities among the PFGE patterns of serotype Saintpaul to serotypes Typhimurium, Typhimurium var. 5-, and I 4,[5],12:i:-; of serotype Hadar to serotype Infantis; and of serotype Muenchen to serotype Newport. The results of the meta-analysis indicated that the pattern similarities/dissimilarities determined the serotype discrimination of PFGE method, and that the possible PFGE markers may have utility for serotype identification. The presence of distinct, serotype specific patterns may provide useful information to aid in the distribution of serotypes in the population and potentially reduce the need for laborious analyses, such as traditional serotyping.

  13. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE of urinary protein in acute kidney injury

    Directory of Open Access Journals (Sweden)

    Sufi M Suhail

    2011-01-01

    Full Text Available Recent experimental and clinical studies have shown the importance of urinary proteomics in acute kidney injury (AKI. We analyzed the protein in urine of patients with clinical AKI using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE for its diagnostic value, and followed them up for 40 months to evaluate prognosis. Urine from 31 consecutive cases of AKI was analyzed with SDS-PAGE to determine the low, middle and high molecular weight proteins. Fractional excretion of sodium (FENa was estimated from serum and urine creatinine and sodium (Na. The cases were followed-up for 40 months from the end of the recruitment of study cases. Glomerular protein was higher in the hematuria group when compared with the non-hematuria group (P <0.04 and in the AKI group than in the acute on chronic renal failure (AKI-on-CRF group (P <0.002. Tubular protein was higher in the AKI-on-CRF group (P <0.003 than in the AKI group. Tubular protein correlated with FENa in groups with diabetes mellitus (DM, AKI-on-CRF, and without hematuria (P <0.03, P <0.02 and P <0.004, respectively. Pattern of protein did not differ between groups with and without DM and clinical acute tubular necrosis (ATN. At the end of 40 months follow-up, category with predominantly glomerular protein progressed to chronic renal failure (CRF or end-stage renal failure in higher proportion (P <0.05. In clinical AKI, we observed that glomerular protein dominated in cases with glomerular insult, as indicated by hematuria. Tubular protein was common in the study cases with CRF, DM and cases without hematuria. This indicates tubulo-interstitial injury for AKI in these cases. Patients with predominantly glomerular protein had an adverse outcome.

  14. Comparative typing of Pseudomonas aeruginosa by random amplification of polymorphic DNA or pulsed-field gel electrophoresis of DNA macrorestriction fragments

    NARCIS (Netherlands)

    N. Renders (Nicole); Y. Romling; A.F. van Belkum (Alex); H.A. Verbrugh (Henri)

    1996-01-01

    textabstractEighty-seven strains of Pseudomonas aeruginosa were typed by random amplification of polymorphic DNA (RAPD) and pulsed-field gel electrophoresis (PFGE) of macrorestriction fragments. Stains were clustered on the basis of interpretative criteria as presented

  15. Random amplified polymorphic DNA assay is less discriminant than pulsed-field gel electrophoresis for typing strains of methicillin-resistant Staphylococcus aureus.

    OpenAIRE

    Saulnier, P; Bourneix, C; Prévost, G; Andremont, A

    1993-01-01

    Twenty-six strains of methicillin-resistant Staphylococcus aureus with different pulsed-field gel electrophoresis fingerprints were tested by random amplified polymorphic DNA assay with three primers, resulting in 15 to 20 different random amplified polymorphic DNA fingerprints. By summing the results for the three primers, the number of different fingerprints increased to 25, but two strains could not be differentiated. We conclude that pulsed-field gel electrophoresis remains the best metho...

  16. DNA-electrophoresis of single cells - a method to screen for irradiated foodstuffs

    International Nuclear Information System (INIS)

    Microelectrophoresis of single cells can be used to detect γ-irradiation over a wide dose range and for a variety of products. It is a simple and rapid test for DNA damages and can be used for screening. The method was tested on cell suspensions of bone marrow and muscle cells from frozen chicken legs, chicken heart, turkey liver, beef and pork irradiated with doses up to 3 kGy. Cell suspensions were prepared by incubation of tissues in EDTA-SDS-buffer at pH 8. Single cell electrophoresis was performed in 0.75% agarose gel. DNA was visualised by silver staining. In unirradiated samples no or only a small amount of DNA penetrated the cell membranes. Cells of irradiated samples appeared like a ''comet'' due to to migration of DNA-fragments out of cell. (orig.)

  17. High-throughput Three-dimensional Gel Electrophoresis for Versatile Utilities: A Stacked Slice-gel System for Separation and Reactions (4SR)

    Institute of Scientific and Technical Information of China (English)

    Md. Salimullah; Masaki Mori; Koichi Nishigaki

    2006-01-01

    A novel high-throughput system, called the stacked slice-gel system for separation and reactions (4SR), was developed for the analysis of DNA/RNA and protein/peptide. The system provides a novel three-dimensional gel electrophoresis approach that exploits the property of stacked slice gels. It allows multiple samples simultaneously to react as well as to be separated, offering a two-dimensional (m×n) sample loading system. For this purpose, high-throughput multi-micro vessels (MMVs) containing variable numbers of wells (100 wells in this paper) have been used, which are made of 25 mm square-size polyacrylamide gels. Furthermore, after electrophoretic separation, a slice gel containing a desired sample can be easily removed and proceeded to the next step. Different biological reactions as well as successive separation of products were effectively carried out dealing with DNA/RNA and protein/peptide. It shows that this system has a diversity of potentials to be developed.

  18. Two-Dimensional Gel Electrophoresis Image Analysis via Dedicated Software Packages.

    Science.gov (United States)

    Maurer, Martin H

    2016-01-01

    Analyzing two-dimensional gel electrophoretic images is supported by a number of freely and commercially available software. Although the respective program is highly specific, all the programs follow certain standardized algorithms. General steps are: (1) detecting and separating individual spots, (2) subtracting background, (3) creating a reference gel and (4) matching the spots to the reference gel, (5) modifying the reference gel, (6) normalizing the gel measurements for comparison, (7) calibrating for isoelectric point and molecular weight markers, and moreover, (8) constructing a database containing the measurement results and (9) comparing data by statistical and bioinformatic methods.

  19. Implementation of Microfluidic Chip Electrophoresis for the Detection of B-cell Clonality

    Directory of Open Access Journals (Sweden)

    Vazan M

    2016-04-01

    Full Text Available Introduction: A clonal population of B-cells is defined as those cells arising from the mitotic division of a single somatic cell with the same rearrangement of immunoglobulin genes. This gives rise to DNA markers for each individual lymphoid cell and its progenies and enables us to study clonality in different B-cell malignancies using multiplex polymerase chain reaction - PCR. The BIOMED-2 protocol has been implemented for clonality detection in lymphoproliferative diseases and exploits multiplex PCR reaction, subsequently analyzed by heteroduplex analysis (HDA using polyacrylamide gel electrophoresis (PAGE. With the advent of miniaturization and automation of molecular biology methods, lab-on-chip technologies were developed and replace partially the conventional approaches. We tested device for microfluidic chip, which is used for B-cells clonality analysis, using a PCR reaction for three subregions called frameworks (FR of the immunoglobulin heavy locus (IGH gene.

  20. Identification of two-dimensional electrophoresis-separated proteins in human hepatoma cell by electrospray ion trap mass spectrometry

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    As one of the most important analytical methods in proteome research, mass spectrometry was utilized to identify proteins separated by two-dimensional electrophoresis in the human hepatoma cell line BEL-7404. The protein spots were excised from the gel, followed by in-gel digestion, and the peptide mappings were analyzed by liquid chromatography electrospray ion trap mass spectrometer. Nine proteins were identified via database searching, according to the molecular weights and amino acid sequences of peptides, among which two proteins have not been identified in the other liver-cell database. The sequence coverage was 21%-72%. Furthermore, the relationship between the expressed proteins and the liver carcinoma was discussed.

  1. Diversity and dynamics of antibiotic-resistant bacteria in cheese as determined by PCR denaturing gradient gel electrophoresis.

    Science.gov (United States)

    Flórez, Ana Belén; Mayo, Baltasar

    2015-12-01

    This work reports the composition and succession of tetracycline- and erythromycin-resistant bacterial communities in a model cheese, monitored by polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE). Bacterial 16S rRNA genes were examined using this technique to detect structural changes in the cheese microbiota over manufacturing and ripening. Total bacterial genomic DNA, used as a template, was extracted from cultivable bacteria grown without and with tetracycline or erythromycin (both at 25 μg ml(-1)) on a non-selective medium used for enumeration of total and viable cells (Plate Count agar with Milk; PCA-M), and from those grown on selective and/or differential agar media used for counting various bacterial groups; i.e., lactic acid bacteria (de Man, Rogosa and Sharpe agar; MRSA), micrococci and staphylococci (Baird-Parker agar; BPA), and enterobacteria (Violet Red Bile Glucose agar; VRBGA). Large numbers of tetracycline- and erythromycin-resistant bacteria were detected in cheese samples at all stages of ripening. Counts of antibiotic-resistant bacteria varied widely depending on the microbial group and the point of sampling. In general, resistant bacteria were 0.5-1.0 Log10 units fewer in number than the corresponding susceptible bacteria. The PCR-DGGE profiles obtained with DNA isolated from the plates for total bacteria and the different bacterial groups suggested Escherichia coli, Lactococcus lactis, Enterococcus faecalis and Staphylococcus spp. as the microbial types resistant to both antibiotics tested. This study shows the suitability of the PCR-DGGE technique for rapidly identifying and tracking antibiotic resistant populations in cheese and, by extension, in other foods.

  2. Proteomic Comparison of Two—Dimensional Gel Electrophoresis Profiles from Human Lung Squamous Carcinoma and Normal Bronchial Epithelial Tissues

    Institute of Scientific and Technical Information of China (English)

    CuiLi; XianquanZhan; MaoyuLi; XiaoyingWu; FengLi; JianlingLi; ZhiqiangXiao; ZhuchuChen; XuepingFeng; PingChen; JingyunXie; SongpingLiang

    2003-01-01

    Differential proteome profiles of human lung squamous carcinoma tissue compared to paired tumor-adjacent normal bronchial epithelial tissue were established and analyzed by means of immobilized pH gradient-based two-dimensional polyacrylamide gel electrophoresis(2-D PAGE)and matrix-assisted laser desorption/ionization time of flight mass spectrometry(MALDI-TOF-MS).The results showed that well-resolved,reproducible 2-DE patterns of human lung squamous carcinoma and adjacent normal bronchial epithelial tissues were obtained under the condition of 0.75-mg protein-load.The average deviation of spot position was 0.733±0.101 mm in IEF direction,and 0.925±0.207mm in SDS-PAGE direction.For tumor tissue,a total of 1241±88 spots were detected,987±65 spots were matched with an average matching rate of 79.5%.For control,a total of 1190±72 spots were detected,and 875±48 spots were matched with an average matching rate of 73.5%.A total of 864±34 spots were matched between tumors and controls.Forth-three differential proteins were characterized:some proteins were related to oncogenes,and others involved in the regulation of cell cycle and signal transduction.It is suggested that the differential proteomic approach is valuable for mass identification of differentially expressed proteins involved in lung carcinogenesis.These data will be used to establish human lung cancer proteome database to further study human lung squamous carcinoma.

  3. Detection of a NotI polymorphism with the pmetH probe by pulsed-field gel electrophoresis.

    OpenAIRE

    Julier, C; White, R.

    1988-01-01

    The pmetH probe, tightly linked to the locus for cystic fibrosis (CF), detected a NotI polymorphism with allele sizes of 1,000 and 550 kb that could be separated by pulsed-field gel electrophoresis. Both alleles were found on chromosomes bearing either the normal or the CF allele. Preliminary data showed that this polymorphism was not in strong linkage disequilibrium with the CF locus. Preliminary large-scale restriction mapping of the fragment showed that the NotI polymorphic site is 200-370...

  4. One-day pulsed-field gel electrophoresis protocol for rapid determination of emetic Bacillus cereus isolates.

    Science.gov (United States)

    Kaminska, Paulina S; Fiedoruk, Krzysztof; Jankowska, Dominika; Mahillon, Jacques; Nowosad, Karol; Drewicka, Ewa; Zambrzycka, Monika; Swiecicka, Izabela

    2015-04-01

    Bacillus cereus, the Gram-positive and spore-forming ubiquitous bacterium, may cause emesis as the result of food intoxication with cereulide, a heat-stable emetic toxin. Rapid determination of cereulide-positive B. cereus isolates is of highest importance due to consequences of this intoxication for human health and life. Here we present a 1-day pulsed-field gel electrophoresis for emetic B. cereus isolates, which allows rapid and efficient determination of their genomic relatedness and helps determining the source of intoxication in case of outbreaks caused by these bacilli.

  5. Pulsed field gel electrophoresis identifies an outbreak of Salmonella enterica serotype Montevideo infection associated with a supermarket hot food outlet.

    Science.gov (United States)

    Threlfall, E J; Hampton, M D; Ward, L R; Richardson, I R; Lanser, S; Greener, T

    1999-09-01

    In February 1996 Salmonella enterica serotype Montevideo infection in a patient in the North Tyneside area was attributed to consumption of cooked chicken bought from a supermarket hot food outlet. Isolates from the patient, leftover food, and environmental samples were indistinguishable by pulsed field gel electrophoresis (PFGE). PFGE also demonstrated that an outbreak of infection with S. Montevideo associated with the hot food outlet had occurred in late 1995 and early 1996. This study shows the importance of microbial strain discrimination in outbreak investigations and illustrates the value of close liaison between microbiologists, epidemiologists, and environmental health officers in the control of salmonella outbreaks.

  6. Using micronuclei test and single cell gel electrophoresis assay to evaluate genotoxicity of pesticides to Pardosa astrigera L.Koch%应用微核试验和单细胞凝胶电泳技术检测农药对蜘蛛的遗传毒性

    Institute of Scientific and Technical Information of China (English)

    李锐; 李生才; 刘佳; 杨怀卿

    2012-01-01

    应用蜘蛛血细胞微核试验和单细胞凝胶电泳试验研究了两种杀虫剂——吡虫啉和阿维菌素对蜘蛛头胸部和腹部的遗传毒性.结果表明:各供试浓度吡虫啉和阿维菌素对蜘蛛血细胞微核率均有明显影响,与对照组相比有显著性差异(P<0.05,P<0.01);且随着两种农药浓度升高,血细胞微核率显著增加,存在明显的剂量-效应关系(吡虫啉浓度与星豹蛛头胸部血细胞微核率相关系数r=0.672 8,腹部为r=0.800 6;阿维菌素与星豹蛛头胸部血细胞微核率相关系数r=0.989 9,腹部为r=0.985 8).吡虫啉和阿维菌素对星豹蛛血细胞DNA损伤有明显的剂量-效应关系(吡虫啉浓度与星豹蛛头胸部血细胞DNA损伤相关系数r=0.948 2,腹部为r=0.970 4;阿维菌素与星豹蛛头胸部血细胞DNA损伤相关系数r=0.978 1,腹部为r=0.975 6).两种农药在同一浓度下,对星豹蛛腹部血细胞微核率和DNA损伤程度明显大于头胸部.%This study combined micronucleus test (MN) and single cell gel electrophoresis technique to assess the genotoxicity of imidacloprid and avermectins to Pardosa astrigera Koch.The micronucleus assay is already widely used in genetictoxicity evaluation due to its clear endpoint,high reproducibility and easy accessibility.The single cell gel electrophoresis technique (comet assay) is a simple,sensitive,reliable,and rapid method to detect DNA damage in eukaryotic cells.P.Astrigera,one of the main natural enemies of destructive insects for cropland,orchard,vegetable fields and forest ecosystems,widely distributed in most areas of South and North China.The objective of the study was to achieve a more comprehensive understanding of the effects and potential risks on the spiders of imidacloprid and avermectins,which are normal pesticides,used in the agricultural and forest ecosystems.The resultsshowed significant differences (P < 0.05,or P < 0.01) in micronuclei frequency of P.Astrigera hemocytes

  7. Development of an open source laboratory information management system for 2-D gel electrophoresis-based proteomics workflow

    Directory of Open Access Journals (Sweden)

    Toda Tosifusa

    2006-10-01

    Full Text Available Abstract Background In the post-genome era, most research scientists working in the field of proteomics are confronted with difficulties in management of large volumes of data, which they are required to keep in formats suitable for subsequent data mining. Therefore, a well-developed open source laboratory information management system (LIMS should be available for their proteomics research studies. Results We developed an open source LIMS appropriately customized for 2-D gel electrophoresis-based proteomics workflow. The main features of its design are compactness, flexibility and connectivity to public databases. It supports the handling of data imported from mass spectrometry software and 2-D gel image analysis software. The LIMS is equipped with the same input interface for 2-D gel information as a clickable map on public 2DPAGE databases. The LIMS allows researchers to follow their own experimental procedures by reviewing the illustrations of 2-D gel maps and well layouts on the digestion plates and MS sample plates. Conclusion Our new open source LIMS is now available as a basic model for proteome informatics, and is accessible for further improvement. We hope that many research scientists working in the field of proteomics will evaluate our LIMS and suggest ways in which it can be improved.

  8. Voltage-programming-based capillary gel electrophoresis for the fast detection of angiotensin-converting enzyme insertion/deletion polymorphism with high sensitivity.

    Science.gov (United States)

    Woo, Nain; Kim, Su-Kang; Kang, Seong Ho

    2016-08-01

    A voltage-programming-based capillary gel electrophoresis method with a laser-induced fluorescence detector was developed for the fast and highly sensitive detection of DNA molecules related to angiotensin-converting enzyme insertion/deletion polymorphism, which has been reported to influence predisposition to various diseases such as cardiovascular disease, high blood pressure, myocardial infarction, and Alzheimer's disease. Various voltage programs were investigated for fast detection of specific DNA molecules of angiotensin-converting enzyme insertion/deletion polymorphism as a function of migration time and separation efficiency to establish the effect of voltage strength to resolution. Finally, the amplified products of the angiotensin-converting enzyme insertion/deletion polymorphism (190 and 490 bp DNA) were analyzed in 3.2 min without losing resolution under optimum voltage programming conditions, which were at least 75 times faster than conventional slab gel electrophoresis. In addition, the capillary gel electrophoresis method also successfully applied to the analysis of real human blood samples, although no polymorphism genes were detected by slab gel electrophoresis. Consequently, the developed voltage-programming capillary gel electrophoresis method with laser-induced fluorescence detection is an effective, rapid analysis technique for highly sensitive detection of disease-related specific DNA molecules.

  9. Analysis of a ribonuclease H digestion of N3'-->P5' phosphoramidate-RNA duplexes by capillary gel electrophoresis.

    Science.gov (United States)

    DeDionisio, L; Gryaznov, S M

    1995-07-01

    Phosphodiester oligonucleotides (ODNs) and their analogs are presently being investigated as potential antisense therapeutics in the treatment of viral infections and various forms of cancer. here, we would like to report results from an investigation of activity for a ribonuclease H (RNase H) mediated RNA digestion assay in the duplexes formed by an ODN or the ODN analog, N3'-->P5' phosphoramidate (3'-phosphoramidate), and complimentary RNA strands. Capillary gel electrophoresis (CGE) proved to be an effective method for determining RNA hydrolysis in the presence of RNase H. RNA and an ODN or RNA and a 3'-phosphoramidate were hybridized in a Tris-HCl, MgCl2 buffer at room temperature (RT) and incubated with RNase H. Digestions were carried out at RT or at 37 degrees C. Control samples were unhybridized RNA with RNase H, RNA without RNase H, and duplexes (RNA-ODN or 3'-phosphoramidate) without RNase H. All controls were incubated in Tris-HCl, MgCl2 buffer, and sample aliquots were analyzed at various time intervals. A homodecamer, (dT)10, was used as an internal standard to determine the relative migration time of the RNA strand. The final digestion products for the duplexes and the various controls were monitored by CGE. In addition, polyacrylamide gel electrophoresis (PAGE) was used in conjunction with Stains-All (staining) and a densitometric analysis to verify CGE results. PMID:7581876

  10. Characterization of royal jelly proteins in both Africanized and European honeybees (Apis mellifera) by two-dimensional gel electrophoresis.

    Science.gov (United States)

    Sano, Osamu; Kunikata, Toshio; Kohno, Keizo; Iwaki, Kanso; Ikeda, Masao; Kurimoto, Masashi

    2004-01-14

    In this study, the proteins contained in royal jelly (RJ) produced by Africanized honeybees and European honeybees (Apis mellifera) haven been analyzed in detail and compared using two-dimensional gel electrophoresis, and the N-terminal amino acid sequence of each spot has been determined. Most spots were assigned to major royal jelly proteins (MRJPs). Remarkable differences were found in the heterogeneity of the MRJPs, in particular MRJP3, in terms of molecular weights and isoelectric points between the two species of RJ. Furthermore, during the determination of the N-terminal amino acid sequence of each spot, for the first time, MRJP4 protein has been identified, the existence of which had been only implied by cloning of its cDNA sequence. The presence of heterogeneous bands of glucose oxidase was also identified. Thus, the results suggest that two-dimensional gel electrophoresis provides a suitable method for the qualitative analysis of the proteins contained in RJ derived from different honeybee species. PMID:14709007

  11. Antigenic profile of heat-killed versus thimerosal-treated Leishmania major using sodium dodecyl sulfate-polyacrylamide gel electrophoresis

    Directory of Open Access Journals (Sweden)

    Reza Arjmand

    2015-01-01

    Full Text Available Background: Leishmania is a parasitic protozoan of trypanosomatidae family which causes a wide spectrum of diseases ranging from self-healing cutaneous lesions to deadly visceral forms. In endemic areas, field trials of different preparations of Leishmania total antigen were tested as leishmaniasis vaccine. Two preparations of killed Leishmania major were produced In Iran, which were heat-killed vaccine called autoclaved L. major (ALM and thimerosal-treated freeze-thawed vaccine called killed L. major (KLM. In this study, the protein content of both ALM and KLM were compared with that of freshly harvested intact L. major promastigotes using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE. Materials and Methods: L. major (MRHO/IR/75/ER from pre-infected Balb/c mice was isolated with modified Novy-MacNeal-Nicolle (NNN medium and then subcultured in liquid RPMI 1640 medium supplemented with fetal calf serum (FCS 20% for mass production. Two preparations of KLM and ALM were produced by Razi Vaccine and Serum Research Institute, Iran, under WHO/TDR supervision. Electrophoresis was performed by SDS-PAGE method and the gel was stained by Coomassie brilliant blue dye. The resultant unit bands were compared using standard molecular proteins. Results: Electrophoresis of the two preparations produced many bands from 10 kDa to 100 kDa. KLM bands were much like those of freshly harvested intact L. major. Conclusion: It is concluded that although there are similar bands in the three forms of Leishmania antigens, there are some variations which might be considered for identification and purification of protective immunogens in a total crude antigen, and detection of their stability is essential for the production and marketing of a putative vaccine.

  12. ASTRO Research Fellow Presentation - A comparison of the comet assay and pulsed-field gel electrophoresis as a predictive assay for radiosensitivity in human fibroblasts

    International Nuclear Information System (INIS)

    Purpose/Objective: To determine whether neutral lysis single-cell gel electrophoresis (comet assay) or pulsed-field gel electrophoresis (PFGE) can be used as a predictive assay for tissue response to radiotherapy as an alternative to clonogenic survival measurements. Materials and Methods: The comet assay has been widely used to measure DNA double strand breaks (dsb) in individual cells, and it has been suggested that it could be used as an alternative to clonogenic assays to measure radiosensitivity. Previous studies in this lab have demonstrated the ability of pulsed-field gel electrophoresis, which also measures DNA dsb, to accurately predict the radiosensitivity of a panel of fibroblasts based on determination of residual DNA dsb. As part of an ongoing study examining the relationship between fibroblast radiosensitivity and normal-tissue radiation reactions, we have compared the sensitivity and accuracy of the comet assay and PFGE on a different panel of non-transformed fibroblasts derived from breast cancer patients who developed severe radiation late effects and from case-matched controls. For the measurement of initial damage, cells were suspended in PBS and irradiated on ice for the comet assay and irradiated in agarose plugs on ice for pFGE. Residual damage was measured following irradiation of confluent cultures at 37 degree sign C and subsequent incubation for four hours prior to preparation of agarose slides and plugs. All irradiations were performed with a 59 TBq 60Co source at a dose rate of 1.7 Gy/min. Electrophoresis was performed following neutral pH cell lysis. Comet images were captured and analyzed using Optimas software with DNA damage quantitated by the comet moment. PFGE gels were analyzed using a phosphor-image analysis system and damage was quantitated based on the percent of activity released from the well. Results: The comet assay was able to detect initial DNA damage at a threshold of 5 Gy and exhibited a linear dose

  13. Determination of damage and In vivo DNA repairing through the unicellular in gel electrophoresis technique; Determinacion del dano y la reparacion del ADN In vivo mediante la tecnica de electroforesis unicelular en gel

    Energy Technology Data Exchange (ETDEWEB)

    Mendiola C, M.T.; Morales R, P. [Instituto Nacional de Investigaciones Nucleares, A.P. 18-1027, 11801 Mexico D.F. (Mexico)

    1997-07-01

    The experimental conditions were standardized for the unicellular in gel electrophoresis technique setting up (EUG) at the Cellular Radiobiology laboratory. Preliminary experiments were realized with human cells and mouse which were exposed to ionizing radiation or hydroxide peroxide (H{sub 2}O{sub 2}) to induce DNA damage and to verify the technique performance. It was analysed the In vivo repairing kinetics of induced damage by gamma radiation in mouse leukocytes which were exposed to {sup 137} Cs source and taking samples of peripheric blood of the tail of each mouse at different exposure times and processing them for EUG. In function of the cells proportion with damage in each time it was determined the existence of fast repairing mechanism at the first 15 minutes followed by a slight increase in the damage and a late repairing stage between 30 and 90 minutes. It was analysed this behavior and the potentiality of this In vivo system. (Author)

  14. Differential Expression of Proteins in Lung Cancer Using Difference in Gel Electrophoresis (DIGE)

    OpenAIRE

    Beckett, P; Aulak, K. S.; Masri, F.

    2011-01-01

    Background: Lung cancer remains the leading cause of cancer-related mortality worldwide. Early detection of lung cancer is problematic due to the lack of a marker with high diagnosis sensitivity and specificity. The purpose of this study was to develop techniques to identify the differential expression protein profiles between tumor and tumor free of lung cancer tissues. Methods: 2-dimensional differential ingel electrophoresis (2D-DIGE) and matrix-assisted laser desorption/ionization time-of...

  15. Molecular Fingerprinting of Dairy Microbial Ecosystems by Use of Temporal Temperature and Denaturing Gradient Gel Electrophoresis

    OpenAIRE

    Ogier, J.-C.; Lafarge, V.; Girard, V.; A. Rault; Maladen, V.; Gruss, A; Leveau, J.-Y.; Delacroix-Buchet, A

    2004-01-01

    Numerous microorganisms, including bacteria, yeasts, and molds, constitute the complex ecosystem present in milk and fermented dairy products. Our aim was to describe the bacterial ecosystem of various cheeses that differ by production technology and therefore by their bacterial content. For this purpose, we developed a rapid, semisystematic approach based on genetic profiling by temporal temperature gradient electrophoresis (TTGE) for bacteria with low-G+C-content genomes and denaturing grad...

  16. Acrylamide gel electrophoresis of proteins, acid phosphatases and RN-ases from three potato varieties

    OpenAIRE

    A. Kubicz; E. Wieczorek; B. Morawiecka

    2015-01-01

    Studies on variety differences in the protein and acid phosphatase patterns as well as ribunuclease activity distribution were carried out by disc electrophoresis on saline extracts of three varieties of the potato Solanum tuberosum (L.). The protein bands varied in number, position and relative abundance. One main zone of the acid phosphatase activity was detected consisting of 2-3 electrophoretically different bands. Variety differences were concerned with the number and relative abundance ...

  17. Restriction landmark cDNA scanning (RLCS): a novel cDNA display system using two-dimensional gel electrophoresis.

    Science.gov (United States)

    Suzuki, H; Yaoi, T; Kawai, J; Hara, A; Kuwajima, G; Wantanabe, S

    1996-01-01

    We have developed a new method, designated restriction landmark cDNA scanning (RLCS), which displays many cDNA species quantitatively and simultaneously as two-dimensional gel spots. In this method cDNA species of uniform length were prepared for each mRNA species using restriction enzymes. After the restriction enzyme sites were radiolabeled as landmarks, the labeled fragments were subjected to high resolution two-dimensional gel electrophoresis. In analyses of cDNA samples from adult mouse liver and brain (cerebral cortex, cerebellum and brain stem) we detected approximately 500 and >1000 discrete gel spots respectively of various intensities at a time. The spot patterns of the three brain regions were very similar, although not identical, but were quite different from the pattern for the liver. RNA blot hybridization analysis using several cloned spot DNAs as probes showed that differences in intensity of the spots among RLCS profiles correlated well with expression levels of the corresponding mRNA species in the brain regions. Because the spots and their intensities reflect distinct mRNA species and their expression level respectively, the RLCS is a novel cDNA display system which provides a great deal of information and should be useful for systematic documentation of differentially expressed genes. PMID:8628652

  18. Random amplified polymorphic DNA assay is less discriminant than pulsed-field gel electrophoresis for typing strains of methicillin-resistant Staphylococcus aureus.

    Science.gov (United States)

    Saulnier, P; Bourneix, C; Prévost, G; Andremont, A

    1993-04-01

    Twenty-six strains of methicillin-resistant Staphylococcus aureus with different pulsed-field gel electrophoresis fingerprints were tested by random amplified polymorphic DNA assay with three primers, resulting in 15 to 20 different random amplified polymorphic DNA fingerprints. By summing the results for the three primers, the number of different fingerprints increased to 25, but two strains could not be differentiated. We conclude that pulsed-field gel electrophoresis remains the best method of typing methicillin-resistant S. aureus strains. PMID:8463406

  19. Exposures of Sus scrofa to a TASER(®) conducted electrical weapon: no effects on 2-dimensional gel electrophoresis patterns of plasma proteins.

    Science.gov (United States)

    Jauchem, James R; Cerna, Cesario Z; Lim, Tiffany Y; Seaman, Ronald L

    2014-12-01

    In an earlier study, we found significant changes in red-blood-cell, leukocyte, and platelet counts, and in red-blood-cell membrane proteins, following exposures of anesthetized pigs to a conducted electrical weapon. In the current study, we examined potential changes in plasma proteins [analyzed via two-dimensional gel electrophoresis (2-DGE)] following two 30 s exposures of anesthetized pigs (Sus scrofa) to a TASER (®) C2 conducted electrical weapon. Patterns of proteins, separated by 2-DGE, were consistent and reproducible between animals and between times of sampling. We determined that the blood plasma collection, handling, storage, and processing techniques we used are suitable for swine blood. There were no statistically significant changes in plasma proteins following the conducted-electrical-weapon exposures. Overall gel patterns of fibrinogen were similar to results of other studies of both pigs and humans (in control settings, not exposed to conducted electrical weapons). The lack of significant changes in plasma proteins may be added to the body of evidence regarding relative safety of TASER C2 device exposures. PMID:25319243

  20. Changes in Predominance of Pulsed-Field Gel Electrophoresis Profiles of Bordetella pertussis Isolates, United States, 2000-2012.

    Science.gov (United States)

    Cassiday, Pamela K; Skoff, Tami H; Jawahir, Selina; Tondella, M Lucia

    2016-03-01

    To clarify the characteristics of circulating Bordetella pertussis isolates, we used pulsed-field gel electrophoresis (PFGE) to analyze 5,262 isolates collected in the United States during 2000-2012. We found 199 PFGE profiles; 5 profiles accounted for 72% of isolates. The most common profile, CDC013, accounted for 35%-46% of isolates tested from 2000-2009; however, the proportion of isolates of this profile rapidly decreased in 2010. Profile CDC237, first seen in 2009, increased rapidly and accounted for 29% of 2012 isolates. No location bias was observed among profiles during 2000-2010, but differences were observed among isolates from different states during 2012. Predominant profiles match those observed in recent European PFGE studies. PFGE profile changes are concurrent with other recent molecular changes in B. pertussis and may be contributing to the reemergence of pertussis in the United States. Continued PFGE monitoring is critical for understanding the changing epidemiology of pertussis.

  1. Separation and identification of Musa acuminate Colla (banana) leaf proteins by two-dimensional gel electrophoresis and mass spectrometry.

    Science.gov (United States)

    Lu, Y; Qi, Y X; Zhang, H; Zhang, H Q; Pu, J J; Xie, Y X

    2013-12-19

    To establish a proteomic reference map of Musa acuminate Colla (banana) leaf, we separated and identified leaf proteins using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS). Tryptic digests of 44 spots were subjected to peptide mass fingerprinting (PMF) by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS. Three spots that were not identified by MALDI-TOF MS analysis were identified by searching against the NCBInr, SwissProt, and expressed sequence tag (EST) databases. We identified 41 unique proteins. The majority of the identified leaf proteins were found to be involved in energy metabolism. The results indicate that 2D-PAGE is a sensitive and powerful technique for the separation and identification of Musa leaf proteins. A summary of the identified proteins and their putative functions is discussed.

  2. Time-based distribution of Staphylococcus saprophyticus pulsed field gel-electrophoresis clusters in community-acquired urinary tract infections

    Directory of Open Access Journals (Sweden)

    Viviane Santos de Sousa

    2013-02-01

    Full Text Available The epidemiology of urinary tract infections (UTI by Staphylococcus saprophyticus has not been fully characterised and strain typing methods have not been validated for this agent. To evaluate whether epidemiological relationships exist between clusters of pulsed field gel-electrophoresis (PFGE genotypes of S. saprophyticus from community-acquired UTI, a cross-sectional surveillance study was conducted in the city of Rio de Janeiro, Brazil. In total, 32 (16% female patients attending two walk-in clinics were culture-positive for S. saprophyticus. Five PFGE clusters were defined and evaluated against epidemiological data. The PFGE clusters were grouped in time, suggesting the existence of community point sources of S. saprophyticus. From these point sources, S. saprophyticus strains may spread among individuals.

  3. Time-based distribution of Staphylococcus saprophyticus pulsed field gel-electrophoresis clusters in community-acquired urinary tract infections.

    Science.gov (United States)

    Sousa, Viviane Santos de; Rabello, Renata Fernandes; Dias, Rubens Clayton da Silva; Martins, Ianick Souto; Santos, Luisa Barbosa Gomes da Silva dos; Alves, Elisabeth Mendes; Riley, Lee Woodford; Moreira, Beatriz Meurer

    2013-02-01

    The epidemiology of urinary tract infections (UTI) by Staphylococcus saprophyticus has not been fully characterised and strain typing methods have not been validated for this agent. To evaluate whether epidemiological relationships exist between clusters of pulsed field gel-electrophoresis (PFGE) genotypes of S. saprophyticus from community-acquired UTI, a cross-sectional surveillance study was conducted in the city of Rio de Janeiro, Brazil. In total, 32 (16%) female patients attending two walk-in clinics were culture-positive for S. saprophyticus. Five PFGE clusters were defined and evaluated against epidemiological data. The PFGE clusters were grouped in time, suggesting the existence of community point sources of S. saprophyticus. From these point sources, S. saprophyticus strains may spread among individuals.

  4. The use of caspase inhibitors in pulsed-field gel electrophoresis may improve the estimation of radiation-induced DNA repair and apoptosis

    International Nuclear Information System (INIS)

    Radiation-induced DNA double-strand break (DSB) repair can be tested by using pulsed-field gel electrophoresis (PFGE) in agarose-encapsulated cells. However, previous studies have reported that this assay is impaired by the spontaneous DNA breakage in this medium. We investigated the mechanisms of this fragmentation with the principal aim of eliminating it in order to improve the estimation of radiation-induced DNA repair. Samples from cancer cell cultures or xenografted tumours were encapsulated in agarose plugs. The cell plugs were then irradiated, incubated to allow them to repair, and evaluated by PFGE, caspase-3, and histone H2AX activation (γH2AX). In addition, apoptosis inhibition was evaluated through chemical caspase inhibitors. We confirmed that spontaneous DNA fragmentation was associated with the process of encapsulation, regardless of whether cells were irradiated or not. This DNA fragmentation was also correlated to apoptosis activation in a fraction of the cells encapsulated in agarose, while non-apoptotic cell fraction could rejoin DNA fragments as was measured by γH2AX decrease and PFGE data. We were able to eliminate interference of apoptosis by applying specific caspase inhibitors, and improve the estimation of DNA repair, and apoptosis itself. The estimation of radiation-induced DNA repair by PFGE may be improved by the use of apoptosis inhibitors. The ability to simultaneously determine DNA repair and apoptosis, which are involved in cell fate, provides new insights for using the PFGE methodology as functional assay

  5. Determination of phosphorus and metals in human brain proteins after isolation by gel electrophoresis by laser ablation inductively coupled plasma source mass spectrometry

    OpenAIRE

    Becker, J. S.; M. Zoriy; Becker, J. Su.; Pickhardt, C.; Przybylski, M.

    2004-01-01

    Phosphorus, sulfur, silicon and metal concentrations (Al, Cu and Zn) were determined in human brain, proteins by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) after separation of protein mixtures by two dimensional (2-D) gel electrophoresis. The analysis of phosphorus, silicon and metals in single protein spots in the gel was' performed with an optimized microanalytical method using a double-focusing sector field inductively coupled plasma mass spectrometer coupled t...

  6. Triclabendazole (Anthelmintic Drug Effects on the Excretory- Secretory Proteome of Fasciola hepatica in Two Dimension Electrophoresis Gel.

    Directory of Open Access Journals (Sweden)

    Ashkan Faridi

    2014-06-01

    Full Text Available The aim of this study was to evaluate the protein spots of excretory - secretory products of Fasciola hepatica using two dimension electrophoresis method in the presence and absence of triclabendazole drug which can be considered to detect the target protein of the drug.F. hepatica parasites were collected from infected cattle livers, divided in two groups and cultivated in RPMI 1640 medium. First group was treated with triclabendazole (TCBZ and second group considered as control. The excretory-secretory (ES products of each group were separated and total protein determined by Bradford method. To provide proteome spots, the ES proteins were precipitated and two dimension electrophoresis (2-DE gel prepared. Protein amounts of two groups were compared using the statistical t-test and protein spots from 2-DE in test and control groups were also statistically analyzed. The protein spots of gels were identified by using protein database.The t-test showed a significant increase of total proteins in treated group (P0.05. Cathepsin L- protein (MW 36.7 pH 5.34, 14-3-3 epsilon 2 isoform (MW 28.2 pH 5.36, Cathepsin L1D (MW 36.5 pH 5.8 and Cathepsin L1D (MW 36.6 pH 6.26 were identified in test group.It seems that, these results can be considered to determine the proteins which the drug acts as a target on them.

  7. Amino Acid Composition, Molecular Weight Distribution and Gel Electrophoresis of Walnut (Juglans regia L. Proteins and Protein Fractionations

    Directory of Open Access Journals (Sweden)

    Xiaoying Mao

    2014-01-01

    Full Text Available As a by-product of oil production, walnut proteins are considered as an additional source of plant protein for human food. To make full use of the protein resource, a comprehensive understanding of composition and characteristics of walnut proteins are required. Walnut proteins have been fractionated and characterized in this study. Amino acid composition, molecular weight distribution and gel electrophoresis of walnut proteins and protein fractionations were analyzed. The proteins were sequentially separated into four fractions according to their solubility. Glutelin was the main component of the protein extract. The content of glutelin, albumin, globulin and prolamin was about 72.06%, 7.54%, 15.67% and 4.73% respectively. Glutelin, albumin and globulin have a balanced content of essential amino acids, except for methionine, with respect to the FAO pattern recommended for adults. SDS-PAGE patterns of albumin, globulin and glutelin showed several polypeptides with molecular weights 14.4 to 66.2 kDa. The pattern of walnut proteins in two-dimension electrophoresis (2-DE showed that the isoelectric point was mainly in the range of 4.8–6.8. The results of size exclusion chromatogram indicated molecular weight of the major components of walnut proteins were between 3.54 and 81.76 kDa.

  8. Amino acid composition, molecular weight distribution and gel electrophoresis of walnut (Juglans regia L.) proteins and protein fractionations.

    Science.gov (United States)

    Mao, Xiaoying; Hua, Yufei; Chen, Guogang

    2014-01-01

    As a by-product of oil production, walnut proteins are considered as an additional source of plant protein for human food. To make full use of the protein resource, a comprehensive understanding of composition and characteristics of walnut proteins are required. Walnut proteins have been fractionated and characterized in this study. Amino acid composition, molecular weight distribution and gel electrophoresis of walnut proteins and protein fractionations were analyzed. The proteins were sequentially separated into four fractions according to their solubility. Glutelin was the main component of the protein extract. The content of glutelin, albumin, globulin and prolamin was about 72.06%, 7.54%, 15.67% and 4.73% respectively. Glutelin, albumin and globulin have a balanced content of essential amino acids, except for methionine, with respect to the FAO pattern recommended for adults. SDS-PAGE patterns of albumin, globulin and glutelin showed several polypeptides with molecular weights 14.4 to 66.2 kDa. The pattern of walnut proteins in two-dimension electrophoresis (2-DE) showed that the isoelectric point was mainly in the range of 4.8-6.8. The results of size exclusion chromatogram indicated molecular weight of the major components of walnut proteins were between 3.54 and 81.76 kDa.

  9. Characterization of Mycoplasma hyosynoviae strains by amplified fragment length polymorphism analysis, pulsed-field gel electrophoresis and 16S ribosomal DNA sequencing

    DEFF Research Database (Denmark)

    Kokotovic, Branko; Friis, N.F.; Ahrens, Peter

    2002-01-01

    , were investigated by analysis of amplified fragment length polymorphisms of the Bgl II and Mfe I restriction sites and by pulsed-field gel electrophoresis of a Bss HII digest of chromosomal DNA. Both methods allowed unambiguous differentiation of the analysed strains and showed similar discriminatory...

  10. Two-dimensional gel electrophoresis pattern (pH 6-11) and identification of water-soluble barley seed and malt proteins by mass spectrometry

    DEFF Research Database (Denmark)

    Bak-Jensen, K.S.; Laugesen, S.; Roepstorff, P.;

    2004-01-01

    A protocol was established for two-dimensional gel electrophoresis (2-DE) of barley seed and malt proteins in the pH range of 6-11. Proteins extracted from flour in a low-salt buffer were focused after cup-loading onto IPG strips. Successful separation in the second dimension was achieved using...

  11. Electrophoresis Gel Quantification with a Flatbed Scanner and Versatile Lighting from a Screen Scavenged from a Liquid Crystal Display (LCD) Monitor

    Science.gov (United States)

    Yeung, Brendan; Ng, Tuck Wah; Tan, Han Yen; Liew, Oi Wah

    2012-01-01

    The use of different types of stains in the quantification of proteins separated on gels using electrophoresis offers the capability of deriving good outcomes in terms of linear dynamic range, sensitivity, and compatibility with specific proteins. An inexpensive, simple, and versatile lighting system based on liquid crystal display backlighting is…

  12. Analysis of bacterial communities in soil by use of denaturing gradient gel electrophoresis and clone libraries, as influenced by different reverse primers

    NARCIS (Netherlands)

    Brons, Jolanda; van Elsas, J.D.

    2008-01-01

    To assess soil bacterial diversity, PCR systems consisting of several slightly different reverse primers together with forward primer F968-GC were used along with subsequent denaturing gradient gel electrophoresis (DGGE) or clone library analyses. In this study, a set of 13 previously used and novel

  13. Comparison between Gradient Gel Electrophoresis and Nuclear Magnetic Resonance Spectroscopy in Estimating Coronary Heart Disease Risk Associated with LDL and HDL Particle Size

    NARCIS (Netherlands)

    B.J. Arsenault; I. Lemieux; J.P. Després; N.J. Wareham; E.S.G. Stroes; J.J.P. Kastelein; K.T. Khaw; S.M. Boekholdt

    2010-01-01

    BACKGROUND: Gradient gel electrophoresis (GGE) and nuclear magnetic resonance (NMR) spectroscopy are both widely accepted methods for measuring LDL and HDL particle size. However, whether or not GGE- or NMR-measured LDL or HDL particle size predicts coronary heart disease (CHD) risk to a similar ext

  14. Comparative proteomics of E. coli O157:H7: two-dimensional gel electrophoresis vs. two-dimensional liquid chromatography separation

    Science.gov (United States)

    The accepted method for comparing bacterial proteomes has traditionally been two-dimensional gel electrophoresis (2-D GE). However, in recent years, new procedures for protein separation have been introduced. One of these new procedures utilizes column-based liquid chromatography (2-D LC) separati...

  15. Proteomics analysis in mature seed of four peanut cultivars using two-dimensional gel electrophoresis reveals distinct differential expression of storage, anti-nutritive, and allergenic proteins

    Science.gov (United States)

    Protein profiles of total seed proteins isolated from mature seeds of four peanut cultivars, New Mexico Valencia C (NM Valencia C), Tamspan 90, Georgia Green, and NC-7, were studied using two-dimensional gel electrophoresis coupled with nano electrospray ionization liquid chromatography tandem mass ...

  16. Random amplification of polymorphic DNA (RAPD), pulsed-field gel electrophoresis (PFGE) and phage-typing in the analysis of a hospital outbreak of Salmonella enteritidis

    DEFF Research Database (Denmark)

    Skibsted, U.; Baggesen, Dorte Lau; Dessau, R.;

    1998-01-01

    Isolates of Salmonella Enteritidis from 81 patients from Herlev Hospital or from Copenhagen County were analysed by random amplification of polymorphic DNA (RAPD), pulsed-field gel electrophoresis (PFGE) and phage-typing. Fourteen polymorphic markers from five decamer primers unambiguously placed...

  17. Resolution and identification of major peanut allergens using a combination of fluorescence two-dimensional differential gel electrophoresis, western blotting and Q-TOF mass spectrometry.

    Science.gov (United States)

    Peanut allergy is triggered by several proteins known as allergens. The matching resolution and identification of major peanut allergens in 2D protein maps, was accomplished by the use of fluorescence two-dimensional differential gel electrophoresis (2D DIGE), Western blotting and quadrupole time-of...

  18. Characterization of vancomycin-resistant and vancomycin-susceptible Enterococcus faecium isolates from humans, chickens and pigs by RiboPrinting and pulsed-field gel electrophoresis

    DEFF Research Database (Denmark)

    Hammerum, Anette Marie; Fussing, Vivian; Aarestrup, Frank Møller;

    2000-01-01

    Forty-eight vancomycin-resistant and 35 vancomycin-sensitive Danish Enterococcus faecium isolates obtained from pigs, chickens and humans, as well as the human vanA reference isolate BM4147, were characterized by EcoRI RiboPrinting and Smal pulsed-field gel electrophoresis. RiboPrinting of the 84...

  19. A comparative method for protein extraction and 2-D gel electrophoresis from different tissues of Cajanus cajan.

    Science.gov (United States)

    Singh, Nisha; Jain, Neha; Kumar, Ram; Jain, Ajay; Singh, Nagendra K; Rai, Vandna

    2015-01-01

    Pigeonpea is an important legume crop with high protein content. However, it is often subjected to various abiotic and biotic stresses. Proteomics is a state-of-the-art technique used to analyze the protein profiling of a tissue for deciphering the molecular entities that could be manipulated for developing crops resistant to these stresses. In this context, developing a comprehensive proteome profile from different vegetative and reproductive tissues has become mandatory. Although several protein extraction protocols from different tissues of diverse plant species have been reported, there is no report for pigeonpea. Here, we report tissue-specific protein extraction protocols representing vegetative (young leaves), and reproductive (flowers and seeds) organs and their subsequent analysis on 2-dimensional gel electrophoresis. The study explicitly demonstrated that the efficacy of a particular protein extraction protocol is dependent on the different tissues, such as leaves, flowers and seeds that differ in their structure and metabolic constituents. For instance, phenol-based protocol showed an efficacy toward higher protein yield, better spot resolution and a minimal streaking on 2-DE gel for both leaves and flowers. Protein extraction from seeds was best achieved by employing phosphate-TCA-acetone protocol. PMID:26300903

  20. Singular value decomposition of genome-scale mRNA lengths distribution reveals asymmetry in RNA gel electrophoresis band broadening.

    Science.gov (United States)

    Alter, Orly; Golub, Gene H

    2006-08-01

    We describe the singular value decomposition (SVD) of yeast genome-scale mRNA lengths distribution data measured by DNA microarrays. SVD uncovers in the mRNA abundance levels data matrix of genes x arrays, i.e., electrophoretic gel migration lengths or mRNA lengths, mathematically unique decorrelated and decoupled "eigengenes." The eigengenes are the eigenvectors of the arrays x arrays correlation matrix, with the corresponding series of eigenvalues proportional to the series of the "fractions of eigen abundance." Each fraction of eigen abundance indicates the significance of the corresponding eigengene relative to all others. We show that the eigengenes fit "asymmetric Hermite functions," a generalization of the eigenfunctions of the quantum harmonic oscillator and the integral transform which kernel is a generalized coherent state. The fractions of eigen abundance fit a geometric series as do the eigenvalues of the integral transform which kernel is a generalized coherent state. The "asymmetric generalized coherent state" models the measured data, where the profiles of mRNA abundance levels of most genes as well as the distribution of the peaks of these profiles fit asymmetric Gaussians. We hypothesize that the asymmetry in the distribution of the peaks of the profiles is due to two competing evolutionary forces. We show that the asymmetry in the profiles of the genes might be due to a previously unknown asymmetry in the gel electrophoresis thermal broadening of a moving, rather than a stationary, band of RNA molecules.

  1. Acrylamide gel electrophoresis of proteins, acid phosphatases and RN-ases from three potato varieties

    Directory of Open Access Journals (Sweden)

    A. Kubicz

    2015-05-01

    Full Text Available Studies on variety differences in the protein and acid phosphatase patterns as well as ribunuclease activity distribution were carried out by disc electrophoresis on saline extracts of three varieties of the potato Solanum tuberosum (L.. The protein bands varied in number, position and relative abundance. One main zone of the acid phosphatase activity was detected consisting of 2-3 electrophoretically different bands. Variety differences were concerned with the number and relative abundance of these bands. RNase activity was detected in 4 main zones, in some of them additional subbands were visible. Differences between the three examined varieties were reflected in the occurence of the particular activity zones or their subbands.

  2. DNA double-strand breaks induced by high-energy neon and iron ions in human fibroblasts. I. Pulsed-field gel electrophoresis method

    International Nuclear Information System (INIS)

    The relative effectiveness of high-energy neon and iron ions for the production of DNA double-strand breaks was measured in one transformed and one nontransformed human fibroblast cell line using pulsed-field gel electrophoresis. The DNA released from the gel plug (fraction of activity released: FAR) as well as the size distribution of the DNA entering the gel were used to compare the effects of the heavy-ion exposure with X-ray exposure. Both methods gave similar results, indicating similar distributions of breaks over megabase-pair distances for the heavy ions and the X rays. The relative biological effectiveness (RBE) compared to 225 kVp X rays of initially induced DNA double-strand breaks was found to be 0.85 for 425 MeV/u neon ions (LET 32 keV/μm) and 0.42-0.55 for 250-600 MeV/u iron ions (LET 190-350 keV/μm). Postirradiation incubation showed less efficient repair of breaks induced by the neon ions and the 600 MeV/u iron ions compared to X rays. Survival experiments demonstrated RBE values larger than one for cell killing by the heavy ions in parallel experiments (neon: RBE = 1.2, iron: RBE = 2.3-3.0, based on D10 values). It is concluded that either the initial yield of DNA double-strand breaks induced by the high-energy particles is lower than the yield for X rays, or the breaks induced by heavy ions are present in clusters that cannot be resolved with the technique used. These results are confirmed in the accompanying paper. 48 refs., 5 figs., 2 tabs

  3. Unfolding of hemoglobin variants--insights from urea gradient gel electrophoresis photon correlation spectroscopy and zeta potential measurements

    Energy Technology Data Exchange (ETDEWEB)

    Bhattacharya, Jaydeep; GhoshMoulick, Ranjita; Choudhuri, Utpal; Chakrabarty, Prantar; Bhattacharya, Pranab K.; Lahiri, Prabir; Chakraborti, Bikas; Dasgupta, Anjan Kr

    2004-09-27

    The unfolding pattern of crystal human hemoglobin and variants of hemoglobin obtained from hemolysate were studied using transverse urea gradient gel electrophoresis (TUGGE). A smooth sigmoid like increase of electrophoretic mobility was observed with increasing urea concentrations. A decrease in electrophoretic mobility resulted, if the protein was unfolded with guanidium hydrochloride (GdnHCl). The anomaly was resolved after the Stoke's radii (obtained using the photon correlation spectroscopy) and zeta potential (measured using laser Doppler velocimetry) measurements were made at different denaturant concentrations. Addition of denaturant led to formation of extended structure, irrespective of the nature of the denaturant, as indicated by increase in Stoke's radii in both cases (urea and GdnHCl). The unexpected increase in electrophoretic mobility in case of urea could be explained in terms of a critical redistribution of negative charge at intermediate stages of the unfolding process. In case of GdnHCl, the higher ionic strength masked the charge effect. The mobility, being solely dependent on size, decreased at higher denaturant concentration. Incidentally, folding loci of other hemoglobin variants (e.g. HbE) or that of post-translationally modified hemoglobin (e.g. HbA1c) could be determined by studying the charge distribution and hydrodynamic radius at varying denaturing stress and in each case the gel migration profile could be approximately scaled by the ratio of charge and hydrodynamic diameter of the protein. While unfolding induced charge effect was most pronounced in HbA0 (and crystal ferrous hemoglobin), the unfolding induced aggregation (manifested by the increase in Stoke's radii) was predominantly observed in the variant forms HbE and HbA1c. Representing the proteins by a plot, in which charge and hydrodynamic diameter are on independent axes, may be a useful way of characterizing protein variants having similar migration profiles on

  4. The Sizes of Double Minutes in Human Ovarian Cancer Cells and Mouse MTX-resistant Cells Determined by Pulsed Field Gradient Gel Electrophoresis and Southern Blotting%人卵巢癌细胞及小鼠MTX抗性细胞中DMs大小的测定

    Institute of Scientific and Technical Information of China (English)

    张钰; 邓新宇; 白静; 李璞; 傅松滨

    2006-01-01

    目的 测定肿瘤细胞及耐药性细胞中双微体(double minutes,DMs)的大小.方法 应用PFGE(Pulsed field gradient gel electrophoresis)与Southern印迹杂交技术,对人卵巢癌细胞UACC-1598及氨甲蝶呤(Methotrexate,MTX)抗性的小鼠胚胎成纤维细胞中DMs的大小进行检测.结果 发现UACC-1598细胞中存在2.8Mb、2.1Mb及1.4Mb的DMs群体,提示多拷贝的扩增基因及其邻近的染色体区域经染色体断裂、易位及重排形成较大的DMs.同时,用浓度逐渐增高的MTX对小鼠胚胎成纤维细胞进行体外诱导,分离出富含DMs的不同MTX抗性程度的细胞群体.在MTX抗性细胞中检测到2.5Mb及1.4Mb的DMs群体,MTX100细胞中以1.4Mb的DMs群体为主,而MTX500细胞中以2.5Mb的DMs群体为主.结论 MTX细胞中产生的扩增子结构在演化过程中趋向于寡聚化或多聚化形成较大片段的DMs.

  5. Caracterização de cepas de referência de Leptospira sp utilizando a técnica de pulsed field gel electrophoresis Characterization of Leptospira sp reference strains using the pulsed field gel electrophoresis technique

    Directory of Open Access Journals (Sweden)

    Lívia Machry

    2010-04-01

    Full Text Available INTRODUÇÃO: A leptospirose é uma zoonose endêmica, mundialmente distribuída, causada por bactérias do gênero Leptospira. Este gênero compreende espécies patogênicas e saprofíticas, com mais de 200 sorovares distintos, dificultando sua caracterização. A técnica de pulsed field gel electrophoresis tem sido empregada como uma ferramenta para auxiliar nesta caracterização. Os objetivos deste trabalho foram padronizar a técnica de PFGE, determinar os perfis moleculares das cepas de referência utilizadas pelo Laboratório de Referência Nacional para Leptospirose/Centro Colaborador da Organização Mundial de Saúde para Leptospirose e criar um banco de dados com estes perfis. MÉTODOS: Foram analisadas, por PFGE, dezenove cepas utilizando a enzima de restrição NotI. RESULTADOS: Cada cepa apresentou um perfil único que pode ser considerado como uma identidade genômica específica, com exceção dos sorovares Icterohaemorrhagiae e Copenhageni, cujos perfis foram indistinguíveis. CONCLUSÕES: Dessa forma, foi possível a criação de um banco de perfis moleculares que está sendo utilizado no Laboratório para a comparação e identificação de cepas isoladas de quadros clínicos.INTRODUCTION: Leptospirosis is an endemic zoonosis of worldwide distribution, caused by bacteria of the genus Leptospira. This genus includes pathogenic and saprophytic species, with more than 200 different serovars, thus making it difficult to characterize. The technique of pulsed field gel electrophoresis has been used as a tool to aid in this characterization. The aims of this study were to standardize the PFGE technique, determine the molecular profiles of reference strains used at the National Reference Laboratory for Leptospirosis/World Health Organization Collaborating Center for Leptospirosis and create a database with these profiles. METHODS: Nineteen strains were analyzed by means of PFGE, using the restriction enzyme NotI. RESULTS: Each strain

  6. Miniaturized movable contactless conductivity detection cell for capillary electrophoresis.

    Science.gov (United States)

    Macka, Miroslav; Hutchinson, Joseph; Zemann, Andreas; Shusheng, Zhang; Haddad, Paul R

    2003-06-01

    A miniaturized capacitively coupled contactless conductivity detector (mini-C(4)D) cell has been designed which is small enough to allow it to slide along the effective capillary length inside the capillary cassette of an Agilent capiillary electrophoresis system (CE) (or other CE brand of similar construction), including the possibility of positioning it close to the point of optical detection (4 cm), or even putting two such detector cells in one cassette. The cell was tested and the performance characteristics (noise, sensitivity, and peak width) were compared with those obtained with the previously used large C(4)D cell. No significant differences were observed. The mini-C(4)D was used in simultaneous separations of common cations and anions where its advantage over a larger C(4)D cell is the ability to vary the point of detection with the mini-C(4)D cell continuously at any point along the capillary length, so that the optimum apparent selectivity can be chosen. Other applications include providing a convenient second point of detection in addition to photometric detection, such as to measure accurately the linear velocity of a zone, or to allow placement of two mini-C(4)D cells in one capillary cassette simultaneously. PMID:12858387

  7. An Economical Electrophoresis Apparatus

    Science.gov (United States)

    Andrews, I. M.

    1975-01-01

    Describes the production of an electrophoresis apparatus from commonly discarded articles. Outlines paper and gel electrophoresis and its application to the separation of amino acids and intestinal enzymes. (GS)

  8. A comprehensive two-dimensional gel protein database of noncultured unfractionated normal human epidermal keratinocytes: towards an integrated approach to the study of cell proliferation, differentiation and skin diseases

    DEFF Research Database (Denmark)

    Celis, J E; Madsen, Peder; Rasmussen, H H;

    1991-01-01

    A two-dimensional (2-D) gel database of cellular proteins from noncultured, unfractionated normal human epidermal keratinocytes has been established. A total of 2651 [35S]methionine-labeled cellular proteins (1868 isoelectric focusing, 783 nonequilibrium pH gradient electrophoresis) were resolved......, melanocytes, fibroblasts, dermal microvascular endothelial cells, peripheral blood mononuclear cells and sweat duct cells. The keratinocyte 2-D gel protein database will be updated yearly in the November issue of Electrophoresis. Udgivelsesdato: 1991-Nov...

  9. Optimized sample preparation for two-dimensional gel electrophoresis of soluble proteins from chicken bursa of Fabricius

    Directory of Open Access Journals (Sweden)

    Zheng Xiaojuan

    2009-10-01

    Full Text Available Abstract Background Two-dimensional gel electrophoresis (2-DE is a powerful method to study protein expression and function in living organisms and diseases. This technique, however, has not been applied to avian bursa of Fabricius (BF, a central immune organ. Here, optimized 2-DE sample preparation methodologies were constructed for the chicken BF tissue. Using the optimized protocol, we performed further 2-DE analysis on a soluble protein extract from the BF of chickens infected with virulent avibirnavirus. To demonstrate the quality of the extracted proteins, several differentially expressed protein spots selected were cut from 2-DE gels and identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS. Results An extraction buffer containing 7 M urea, 2 M thiourea, 2% (w/v 3-[(3-cholamidopropyl-dimethylammonio]-1-propanesulfonate (CHAPS, 50 mM dithiothreitol (DTT, 0.2% Bio-Lyte 3/10, 1 mM phenylmethylsulfonyl fluoride (PMSF, 20 U/ml Deoxyribonuclease I (DNase I, and 0.25 mg/ml Ribonuclease A (RNase A, combined with sonication and vortex, yielded the best 2-DE data. Relative to non-frozen immobilized pH gradient (IPG strips, frozen IPG strips did not result in significant changes in the 2-DE patterns after isoelectric focusing (IEF. When the optimized protocol was used to analyze the spleen and thymus, as well as avibirnavirus-infected bursa, high quality 2-DE protein expression profiles were obtained. 2-DE maps of BF of chickens infected with virulent avibirnavirus were visibly different and many differentially expressed proteins were found. Conclusion These results showed that method C, in concert extraction buffer IV, was the most favorable for preparing samples for IEF and subsequent protein separation and yielded the best quality 2-DE patterns. The optimized protocol is a useful sample preparation method for comparative proteomics analysis of chicken BF tissues.

  10. 2-D GEL ELECTROPHORESIS MAP OF METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS TREATED WITH QUERCUS INFECTORIA GALL EXTRACT

    Directory of Open Access Journals (Sweden)

    Dayang Fredalina Basri

    2013-01-01

    Full Text Available The widespread outbreak of Methicillin-Resistant Staphylococcus Aureus (MRSA has caused clinical and epidemiological concern in hospital environment. The emergence of Vancomycin-Intermediate S. Aureus (VISA and, more recently, Vancomycin-Resistant S. Aureus (VRSA has further alarmed clinician and scientist worlwide. The objective of this study is to determine the optimum concentration of sample protein from MRSA after treatment with acetone extract from Quercus infectoria gall. Comparison of the Protein Expression Profile (PEP between the treated MRSA and untreated strain as control was obtained using 2-dimensional gel electrophoresis. The Minimum Inhibitory Concentration (MIC value of acetone extract of galls from Q. infectoria against two strains of MRSA; ATCC 33591 and PPUKM clinical isolate was determined by broth microdilution method. The MIC value of acetone extracts against both strains of MRSA was 0.3125 mg mL-1 compared to vancomycin (0.00195 mg mL-1. The optimum concentration of MRSA protein that produced the best resolution was 100 µg. Manifold technique was observed to produce a gel with better resolution and greater number of spot compared with the strip holder technique. This study showed that there were 7 protein spots that represented the increased in the protein expression of more than 2-fold in the MRSA treated with acetone extract of galls Q. infectoria compared to the untreated group. This preliminary study on the PEP of Q. infectoria galls extract-treated MRSA may provide an insight of its antimicrobial mechanism which could lead to the identification of target protein in the future development of a new effective regimen for the treatment of MRSA infections.

  11. A multifaceted analysis of viperid snake venoms by two-dimensional gel electrophoresis: an approach to understanding venom proteomics.

    Science.gov (United States)

    Serrano, Solange M T; Shannon, John D; Wang, Deyu; Camargo, Antonio C M; Fox, Jay W

    2005-02-01

    The complexity of Viperid venoms has long been appreciated by investigators in the fields of toxinology and medicine. However, it is only recently that the depth of that complexity has become somewhat quantitatively and qualitatively appreciated. With the resurgence of two-dimensional gel electrophoresis (2-DE) and the advances in mass spectrometry virtually all venom components can be visualized and identified given sufficient effort and resources. Here we present the use of 2-DE for examining venom complexity as well as demonstrating interesting approaches to selectively delineate subpopulations of venom proteins based on particular characteristics of the proteins such as antibody cross-reactivity or enzymatic activities. 2-DE comparisons between venoms from different species of the same genus (Bothrops) of snake clearly demonstrated both the similarity as well as the apparent diversity among these venoms. Using liquid chromatography/tandem mass spectrometry we were able to identify regions of the two-dimensional gels from each venom in which certain classes of proteins were found. 2-DE was also used to compare venoms from Crotalus atrox and Bothrops jararaca. For these venoms a variety of staining/detection protocols was utilized to compare and contrast the venoms. Specifically, we used various stains to visualize subpopulations of the venom proteomes of these snakes, including Coomassie, Silver, Sypro Ruby and Pro-Q-Emerald. Using specific antibodies in Western blot analyses of 2-DE of the venoms we have examined subpopulations of proteins in these venoms including the serine proteinase proteome, the metalloproteinase proteome, and the phospholipases A2 proteome. A functional assessment of the gelatinolytic activity of these venoms was also performed by zymography. These approaches have given rise to a more thorough understanding of venom complexity and the toxins comprising these venoms and provide insights to investigators who wish to focus on these venom

  12. Heterogeneity of human alpha-fetoprotein (HAFP) as revealed by agarose gel electrophoresis and isoelectric focusing in urea-acrylamide gels

    Energy Technology Data Exchange (ETDEWEB)

    Lester, E. P.; Miller, J. B.; Yachnin, S.

    1977-01-01

    HAFP was purified from five patients with hepatoma, one with gastric cancer, and one with an embryonal cell tumor, as well as from fetal liver and a monkey tumor cell line grown in tissue culture. The pattern of microheterogeneity of purified HAFP was defined for each HAFP isolate, and was demonstrated to be present in native sera, using crossed immunoelectrophoresis in agarose gels and isoelectric focusing in polyacrylamide gels containing 8 M urea. Three, and in one case four, species were seen in agarose, and were further resolved to reveal 6 major species with isoelectric focusing which could be correlated with the agarose gel variants. We have demonstrated a relationship between the immunosuppressive potency of certain HAFP preparations and the proportion of specific HAFP isomers which they contain as shown by these techniques. We have desialylated each of our preparations and demonstrated that this does not alter immunosuppressive potency but leaves residual complex microheterogeneity. Desialylated HAFP isolates contain six major HAFP isomers by isoelectric focusing, indicating that HAFP heterogeneity is based upon multiple charge differences in the HAFP molecule, apart from sialic acid content. The nature of these charge differences remain to be determined. We postulate that these charge differences modulate the immunosuppressive potency of HAFP.

  13. Heterogeneity of Campylobacter species isolated from serial stool specimens of Egyptian children using pulsed field gel electrophoresis

    Directory of Open Access Journals (Sweden)

    Atef M. El-Gendy

    2013-03-01

    Full Text Available Background: The genus Campylobacter spp. is a common cause of human acute bacteria lenteritis and travellers’ diarrhoea worldwide.Objective: To determine whether multiple serial isolations of Campylobacter spp., when obtained from a single child, represented the same or a different organism.Methods: In a birth cohort study conducted in Egypt, numerous children showed serial isolations of Campylobacter spp. Of these, 13 children were selected from different households based on the successive isolation of six or more Campylobacter isolates from stool samples.Results: Eighty isolates were recovered and identified as either Campylobacter coli (n = 25 or Campylobacter jejuni (n = 55. Pulsed-field gel electrophoresis (PFGE revealed the presence of 38 unique C. jejuni and 24 C. coli profiles at a similarity level of ≥ 90%. Although no seriallyidentical isolates were detected in six children, others demonstrated at least one identical couple of isolates; all identified serially between one to six weeks. Two children demonstrated > 80% similar couples of isolates that appeared seven months apart. PFGE could be a useful tool for differentiating reinfection, relapse and convalescent excretion phases.Conclusion: Our data suggest that Campylobacter infection in children is a complex process; children are exposed to multiple species in endemic environments and strains of the same bacterium appear to be shed serially between one to six weeks after the first exposure. Isolates that persisted for longer periods were relatively less similar, as shown from the results of this study.

  14. Frequencies of virulence genes and pulse field gel electrophoresis fingerprints in Escherichia coli isolates from canine pyometra.

    Science.gov (United States)

    Maluta, Renato P; Borges, Clarissa A; Beraldo, Lívia G; Cardozo, Marita V; Voorwald, Fabiana A; Santana, André M; Rigobelo, Everlon C; Toniollo, Gilson H; Avila, Fernando A

    2014-11-01

    Escherichia coli is the most common bacterial agent isolated from canine pyometra. The frequencies of 24 virulence genes and pulsed field gel electrophoresis (PFGE) profiles were determined for 23 E. coli isolates from cases of canine pyometra in Brazil. The frequencies of virulence genes were 91.3% fimH, 91.3% irp-2, 82.6% fyuA, 56.5% iroN, 47.8% traT, 39.1% usp, 34.8% sfaD/E, 34.8% tsh, 30.4% papC, 30.4% hlyA, 26.1% papGIII, 26.1% cnf-1, 21.7% papE/F, 21.7% iss, 17.4% iutA, 17.4% ompT, 17.4% cvaC, 17.4% hlyF, 17.4% iucD, 13.0% iucC, 13.0% astA, 4.3% papGII, 0% afaB/C and 0% papGI. The high frequency of yersiniabactin (fyuA and irp2) and salmochelin (iroN) genes suggests that iron uptake systems might be important in the pathogenesis of canine pyometra. PFGE profiles of 19 isolates were heterogeneous, confirming that E. coli isolates from canine pyometra are unlikely to be epidemic clones. PMID:25201253

  15. Diversity of pulsed-field gel electrophoresis patterns of cereulide-producing isolates of Bacillus cereus and Bacillus weihenstephanensis.

    Science.gov (United States)

    Castiaux, Virginie; N'guessan, Elise; Swiecicka, Izabela; Delbrassinne, Laurence; Dierick, Katelijne; Mahillon, Jacques

    2014-04-01

    Bacillus cereus is an important foodborne pathogen causing diarrhoea, emesis and in, rare cases, lethal poisonings. The emetic syndrome is caused by cereulide, a heat-stable toxin. Originally considered as a rather homogenous group, the emetic strains have since been shown to display some diversity, including the existence of two clusters of mesophilic B. cereus and psychrotolerant B. weihenstephanensis. Using pulsed-field gel electrophoresis (PFGE) analysis, this research aimed to better understand the diversity and spatio-temporal occurrence of emetic strains originating from environmental or food niches vs. those isolated from foodborne cases. The diversity was evaluated using a set of 52 B. cereus and B. weihenstephanensis strains isolated between 2000 and 2011 in ten countries. PFGE analysis could discriminate 17 distinct profiles (pulsotypes). The most striking observations were as follows: (1) more than one emetic pulsotype can be observed in a single outbreak; (2) the number of distinct isolates involved in emetic intoxications is limited, and these potentially clonal strains frequently occurred in successive and independent food poisoning cases; (3) isolates from different countries displayed identical profiles; and (4) the cereulide-producing psychrotolerant B. weihenstephanensis were, so far, only isolated from environmental niches.

  16. Triton X-114 cloud point extraction to subfractionate blood plasma proteins for two-dimensional gel electrophoresis.

    Science.gov (United States)

    Jessen, Flemming; Wulff, Tune

    2015-09-15

    A simple and reproducible procedure for enrichment of a plasma protein subfraction suitable for two-dimensional polyacrylamide gel electrophoresis (2DE) was developed, using a Triton X-114-based cloud point extraction (CPE). Appropriate conditions for such a CPE procedure were found by SDS-PAGE to be a plasma protein concentration of about 10mg/ml in 3% (w/v) Triton X-114. 2DE of proteins obtained by CPE of 400 μl of human plasma revealed about 200 spots constituting a spot pattern very different from the pattern of total plasma. The CPE procedure only had a limited contribution to the technical variation. Identification of about 60 spots, representing only 22 proteins, revealed that several proteins in the obtained subfraction were present in more isoforms or modifications. Among these were apolipoproteins (A-1, D, E, L1, and M), haptoglobin-related protein, phosphatidylcholine-sterol acyltransferase, serum amyloid A, and serum paraoxonase/arylesterase 1, which are proteins of a hydrophobic nature, as in plasma they relate to lipoprotein particles. Thus, Triton X-114-based CPE is a simple plasma prefractionation tool, attractive for detailed 2DE studies of hydrophobic plasma proteins and their isoforms or modifications.

  17. Denaturing gradient gel electrophoresis (DGGE as a powerful novel alternative for differentiation of epizootic ISA virus variants.

    Directory of Open Access Journals (Sweden)

    Marisela Carmona

    Full Text Available Infectious Salmon Anemia is a devastating disease critically affecting world-wide salmon production. Chile has been particularly stricken by this disease which in all cases has been directly related with its causative agent, a novel orthomyxovirus which presents specific and distinctive infective features. Among these, two molecular markers have been directly associated with pathogenicity in two of the eight RNA sub genomic coding units of the virus: an insertion hot spot region present in viral segment 5 and a Highly Polymorphic Region (HPR located in viral segment 6. Here we report the successful adaptation of a PCR-dependent denaturing gel electrophoresis technique (DGGE, which enables differentiation of selected reported HPR epizootic variants detected in Chile. At the same time, the technique allows us to distinguish one nucleotide differences in sequences associated with the intriguing, and still not well-understood, insertion events which tend to occur on RNA Segment 5. Thus, the versatility of the technique opens new opportunities for improved understanding of the complex biology of all ISA variants as well as possible applications to other highly variable pathogens.

  18. Monitoring of the microbial communities involved in the soy sauce manufacturing process by PCR-denaturing gradient gel electrophoresis.

    Science.gov (United States)

    Tanaka, Yasushi; Watanabe, Jun; Mogi, Yoshinobu

    2012-08-01

    Soy sauce is a traditional seasoning produced through the fermentation of soybeans and wheat using microbes. In this study, the microbial communities involved in the soy sauce manufacturing process were analyzed by PCR-Denaturing Gradient Gel Electrophoresis (PCR-DGGE). The bacterial DGGE profile indicated that the bacterial microbes in the koji were Weissella cibaria (Weissella confusa, Weissella kimchii, Weissella salipiscis, Lactobacillus fermentum, Lactobacillus plantarum, Lactobacillus iners, or Streptococcus thermophilus), Staphylococcus gallinarum (or Staphylococcus xylosus), and Staphylococcus kloosii. In addition to these bacteria, Tetragenococcus halophilus was also detected in the mash during lactic acid fermentation. The fungal DGGE profile indicated that the fungal microbes in the koji were not only Aspergillus oryzae but also several yeasts. In the mash, Zygosaccharomyces rouxii appeared in the early fermentation stage, Candida etchellsii (or Candida nodaensis) and Candida versatilis were detected at the middle fermentation stage, and Candida etchellsii was detected at the mature fermentation stage. These results suggest that the microbial communities present during the soy sauce manufacturing process change drastically throughout its production. This is the first report to reveal the microbial communities involved in the soy sauce manufacturing process using a culture-independent method. PMID:22475947

  19. Analysis of microbial communities in doenjang, a Korean fermented soybean paste, using nested PCR-denaturing gradient gel electrophoresis.

    Science.gov (United States)

    Kim, Tae-Woon; Lee, Jun-Hwa; Kim, Sung-Eon; Park, Min-Hee; Chang, Hae Choon; Kim, Hae-Yeong

    2009-05-31

    Doenjang is a traditional Korean fermented soybean paste that provides a major source of protein. The microbial diversity of 10 samples of doenjang (5 commercially manufactured products and 5 homemade products) was investigated using nested PCR-denaturing gradient gel electrophoresis (DGGE). In the first step, the nearly complete 16S rRNA and 18S rRNA genes were amplified using universal primers. Subsequently, these products were used as a template in a nested PCR to obtain fragments suitable for DGGE. The bacterial DGGE profile targeting the V3 region of the 16S rRNA gene indicated that lactic acid bacteria such as Leuconostoc mesenteroide, Tetragenococcus halophilus, and Enterococcus faecium were the predominant species. However, bands corresponding to Bacillus species, known to be the main organisms in doenjang, were not detected under the conditions described above. When selective PCR was conducted using a primer specific for Bacillus species, Bacillus subtilis and B. licheniformis were detected in several doenjang samples. In analysis of fungi, Mucor plumbeus, Aspergillus oryzae, and Debaryomyces hansenii were the most common species in the doenjang samples. On the basis of DGGE, a few differences in community structure were found for different samples. Also, cluster analysis of the DGGE profile revealed that the microbial diversity did not differ clearly between commercially manufactured and homemade products. The nested PCR-DGGE technique was used for the first time in this study to asses a microbial community in doenjang and proved to be effective in profiling microbial diversity. PMID:19324443

  20. Investigating the fate of activated sludge extracellular proteins in sludge digestion using sodium dodecyl sulfate polyacrylamide gel electrophoresis.

    Science.gov (United States)

    Park, Chul; Helm, Richard F; Novak, John T

    2008-12-01

    The fate of activated sludge extracellular proteins in sludge digestion was investigated using three different cation-associated extraction methods and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Extraction methods used were the cation exchange resin (CER) method for extracting calcium (Ca2+) and magnesium (Mg2+), sulfide extraction for removing iron, and base treatment (pH 10.5) for dissolving aluminum. Extracellular polymeric substances extracted were then subjected to SDS-PAGE, and the resultant protein profiles were examined before and after sludge digestion. The SDS-PAGE results showed that three methods led to different SDS-PAGE profiles for both undigested and digested sludges. The results further revealed that CER-extracted proteins remained mainly undegraded in anaerobic digestion, but were degraded in aerobic digestion. While the fate of sulfide- and base-extracted proteins was not clear for aerobic digestion, their changes in anaerobic digestion were elucidated. Most sulfide-extracted proteins were removed by anaerobic digestion, while the increase in protein band intensity and diversity was observed for base-extracted proteins. These results suggest that activated sludge flocs contain different fractions of proteins that are distinguishable by their association with certain cations and that each fraction undergoes different fates in anaerobic and aerobic digestion. The proteins that were resistant to degradation and generated during anaerobic digestion were identified by liquid chromatography tandem mass spectrometry. Protein identification results and their putative roles in activated sludge and anaerobic digestion are discussed in this study. PMID:19146099

  1. Variations among Japanese of the factor IX gene (F9) detected by PCR-denaturing gradient gel electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Satoh, Chiyoko; Takahashi, Norio; Asakawa, Junichi; Hiyama, Keiko; Kodaira, Meiko (Radiation Effects Research Foundation, Hiroshima (Japan))

    1993-01-01

    In the course of feasibility studies to examine the efficiencies and practicalities of various techniques for screening for genetic variations, the human coagulation factor IX (F9) genes of 63 Japanese families were examined by PCR-denaturing gradient gel electrophoresis (PCR-DGGE). Four target sequences with lengths of 983-2,891 bp from the F9 genes of 126 unrelated individuals from Hiroshima and their 100 children were amplified by PCR, digested with restriction enzymes to approximately 500-bp fragments, and examined by DGGE - a total of 6,724 bp being examined per individual. GC-rich sequences (GC-clamps) of 40 bp were attached to both ends of the target sequences, as far as was feasible. Eleven types of new nucleotide substitutions were detected in the population, none of which produced RFLPs or caused hemophilia B. By examining two target sequences in a single lane, approximately 8,000 bp in a diploid individual could be examined. This approach is very effective for the detection of variations in DNA and is applicable to large-scale population studies. 46 refs., 3 figs., 1 tab.

  2. Denaturing gradient gel electrophoresis and barcoded pyrosequencing reveal unprecedented archaeal diversity in mangrove sediment and rhizosphere samples.

    Science.gov (United States)

    Pires, Ana C C; Cleary, Daniel F R; Almeida, Adelaide; Cunha, Angela; Dealtry, Simone; Mendonça-Hagler, Leda C S; Smalla, Kornelia; Gomes, Newton C M

    2012-08-01

    Mangroves are complex ecosystems that regulate nutrient and sediment fluxes to the open sea. The importance of bacteria and fungi in regulating nutrient cycles has led to an interest in their diversity and composition in mangroves. However, very few studies have assessed Archaea in mangroves, and virtually nothing is known about whether mangrove rhizospheres affect archaeal diversity and composition. Here, we studied the diversity and composition of Archaea in mangrove bulk sediment and the rhizospheres of two mangrove trees, Rhizophora mangle and Laguncularia racemosa, using denaturing gradient gel electrophoresis (DGGE) and pyrosequencing of archaeal 16S rRNA genes with a nested-amplification approach. DGGE profiles revealed significant structural differences between bulk sediment and rhizosphere samples, suggesting that roots of both mangrove species influence the sediment archaeal community. Nearly all of the detected sequences obtained with pyrosequencing were identified as Archaea, but most were unclassified at the level of phylum or below. Archaeal richness was, furthermore, the highest in the L. racemosa rhizosphere, intermediate in bulk sediment, and the lowest in the R. mangle rhizosphere. This study shows that rhizosphere microhabitats of R. mangle and L. racemosa, common plants in subtropical mangroves located in Rio de Janeiro, Brazil, hosted distinct archaeal assemblages. PMID:22660713

  3. Investigation of two different anoxia models by 2-dimensional gel electrophoresis

    DEFF Research Database (Denmark)

    Wulff, Tune; Jessen, Flemming; Hoffmann, Else Kay

    2006-01-01

    This study presents a broad investigation of the effects of different types of anoxia in the Rainbow Trout Hypodermal Fibroblasts cell line, including a comparison of two widely used anoxia models. Anoxia was obtained either by flushing with N2 (FN) or by adding NaN3 to the medium, since chemical...... of molecular masses from 10 to 120 kDa and pI values from 4 to 7. In response to 24 h of anoxia obtained by FN we found that the sexpression of more than 30 proteins changed, including proteins involved in cell metabolism as well as protective proteins. Chemical anoxia for 30 minutes and subsequent...

  4. Two dimensional gel electrophoresis using narrow pH 3-5.6 immobilised pH gradient strips identifies potential novel disease biomarkers in plasma or serum

    OpenAIRE

    sprotocols

    2015-01-01

    Authors: Bevin Gangadharan & Nicole Zitzmann ### Abstract Two-dimensional gel electrophoresis (2-DE) is a protein separation technique often used to separate plasma or serum proteins in an attempt to identify novel biomarkers. This protocol describes how to run 2-DE gels using narrow pH 3-5.6 immobilised pH gradient strips to separate 2 mg of serum proteins. pH 3-6 ampholytes are used to enhance the solubility of proteins in this pH range before the serum proteins are separated in...

  5. Analysis of proteins in the extracellular matrix of the plant pathogenic fungus Bipolaris sorokiniana using 2-D gel electrophoresis and MS/MS.

    Science.gov (United States)

    Apoga, D; Ek, B; Tunlid, A

    2001-04-13

    A method was developed for isolating and sequencing proteins present in the extracellular matrix (ECM) of germlings and hyphae of filamentous fungi. Surface proteins of the cereal pathogen Bipolaris sorokiniana were labelled with a membrane impermeable biotinylating agent and extracted using a glycine-HCl buffer. Extracted proteins were purified by affinity binding to streptavidin-conjugated magnetic beads or by two-dimensional gel electrophoresis. Four of the biotinylated proteins from the ECM of B. sorokiniana were isolated, in gel digested with trypsin and partly sequenced by tandem mass spectrometry. No significant sequence similarities to proteins in databases were obtained.

  6. Dynamics of the microbial community responsible for traditional sour cassava starch fermentation studied by denaturing gradient gel electrophoresis and quantitative rRNA hybridization

    OpenAIRE

    Ampe, Frédéric; Sirvent, A.; Zakhia, N.

    2001-01-01

    The microbial community developing during the spontaneous fermentation of sour cassava starch was investigated by cultivation-independent methods. Denaturing gradient gel electrophoresis (DGGE) of partially amplified 16S rDNA followed by sequencing of the most intense bands showed that the dominant organisms were all lactic acid bacteria (LAB), mainly close relatives of #Bifidobacterium minimum$, #Lactococcus lactis$, #Streptoccocus$ sp., #Enteroccucus saccharolyticus$ and #Lactobacillus plan...

  7. Selective Discrimination of Listeria monocytogenes Epidemic Strains by a Mixed-Genome DNA Microarray Compared to Discrimination by Pulsed-Field Gel Electrophoresis, Ribotyping, and Multilocus Sequence Typing

    OpenAIRE

    Borucki, Monica K.; Kim, So Hyun; Call, Douglas R.; Smole, Sandra C.; Pagotto, Franco

    2004-01-01

    Listeria monocytogenes can cause serious illness in humans, and subsequent epidemiological investigation requires molecular characterization to allow the identification of specific isolates. L. monocytogenes is usually characterized by serotyping and is subtyped by using pulsed-field gel electrophoresis (PFGE) or ribotyping. DNA microarrays provide an alternative means to resolve genetic differences among isolates, and unlike PFGE and ribotyping, microarrays can be used to identify specific g...

  8. Temporal study of staphylococcal species on the skin of human subjects in isolation and clonal analysis of Staphylococcus capitis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis.

    OpenAIRE

    Maggs, A F; Pennington, T H

    1989-01-01

    The staphylococcal skin floras of an isolated group of subjects were studied for 1 year. A wide variation in isolation patterns was found for different species. Staphylococcus intermedius, previously thought to be of veterinary origin, was found to be part of the resident flora of some subjects, and this may indicate a wider role for it in clinical infection. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis of S. capitis isolates indicated persistent skin coloniza...

  9. Molecular Fingerprinting by PCR-Denaturing Gradient Gel Electrophoresis Reveals Differences in the Levels of Microbial Diversity for Musty-Earthy Tainted Corks ▿

    OpenAIRE

    Prat, Chantal; Ruiz-Rueda, Olaya; Trias, Rosalia; Anticó, Enriqueta; Capone, Dimitra; Sefton, Mark; Bañeras, Lluís

    2009-01-01

    The microbial community structure of cork with marked musty-earthy aromas was analyzed using denaturing gradient gel electrophoresis of amplified ribosomal DNA. Cork stoppers and discs were used for DNA extraction and were analyzed by using selective primers for bacteria and fungi. Stoppers clearly differed from discs harboring a different fungal community. Moreover, musty-earthy samples of both types were shown to have a specific microbiota. The fungi Penicillium glabrum and Neurospora spp. ...

  10. Proteomic analysis of halotolerant proteins under high and low salt stress in Dunaliella salina using two-dimensional differential in-gel electrophoresis

    Directory of Open Access Journals (Sweden)

    Yan-Long Jia

    2016-01-01

    Full Text Available Abstract Dunaliella salina, a single-celled marine alga with extreme salt tolerance, is an important model organism for studying fundamental extremophile survival mechanisms and their potential practical applications. In this study, two-dimensional differential in-gel electrophoresis (2D-DIGE was used to investigate the expression of halotolerant proteins under high (3 M NaCl and low (0.75 M NaCl salt concentrations. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF/TOF MS and bioinformatics were used to identify and characterize the differences among proteins. 2D-DIGE analysis revealed 141 protein spots that were significantly differentially expressed between the two salinities. Twenty-four differentially expressed protein spots were successfully identified by MALDI-TOF/TOF MS, including proteins in the following important categories: molecular chaperones, proteins involved in photosynthesis, proteins involved in respiration and proteins involved in amino acid synthesis. Expression levels of these proteins changed in response to the stress conditions, which suggests that they may be involved in the maintenance of intracellular osmotic pressure, cellular stress responses, physiological changes in metabolism, continuation of photosynthetic activity and other aspects of salt stress. The findings of this study enhance our understanding of the function and mechanisms of various proteins in salt stress.

  11. Pulsed-Field Gel Electrophoresis characterization of Listeria monocytogenes isolates from cheese manufacturing plants in São Paulo, Brazil.

    Science.gov (United States)

    Barancelli, Giovana V; Camargo, Tarsila M; Gagliardi, Natália G; Porto, Ernani; Souza, Roberto A; Campioni, Fabio; Falcão, Juliana P; Hofer, Ernesto; Cruz, Adriano G; Oliveira, Carlos A F

    2014-03-01

    This study aimed to evaluate the occurrence of Listeria monocytogenes in cheese and in the environment of three small-scale dairy plants (A, B, C) located in the Northern region state of São Paulo, Brazil, and to characterize the isolates using conventional serotyping and PFGE. A total of 393 samples were collected and analyzed from October 2008 to September 2009. From these, 136 came from dairy plant A, where only L. seeligeri was isolated. In dairy plant B, 136 samples were analyzed, and L. innocua, L. seeligeri and L. welshimeri were isolated together with L. monocytogenes. In dairy plant C, 121 samples were analyzed, and L. monocytogenes and L. innocua were isolated. Cheese from dairy plants B and C were contaminated with Listeria spp, with L. innocua being found in Minas frescal cheese from both dairy plants, and L. innocua and L. monocytogenes in Prato cheese from dairy plant C. A total of 85 L. monocytogenes isolates were classified in 3 serotypes: 1/2b, 1/2c, and 4b, with predominance of serotype 4b in both dairy plants. The 85 isolates found in the dairy plants were characterized by genomic macrorestriction using ApaI and AscI with Pulsed Field Gel Electrophoresis (PFGE). Macrorestriction yielded 30 different pulsotypes. The presence of indistinguishable profiles repeatedly isolated during a 12-month period indicated the persistence of L. monocytogenes in dairy plants B and C, which were more than 100 km away from each other. Brine used in dairy plant C contained more than one L. monocytogenes lineage. The routes of contamination were identified in plants B and C, and highlighted the importance of using molecular techniques and serotyping to track L. monocytogenes sources of contamination, distribution, and routes of contamination in dairy plants, and to develop improved control strategies for L. monocytogenes in dairy plants and dairy products.

  12. Plasmid profile and pulsed-field gel electrophoresis analysis of Salmonella enterica isolates from humans in Turkey.

    Directory of Open Access Journals (Sweden)

    Kerem Ozdemir

    Full Text Available This study was conducted for typing Salmonella enterica subspecies enterica strains in Turkey using pulsed-field gel electrophoresis (PFGE and plasmid DNA profile analysis. Fourty-two strains were isolated from clinical samples obtained from unrelated patients with acute diarrhea. The samples were collected from state hospitals and public health laboratories located at seven provinces in different regions of Turkey at different times between 2004 and 2010. The strains were determined to belong to 4 different serovars. The Salmonella enterica strains belonged to the serovars Salmonella Enteritidis (n = 23, Salmonella Infantis (n = 14, Salmonella Munchen (n = 2, and Salmonella Typhi (n = 3. Forty-two Salmonella enterica strains were typed with PFGE methods using XbaI restriction enzyme and plasmid analysis. At the end of typing, 11 different PFGE band profiles were obtained. Four different PFGE profiles (type 1, 4, 9, and 10 were found among serotype S. Enteritidis species, 3 different PFGE profiles (type 3, 5, 6 were found among S. Infantis species, 2 different PFGE profiles were found among S. Typhi species (type 2 and 11, and 2 different PFGE profiles were found among S. Munchen species (type 7, 8. The UPGMA dendrogram was built on the PFGE profiles. In this study, it was determined that 4 strains of 42 Salmonella enterica strains possess no plasmid, while the isolates have 1-3 plasmids ranging from 5.0 to 150 kb and making 12 different plasmid profiles (P1-P12. In this study, we have applied the analysis of the PFGE patterns and used bioinformatics methods to identify both inter and intra serotype relationships of 4 frequently encountered serotypes for the first time in Turkey.

  13. Pulsed-field gel electrophoresis analysis of Bordetella pertussis isolates circulating in Europe from 1998 to 2009.

    Science.gov (United States)

    Advani, Abdolreza; Hallander, Hans O; Dalby, Tine; Krogfelt, Karen Angeliki; Guiso, Nicole; Njamkepo, Elisabeth; von Könnig, Carl Heinz Wirsing; Riffelmann, Marion; Mooi, Frits R; Sandven, Per; Lutynska, Anna; Fry, Norman K; Mertsola, Jussi; He, Qiushui

    2013-02-01

    Between 1998 and 2009, Bordetella pertussis clinical isolates were collected during three periods, i.e., 1998 to 2001 (n = 102), 2004 to 2005 (n = 154), and 2007 to 2009 (n = 140), from nine countries with distinct vaccination programs, i.e., Denmark, Finland, France, Germany, The Netherlands, Norway, Poland, Sweden, and the United Kingdom. Pulsed-field gel electrophoresis (PFGE) analysis was performed according to standardized recommendations for epidemiological typing of B. pertussis. There were 81 different PFGE profiles, five of which (BpSR3, BpSR5, BpSR10, BpSR11, and BpSR12) were observed in 61% of the 396 isolates and shown to be predominant in almost all countries. The major profile, BpSR11, showed a decreasing trend from 25% to 30% in 1998 to 2005 to 13% in 2007 to 2009, and there were increases in BpSR3 and BpSR10 from 0% and 8% to 21% and 22%, respectively. One difference between these profiles is that BpSR11 contains isolates harboring the fim3-2 allele and BpSR3 and BpSR10 contain isolates harboring the fim3-1 allele. The total proportion of the five predominant profiles increased from 44% in 1998 to 2001 to 63% in 2004 to 2005 to 70% in 2007 to 2009. In conclusion, common PFGE profiles were identified in B. pertussis populations circulating in European countries with different vaccination programs and different vaccine coverages. These prevalent isolates contain the novel pertussis toxin promoter ptxP3 allele. However, there is evidence for diversifying selection between ptxP3 strains characterized by distinct PFGE profiles. This work shows that, even within a relatively short time span of 10 years, successful isolates which spread through Europe and cause large shifts in B. pertussis populations may emerge.

  14. Comparison of multilocus sequence typing and pulsed-field gel electrophoresis for Salmonella spp. identification in surface water

    Science.gov (United States)

    Kuo, Chun Wei; Hao Huang, Kuan; Hsu, Bing Mu; Tsai, Hsien Lung; Tseng, Shao Feng; Kao, Po Min; Shen, Shu Min; Chou Chiu, Yi; Chen, Jung Sheng

    2013-04-01

    Salmonella is one of the most important pathogens of waterborne diseases with outbreaks from contaminated water reported worldwide. In addition, Salmonella spp. can survive for long periods in aquatic environments. To realize genotypes and serovars of Salmonella in aquatic environments, we isolated the Salmonella strains by selective culture plates to identify the serovars of Salmonella by serological assay, and identify the genotypes by Multilocus sequence typing (MLST) based on the sequence data from University College Cork (UCC), respectively. The results show that 36 stream water samples (30.1%) and 18 drinking water samples (23.3%) were confirmed the existence of Salmonella using culture method combined PCR specific invA gene amplification. In this study, 24 cultured isolates of Salmonella from water samples were classified to fifteen Salmonella enterica serovars. In addition, we construct phylogenetic analysis using phylogenetic tree and Minimum spanning tree (MST) method to analyze the relationship of clinical, environmental, and geographical data. Phylogenetic tree showed that four main clusters and our strains can be distributed in all. The genotypes of isolates from stream water are more biodiversity while comparing the Salmonella strains genotypes from drinking water sources. According to MST data, we can found the positive correlation between serovars and genotypes of Salmonella. Previous studies revealed that the result of Pulsed field gel electrophoresis (PFGE) method can predict the serovars of Salmonella strain. Hence, we used the MLST data combined phylogenetic analysis to identify the serovars of Salmonella strain and achieved effectiveness. While using the geographical data combined phylogenetic analysis, the result showed that the dominant strains were existed in whole stream area in rainy season. Keywords: Salmonella spp., MLST, phylogenetic analysis, PFGE

  15. Serum sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of patients with membranous nephropathy and focal and segmental glomerulosclerosis

    Directory of Open Access Journals (Sweden)

    Pragya Pant

    2016-01-01

    Full Text Available Diagnosis of membranous nephropathy (MN and focal and segmental glomerulo- sclerosis (FSGS needs a renal biopsy, which is an invasive procedure with potentially serious complications. Proteomics may be applied for the development of a biomarker for these diseases which will obviate the need of biopsy. Serum sodium dodecyl sulfate-polyacrylamide gel electro-phoresis (SDS-PAGE analysis gives an idea of the various proteins with different molecular weights (MWs in a given sample. This study was conducted to analyze proteins with different MWs in patients with MN and FSGS and to compare the two groups with regard to their protein profile. This was a comparative, experimental study performed from June 2013 to July 2014 in the Department of Nephrology, Sir Sunderlal Hospital, Banaras Hindu University, Varanasi. Twenty-three histologically diagnosed cases of primary MN and 25 cases of FSGS were included in the study. Patients were categorized as having mild, moderate, and severe proteinuria with 24 h urinary protein levels of <4, 4- 8 and ≥8 g/24 h, respectively. SDS-PAGE analysis was performed by the method of Laemmli and revealed a significantly higher number of patients with FSGS (80% having a protein corresponding to 29 kDa MW, than those with MN (39.1% (P = 0.004. Protein of 5 kDa MW was present in a significantly higher number of patients with moderate (80% and severe (100% proteinuria than those with mild proteinuria (25% (P <0.001. Thus, protein of MW 29 kDa may be a marker for FSGS and needs further characterization. Similarly, 5 kDa protein, present in patients with moderate and severe proteinuria, might be either contributing to or be a marker of severe illness.

  16. Serum sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of patients with membranous nephropathy and focal and segmental glomerulosclerosis.

    Science.gov (United States)

    Pant, Pragya; Singh, R G; Singh, Santosh K; Singh, Vijay P; Doley, Prodip K; Sivasankar, M

    2016-05-01

    Diagnosis of membranous nephropathy (MN) and focal and segmental glomerulo- sclerosis (FSGS) needs a renal biopsy, which is an invasive procedure with potentially serious complications. Proteomics may be applied for the development of a biomarker for these diseases which will obviate the need of biopsy. Serum sodium dodecyl sulfate-polyacrylamide gel electro-phoresis (SDS-PAGE) analysis gives an idea of the various proteins with different molecular weights (MWs) in a given sample. This study was conducted to analyze proteins with different MWs in patients with MN and FSGS and to compare the two groups with regard to their protein profile. This was a comparative, experimental study performed from June 2013 to July 2014 in the Department of Nephrology, Sir Sunderlal Hospital, Banaras Hindu University, Varanasi. Twenty-three histologically diagnosed cases of primary MN and 25 cases of FSGS were included in the study. Patients were categorized as having mild, moderate, and severe proteinuria with 24 h urinary protein levels of <4, 4- 8 and ≥8 g/24 h, respectively. SDS-PAGE analysis was performed by the method of Laemmli and revealed a significantly higher number of patients with FSGS (80%) having a protein corresponding to 29 kDa MW, than those with MN (39.1%) (P = 0.004). Protein of 5 kDa MW was present in a significantly higher number of patients with moderate (80%) and severe (100%) proteinuria than those with mild proteinuria (25%) (P <0.001). Thus, protein of MW 29 kDa may be a marker for FSGS and needs further characterization. Similarly, 5 kDa protein, present in patients with moderate and severe proteinuria, might be either contributing to or be a marker of severe illness.

  17. Monitoring of microbial community structure and succession in the biohydrogen production reactor by denaturing gradient gel electrophoresis (DGGE)

    Institute of Scientific and Technical Information of China (English)

    XING; Defeng; REN; Nanqi; GONG; Manli; LI; Jianzheng; LI; Q

    2005-01-01

    To study the structure of microbial communities in the biological hydrogen production reactor and determine the ecological function of hydrogen producing bacteria, anaerobic sludge was obtained from the continuous stirred tank reactor (CSTR) in different periods of time, and the diversity and dynamics of microbial communities were investigated by denaturing gradient gel electrophoresis (DGGE). The results of DGGE demonstrated that an obvious shift of microbial population happened from the beginning of star-up to the 28th day, and the ethanol type fermentation was established. After 28 days the structure of microbial community became stable, and the climax community was formed. Comparative analysis of 16S rDNA sequences from reamplifying and sequencing the prominent bands indicated that the dominant population belonged to low G+C Gram-positive bacteria (Clostridium sp. And Ethanologenbacterium sp.), β- proteobacteria (Acidovorax sp.), γ-proteobacteria (Kluyvera sp.), Bacteroides (uncultured bacterium SJA-168), and Spirochaetes (uncultured eubacterium E1-K13), respectively. The hydrogen production rate increased obviously with the increase of Ethanologenbacterium sp., Clostridium sp. And uncultured Spirochaetes after 21 days, meanwhile the succession of ethanol type fermentation was formed. Throughout the succession the microbial diversity increased however it decreased after 21 days. Some types of Clostridium sp. Acidovorax sp., Kluyvera sp., and Bacteroides were dominant populations during all periods of time. These special populations were essential for the construction of climax community. Hydrogen production efficiency was dependent on both hydrogen producing bacteria and other populations. It implied that the co-metabolism of microbial community played a great role of biohydrogen production in the reactors.

  18. Monitoring of microbial community structure and succession in the biohydrogen production reactor by denaturing gradient gel electrophoresis (DGGE).

    Science.gov (United States)

    Xing, Defeng; Ren, Nanqi; Gong, Manli; Li, Jianzheng; Li, Qiubo

    2005-04-01

    To study the structure of microbial communities in the biological hydrogen production reactor and determine the ecological function of hydrogen producing bacteria, anaerobic sludge was obtained from the continuous stirred tank reactor (CSTR) in different periods of time, and the diversity and dynamics of microbial communities were investigated by denaturing gradient gel electrophoresis (DGGE). The results of DGGE demonstrated that an obvious shift of microbial population happened from the beginning of star-up to the 28th day, and the ethanol type fermentation was established. After 28 days the structure of microbial community became stable, and the climax community was formed. Comparative analysis of 16S rDNA sequences from reamplifying and sequencing the prominent bands indicated that the dominant population belonged to low G+C Gram-positive bacteria (Clostridium sp. and Ethanologenbacterium sp.), beta-proteobacteria (Acidovorax sp.), gamma-proteobacteria (Kluyvera sp.), Bacteroides (uncultured bacterium SJA-168), and Spirochaetes (uncultured eubacterium E1-K13), respectively. The hydrogen production rate increased obviously with the increase of Ethanologenbacterium sp., Clostridium sp. and uncultured Spirochaetes after 21 days, meanwhile the succession of ethanol type fermentation was formed. Throughout the succession the microbial diversity increased however it decreased after 21 days. Some types of Clostridium sp. Acidovorax sp., Kluyvera sp., and Bacteroides were dominant populations during all periods of time. These special populations were essential for the construction of climax community. Hydrogen production efficiency was dependent on both hydrogen producing bacteria and other populations. It implied that the co-metabolism of microbial community played a great role of biohydrogen production in the reactors.

  19. Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed.

    Science.gov (United States)

    Smalla, K; Wieland, G; Buchner, A; Zock, A; Parzy, J; Kaiser, S; Roskot, N; Heuer, H; Berg, G

    2001-10-01

    The bacterial rhizosphere communities of three host plants of the pathogenic fungus Verticillium dahliae, field-grown strawberry (Fragaria ananassa Duch.), oilseed rape (Brassica napus L.), and potato (Solanum tuberosum L.), were analyzed. We aimed to determine the degree to which the rhizosphere effect is plant dependent and whether this effect would be increased by growing the same crops in two consecutive years. Rhizosphere or soil samples were taken five times over the vegetation periods. To allow a cultivation-independent analysis, total community DNA was extracted from the microbial pellet recovered from root or soil samples. 16S rDNA fragments amplified by PCR from soil or rhizosphere bacterium DNA were analyzed by denaturing gradient gel electrophoresis (DGGE). The DGGE fingerprints showed plant-dependent shifts in the relative abundance of bacterial populations in the rhizosphere which became more pronounced in the second year. DGGE patterns of oilseed rape and potato rhizosphere communities were more similar to each other than to the strawberry patterns. In both years seasonal shifts in the abundance and composition of the bacterial rhizosphere populations were observed. Independent of the plant species, the patterns of the first sampling times for both years were characterized by the absence of some of the bands which became dominant at the following sampling times. Bacillus megaterium and Arthrobacter sp. were found as predominant populations in bulk soils. Sequencing of dominant bands excised from the rhizosphere patterns revealed that 6 out of 10 bands resembled gram-positive bacteria. Nocardia populations were identified as strawberry-specific bands. PMID:11571180

  20. DNA double-strand breaks measured by pulsed-field gel electrophoresis in irradiated lymphocytes from normal humans and those with Alzheimer's disease

    International Nuclear Information System (INIS)

    The authors previously found that radiation-induced chromosome aberrations (dicentrics) are more numerous in lymphocytes from Alzheimer's disease (AD) patients than in those from age-matched normal individuals (Tobi et al. 1990). They have examined double-strand breaks (dsb) produced by gamma-irradiation in the DNA of AD and normal lymphocytes by using pulsed-field gel electrophoresis. The percentage of DNA migrating into the gels is an indirect measure of the number of dsb; DNA content of sequential slices of the gel was assayed by direct fluorometry and the percentage migrating was dose dependent. Results show that the level of damage is similar in AD and normal lymphocytes and preliminary assays of the rate of repair suggest that the half-time is also similar, the value being > 1 h. The latter is consistent with the known rate of rejoining of chromosome fragments in interphase lymphocytes (Pantelias and Maillie 1985). (Author)

  1. Comparison of Virulence Gene Identification, Ribosomal Spacer PCR, and Pulsed-Field Gel Electrophoresis for Typing of Staphylococcus aureus Strains Isolated from Cases of Subclinical Bovine Mastitis in the United States.

    Science.gov (United States)

    Adkins, Pamela R F; Middleton, John R; Fox, Lawrence K

    2016-07-01

    Staphylococcus aureus is one of the most important pathogens causing contagious mastitis in dairy cattle worldwide. The objectives of this study were to determine if recently described S. aureus genotype B was present among previously characterized isolates from cases of bovine intramammary infection in the United States and to compare pulsed-field gel electrophoresis (PFGE) to the combination of ribosomal spacer PCR (RS-PCR) and virulence gene identification for typing of S. aureus strains. The hypothesis was that isolates that were previously characterized as contagious would be identified as genotype B and that the results of the two strain-typing methods would be comparable. Isolates were selected from a collection of S. aureus isolates from eight dairy farms. Mammary quarter milk somatic cell count (SCC) and N-acetyl-β-d-gluconaminidase (NAGase) activity data were known and used to evaluate strain pathogenicity. RS-PCR was performed with conventional gel electrophoresis, and PCR was used for toxin gene identification. RS-PCR patterns were associated with a specific virulence gene pattern, as previously reported. Five RS-PCR banding patterns were identified. None of the isolates were characterized as genotype B. No association between RS-PCR types and milk SCC was found; however, NAGase activity was significantly higher in milk from mammary glands infected with RS-PCR banding type 1 (RSP type 1) than in milk from those infected with RSP type 2. The discriminatory power values were 1.0 and 0.46 for PFGE and RS-PCR, respectively. These data suggest that genotype B may have a limited geographic distribution and that PFGE is more discriminatory than RS-PCR performed with conventional gel electrophoresis for typing of S. aureus isolates of bovine origin.

  2. Comparison of Virulence Gene Identification, Ribosomal Spacer PCR, and Pulsed-Field Gel Electrophoresis for Typing of Staphylococcus aureus Strains Isolated from Cases of Subclinical Bovine Mastitis in the United States.

    Science.gov (United States)

    Adkins, Pamela R F; Middleton, John R; Fox, Lawrence K

    2016-07-01

    Staphylococcus aureus is one of the most important pathogens causing contagious mastitis in dairy cattle worldwide. The objectives of this study were to determine if recently described S. aureus genotype B was present among previously characterized isolates from cases of bovine intramammary infection in the United States and to compare pulsed-field gel electrophoresis (PFGE) to the combination of ribosomal spacer PCR (RS-PCR) and virulence gene identification for typing of S. aureus strains. The hypothesis was that isolates that were previously characterized as contagious would be identified as genotype B and that the results of the two strain-typing methods would be comparable. Isolates were selected from a collection of S. aureus isolates from eight dairy farms. Mammary quarter milk somatic cell count (SCC) and N-acetyl-β-d-gluconaminidase (NAGase) activity data were known and used to evaluate strain pathogenicity. RS-PCR was performed with conventional gel electrophoresis, and PCR was used for toxin gene identification. RS-PCR patterns were associated with a specific virulence gene pattern, as previously reported. Five RS-PCR banding patterns were identified. None of the isolates were characterized as genotype B. No association between RS-PCR types and milk SCC was found; however, NAGase activity was significantly higher in milk from mammary glands infected with RS-PCR banding type 1 (RSP type 1) than in milk from those infected with RSP type 2. The discriminatory power values were 1.0 and 0.46 for PFGE and RS-PCR, respectively. These data suggest that genotype B may have a limited geographic distribution and that PFGE is more discriminatory than RS-PCR performed with conventional gel electrophoresis for typing of S. aureus isolates of bovine origin. PMID:27194685

  3. Database of two-dimensional polyacrylamide gel electrophoresis of proteins labeled with CyDye DIGE Fluor saturation dye.

    Science.gov (United States)

    Fujii, Kazuyasu; Kondo, Tadashi; Yokoo, Hideki; Okano, Tetsuya; Yamada, Masayo; Yamada, Tesshi; Iwatsuki, Keiji; Hirohashi, Setsuo

    2006-03-01

    CyDye DIGE Fluor saturation dye (saturation dye, GE Healthcare Amersham Biosciences) enables highly sensitive 2-D PAGE. As the dye reacts with all reduced cysteine thiols, 2-D PAGE can be performed with a lower amount of protein, compared with CyDye DIGE Fluor minimal dye (GE Healthcare Amersham Biosciences), the sensitivity of which is equivalent to that of silver staining. We constructed a 2-D map of the saturation dye-labeled proteins of a liver cancer cell line (HepG2) and identified by MS 92 proteins corresponding to 123 protein spots. Functional classification revealed that the identified proteins had chaperone, protein binding, nucleotide binding, metal ion binding, isomerase activity, and motor activity. The functional distribution and the cysteine contents of the proteins were similar to those in the most comprehensive 2-D database of hepatoma cells (Seow et al.., Electrophoresis 2000, 21, 1787-1813), where silver staining was used for protein visualization. Hierarchical clustering on the basis of the quantitative expression profiles of the 123 characterized spots labeled with two charge- and mass-matched saturation dyes (Cy3 and Cy5) discriminated between nine hepatocellular carcinoma cell lines and primary cultured hepatocytes from five individuals, suggesting the utility of saturation dye and our database for proteomic studies of liver cancer.

  4. 地衣芽孢杆菌总蛋白双向电泳方法的建立和优化%Establishment and optimization of two-dimensional gel electrophoresis of total proteins from Bacillus lincheniformis

    Institute of Scientific and Technical Information of China (English)

    江慎华; 陈惠; 陈静; 汪涛; 姚中平; 周英棠

    2013-01-01

    探索建立有效的地衣芽孢杆菌蛋白质组双向电泳体系,为进一步揭示地衣芽孢杆菌促进氧化葡萄糖酸杆菌产酸的作用机制奠定基础.以地衣芽孢杆菌为材料,比较蛋白质制备超声破壁时间、新型细胞裂解液、pH梯度和不同上样量对地衣芽孢杆菌蛋白双向电泳结果的影响.结果显示:采用15min超声破壁提取地衣芽孢杆菌总蛋白,选用新型蛋白质裂解,用长24cm、pH4~7的IPG胶条,在上样量为80μg进行等电聚焦,于60V 15min、120V 6h条件下进行SDS-PAGE垂直电泳,可以获得背景清晰、重复性好的双向电泳图谱.在探索出一种新型可行的新型细胞裂解液的同时,建立一套用于地衣芽孢杆菌蛋白质组分析的双向电泳方法.%A two dimensional gel electrophoresis protocol proteomic study of Bacillus lincheniformis and offer further information how Bacillus cereus stimulate the growth of Gluconobacter oxydans to produce 2-keto-L-gulonic acid (2-KLG) after entering into stationary phase was established.Different parameters,including protein preparation by different ultrasonic broken time,new type lysis,pH gradient and different sample of Bacillus lincheniformis protein,were used to evaluate the effect of two-dimensional electrophoresis of Bacillus lincheniformis proteins.Results showed that the clear background and reproducibility of two dimensional gel electrophoresis were established on the condition of using 15min of ultrasonic broken extraction,selection of protein cleavage I,pH4~7 24cm IPG strips,80 μg loading volume,isoelectric focus at 60V 15min,120V 6h.The aim of this study was not only to explore a novel cell lysate in two-dimensional gel electrophoresis,but also to establish a method of proteome analysis for two-dimensional electrophoresis of Bacillus licheniformis.

  5. Pulsed Field Gel Electrophoresis (PFGE: a DNA finger printing technique to study the genetic diversity of blood disease bacterium of banana

    Directory of Open Access Journals (Sweden)

    HADIWIYONO

    2011-01-01

    Full Text Available Hadiwiyono, Widada J, Subandiyah S, Fegan F (2011 Pulsed Field Gel Electrophoresis (PFGE: a DNA finger printing technique to study the genetic diversity of blood disease bacterium of banana. Biodiversitas 12: 12-16. Blood disease bacterium (BDB is the most important pathogen of bananas in Indonesia. In some field, the disease incidence reaches over 80%. Epidemiologically, the disease is similar to moko disease in South America and bugtok disease in the Philippines caused by Ralstonia solanacearum race 2. However, BDB is different in phenotype and genotype from the two diseases. Previously BDB was limited in South Sulawesi since 1920s – 1980s and recently was reported in 27 of 30 provinces in Indonesia. Pulsed-Field Gel Electrophoresis (PFGE is a genomic DNA fingerprinting method, which employs rare cutting restriction endonucleases to digest genome prior to electrophoresis using specialized condition to separate of large DNA fragments. The results showed that PFGE analysis was a discriminative tool to study the genetic diversity of BDB. Based on the PFGE analysis, BDB isolates obtained from different localities in Yogyakarta and Central Java were quit diverse.

  6. Shigella sonnei biotype g carrying class 2 integrons in southern Italy: a retrospective typing study by pulsed field gel electrophoresis

    Directory of Open Access Journals (Sweden)

    Romani Cristina

    2006-07-01

    Full Text Available Abstract Background Emergence and global dissemination of multiresistant strains of enteric pathogens is a very concerning problem from both epidemiological and Public Health points of view. Shigella sonnei is the serogroup of Shigella most frequently responsible for sporadic and epidemic enteritis in developed countries. The dissemination is associated most often to human to human transmission, but foodborne episodes have also been described. In recent years the circulation of multiresistant strains of S. sonnei biotype g carrying a class 2 integron has been reported in many countries worldwide. In southern Italy a strain with similar properties has been responsible for a large community outbreak occurred in 2003 in Palermo, Sicily. The objective of this study was to date the emergence of the biotype g strain carrying the class 2 integron in southern Italy and to evaluate the genetic heterogeneity of biotype g S. sonnei isolated throughout an extended interval of time. Methods A total of 31 clinical isolates of S. sonnei biotype g identified in southern Italy during the years 1971–2000 were studied. The strains were identified at the serogroup level, characterized by biochemical tests and submitted to antimicrobial susceptibility testing. Molecular typing was performed by pulsed field gel electrophoresis (PFGE after digestion of DNA by XbaI. Carriage of class 2 integrons was investigated by polymerase chain reaction (PCR with specific primers and confirmed by restriction endonuclease analysis of amplicons. Results The 15 isolates of S. sonnei biotype g identified in the decade 1971–1980 showed highly heterogeneous drug resistance profiles and pulsotypes. None of the isolates was simultaneous resistant to streptomycin and trimethoprim and none was class 2 integron positive. On the contrary, this resistance phenotype and class 2 integron carriage were very common among the 16 strains of biotype g identified in the following two decades

  7. Population Genetic Structure of Listeria monocytogenes Strains as Determined by Pulsed-Field Gel Electrophoresis and Multilocus Sequence Typing

    Science.gov (United States)

    Henri, Clémentine; Félix, Benjamin; Guillier, Laurent; Leekitcharoenphon, Pimlapas; Michelon, Damien; Mariet, Jean-François; Aarestrup, Frank M.; Mistou, Michel-Yves; Hendriksen, René S.

    2016-01-01

    ABSTRACT Listeria monocytogenes is a ubiquitous bacterium that may cause the foodborne illness listeriosis. Only a small amount of data about the population genetic structure of strains isolated from food is available. This study aimed to provide an accurate view of the L. monocytogenes food strain population in France. From 1999 to 2014, 1,894 L. monocytogenes strains were isolated from food at the French National Reference Laboratory for L. monocytogenes and classified according to the five risk food matrices defined by the European Food Safety Authority (EFSA). A total of 396 strains were selected on the basis of different pulsed-field gel electrophoresis (PFGE) clusters, serotypes, and strain origins and typed by multilocus sequence typing (MLST), and the MLST results were supplemented with MLST data available from Institut Pasteur, representing human and additional food strains from France. The distribution of sequence types (STs) was compared between food and clinical strains on a panel of 675 strains. High congruence between PFGE and MLST was found. Out of 73 PFGE clusters, the two most prevalent corresponded to ST9 and ST121. Using original statistical analysis, we demonstrated that (i) there was not a clear association between ST9 and ST121 and the food matrices, (ii) serotype IIc, ST8, and ST4 were associated with meat products, and (iii) ST13 was associated with dairy products. Of the two major STs, ST121 was the ST that included the fewest clinical strains, which might indicate lower virulence. This observation may be directly relevant for refining risk analysis models for the better management of food safety. IMPORTANCE This study showed a very useful backward compatibility between PFGE and MLST for surveillance. The results enabled better understanding of the population structure of L. monocytogenes strains isolated from food and management of the health risks associated with L. monocytogenes food strains. Moreover, this work provided an accurate view

  8. Vibrational spectroscopy and electrophoresis as a "golden means" in monitoring of polysaccharides in medical plant and gels

    Science.gov (United States)

    Pielesz, A.

    In recent years, some bioactive polysaccharides isolated from natural sources have attracted much attention in the field of biochemistry and pharmacology. Of them, polysaccharides or their glycoconjugates were shown to exhibit multiple biological activities including anticarcinogenic, anticoagulant, immunostimulating, antioxidant, etc. Pharmacotherapy using plant-derived substances can be currently regarded as a very promising future alternative to conventional therapy. The advanced biotechnologies available today enable chemical investigation of well-defined bioactive plant components as sources of novel drugs. The need for safer drugs without side effects has led to the use of natural ingredients with proven safety. Special interest is focused on plant polysaccharides. This article attempts to review the current structural and conformational characterization of some importantly bioactive monosaccharides isolated from following plant cell-wall: Symphytum officinale (comfrey), Thymus pulegioides (thyme), Trigonella foenum-graecum L. (fenugreek), Tussilago farfara L. (coltsfoot), Hyssopus officinalis (hyssop), Althaea officinalis L. (marshmallow) and Equisetum arvense L. (horsetail). The chemical structures of monosaccharides were analysed using FTIR and Raman spectroscopies as well as cellulose acetate membrane electrophoresis (CAE). The dried plant samples were gently hydrolysed with sulphuric acid. The presence of glucuronic acid, galacturonic acid, alginic acid, glucose, mannose and xylose in the hydrolysates of reference substances and non-defatted plant films was proved. The possibility of a taxonomic classification of plant cell walls based on infrared and Raman spectroscopies and the use of spectral fingerprinting for authentication and detection of adulteration of products rich in cell-wall materials are discussed. Individual bands were selected to monitor the sugar content in medical plant cell walls and to confirm the identity of the analysed plants.

  9. Native gel analysis of macromolecular protein complexes in cultured mammalian cells.

    Science.gov (United States)

    Munawar, Nayla; Olivero, Giorgio; Jerman, Emilia; Doyle, Benjamin; Streubel, Gundula; Wynne, Kieran; Bracken, Adrian; Cagney, Gerard

    2015-11-01

    Native gel electrophoresis enables separation of cellular proteins in their non-denatured state. In experiments aimed at analysing proteins in higher order or multimeric assemblies (i.e. protein complexes) it offers some advantages over rival approaches, particularly as an interface technology with mass spectrometry. Here we separated fractions from HEK293 cells by native electrophoresis in order to survey protein complexes in the cytoplasmic, nuclear and chromatin environments, finding 689 proteins distributed among 217 previously described complexes. As expected, different fractions contained distinct combinations of macromolecular complexes, with subunits of the same complex tending to co-migrate. Exceptions to this observation could often be explained by the presence of subunits shared among different complexes. We investigated one identified complex, the Polycomb Repressor Complex 2 (PRC2), in more detail following affinity purification of the EZH2 subunit. This approach resulted in the identification of all previously reported members of PRC2. Overall, this work demonstrates that the use of native gel electrophoresis as an upstream separating step is an effective approach for analysis of the components and cellular distribution of protein complexes. PMID:26223664

  10. An accurate determination of human grawth hormone content in different pituitary extracts, using a radioimmunoassay with polyacrylamide gel electrophoresis as a bound-free separation system

    International Nuclear Information System (INIS)

    Human growth hormone was extracted and purified according to the method of Roos et al. A first control of its purification and integrity was performed through molecular weight determination by gel filtration on Sephadex G-100 and on plyacrylamide gel electrophoresis (PAGE). Its biological activity was confirmed by the growth promoted in non-hypophysectomized rats at plateau. The main object, however, was the setting up of an accurate, reproducible method that could furnish the more absolute and comparable value of rafioimmunoassayable HGH content in perfect agreement with the results obtained by other laboratories. This was accomplished through a radioimmunoassay system that uses HGH labelled with 125I, where the separation of the bound from the free antigen is achieved on polyacrylamide gel electrophoresis, by a modification introduced in the original method of Davis. The resulting values, extremely close to that stated by the KABI-Laboratories (Stockolm), through obtained in quite different conditions of incubation, antibody concentration and with no use of second antibody, represent a confident approach to a comparable measure of this hormone in extract, which can also be applied to plasma determinations

  11. Characterization of wild-type human medium-chain acyl-CoA dehydrogenase (MCAD) and mutant enzymes present in MCAD-deficient patients by two-dimensional gel electrophoresis

    DEFF Research Database (Denmark)

    Bross, P; Jensen, T G; Andresen, B S;

    1994-01-01

    Two-dimensional gel electrophoresis was used to study and compare wild-type medium-chain acyl-CoA dehydrogenase (MCAD; EC 1.3.99.3) and mis-sense mutant enzyme found in patients with MCAD deficiency. By comparing the patterns for wild-type and mutant MCAD expressed in Escherichia coli or in eukar......Two-dimensional gel electrophoresis was used to study and compare wild-type medium-chain acyl-CoA dehydrogenase (MCAD; EC 1.3.99.3) and mis-sense mutant enzyme found in patients with MCAD deficiency. By comparing the patterns for wild-type and mutant MCAD expressed in Escherichia coli...... of one aspartic acid residue per monomer. Comparison of pulse labeling and steady-state amounts of MCAD protein in overexpressing COS-7 cells confirms that K304E MCAD is synthesized and transported into mitochondria in amounts similar to the wild-type protein, but is degraded much more readily. For wild...

  12. DNA double-strand break rejoining in radioadapted human lymphocytes: evaluation by neutral comet assay and pulse-field gel electrophoresis

    International Nuclear Information System (INIS)

    Adaptive response (AR), an enhanced resistance to a high dose of ionising radiation acquired after pretreatment with a very low dose, was estimated in normal human lymphocytes. The question posed was whether the extent of radioadaptation, assessed by micronucleus test, would be related to the rate of DNA double-strand break (DSB) rejoining. Phytohemagglutinin-stimulated G1-lymphocytes from 5 healthy male volunteers were pre-treated (or not) with an adaptive (5 cGy) dose of X-rays, followed by a higher (5 or 10 Gy) challenge dose after 20-22 h. DSB rejoining after the challenge dose was monitored with the use of two methods: neutral comet assay, modified to reduce the contribution of singlestrand breaks (SSBs) and thermolabile sites, and pulse-field gel electrophoresis (PFGE), specific for DSBs. At the level of micronuclei, an AR was observed in lymphocytes of 3 of 5 donors. Up to 60 min, comet assay showed no statistically significant differences in DNA break rejoining between adapted and non-adapted lymphocytes, independently of AR appearance. PFGE gave similar results, although in three donors it revealed secondary increases in DSBs levels at 30 min and/or 60 min post-irradiation in the adapted vs. the non-adapted samples. Failure to demonstrate changes in DSBs rejoining rate in the adapted lymphocytes could be due to diversity of AR intensity/timing at the level of DNA repair in not fully homogenous cell populations. Also, '' rare '' DNA cuts characteristic of early apoptosis/necrosis could overlap the process of DNA break rejoining. (authors)

  13. Transcription factor proteomics: identification by a novel gel mobility shift-three-dimensional electrophoresis method coupled with southwestern blot and high-performance liquid chromatography-electrospray-mass spectrometry analysis.

    Science.gov (United States)

    Jiang, Daifeng; Jia, Yinshan; Jarrett, Harry W

    2011-09-28

    Transcription factor (TF) purification and identification is an important step in elucidating gene regulatory mechanisms. In this study, we present two new electrophoretic mobility shift assay (EMSA)-based multi-dimensional electrophoresis approaches to isolate and characterize TFs, using detection with either southwestern or western blotting and HPLC-nanoESI-MS/MS analysis for identification. These new techniques involve several major steps. First, EMSA is performed with agents that diminish non-specific DNA-binding and the DNA-protein complex is separated by native PAGE gel. The gel is then electrotransferred to PVDF membrane and visualized by autoradiography. Next, the DNA-protein complex, which has been transferred onto the blot, is extracted using a detergent-containing elution buffer. Following detergent removal, concentrated extract is separated by SDS-PAGE (EMSA-2DE), followed by in-gel trypsin digestion and HPLC-nanoESI-MS/MS analysis, or the concentrated extract is separated by two-dimensional gel electrophoresis (EMSA-3DE), followed by southwestern or western blot analysis to localize DNA binding proteins on blot which are further identified by on-blot trypsin digestion and HPLC-nanoESI-MS/MS analysis. Finally, the identified DNA binding proteins are further validated by EMSA-immunoblotting or EMSA antibody supershift assay. This approach is used to purify and identify GFP-C/EBP fusion protein from bacterial crude extract, as well as purifying AP1 and CEBP DNA binding proteins from a human embryonic kidney cell line (HEK293) nuclear extract. AP1 components, c-Jun, Jun-D, c-Fos, CREB, ATF1 and ATF2 were successfully identified from 1.5 mg of nuclear extract (equivalent to 3×10(7) HEK293 cells) with AP1 binding activity of 750 fmol. In conclusion, this new strategy of combining EMSA with additional dimensions of electrophoresis and using southwestern blotting for detection proves to be a valuable approach in the identification of transcriptional complexes

  14. Recent advances in preparative electrophoresis

    Science.gov (United States)

    Mosher, Richard A.; Thormann, Wolfgang; Egen, Ned B.; Couasnon, Pascal; Sammons, David W.

    1987-01-01

    Various approaches for preparative electrophoresis, and three new instruments for preparative electrophoresis are discussed. Consideration is given to isoelectric focusing, isotachophoresis, and zone electrophoresis, three gel-based electrophoresis methods. The design, functions, and performance of the Elphor VaP 21 device of Hannig (1982), the shear-stabilized BIOSTREAM separator of Thompson (1983), and the recycling isoelectric focusing device are described.

  15. Investigation and Comparison of Leishmania major Promastigote and Amastigote Protein Content by Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis

    Directory of Open Access Journals (Sweden)

    S. Soleimanifard

    2013-04-01

    Full Text Available ntroduction & Objective: Leishmania is a protozoan of the trypanosomatidae family. This pro-tozoan has two stages in its life cycle, promastigote form in sand flies and amastigote form in macrophage of mammalian hosts. The purpose of this study was identification and compari-son of proteins of Leishmania amastigote and promastigote stages. Materials & Methods: The present study is a cross sectional study of two forms of Leishmania major. To culture promastigotes , L.major (MRHO/IR/75/ER from previously infected Balb/c mice was transferred to modified N.N.N medium with overlay of liquid BHI and then transferred to RPMI-1640 at 26oc ± 1 for mass production. After isolation and growth, pro-mastigotes were transferred to liquid cell culture medium RPMI-1640 with pH 5.5 and incu-bated at 5% CO2 at 37oc for 72 hours until promastigote to amastigote transformation. Elec-trophoresis was performed with SDS-PAGE method to find and compare the molecular weight of the antigens of two stages. Results: The molecular weights of the bands observed in both forms were as follows: 19, 36, 50, 63, 65, 80, 90, 94, 96, 110- 130 KDa. The proteins in the surface of only promastigote were 22, 28 and 46 KDa and special proteins in the surface of amastigote were 12 and 32 KDa. Conclusion : According to this study Leishmania parasite has stage specific proteins. Various studies have shown that axenic amastigotes and tissue amastigotes are similar in their protein content. Therefore, based on stage specific proteins ,effective drugs and vaccines can be de-signed against leishmaniasis. (Sci J Hamadan Univ Med Sci 2013; 20 (1:1-8

  16. Tracing outbreaks of Streptococcus equi infection (strangles) in horses using sequence variation in the seM gene and pulsed-field gel electrophoresis.

    Science.gov (United States)

    Lindahl, Susanne; Söderlund, Robert; Frosth, Sara; Pringle, John; Båverud, Viveca; Aspán, Anna

    2011-11-21

    Strangles is a serious respiratory disease in horses caused by Streptococcus equi subspecies equi (S. equi). Transmission of the disease occurs by direct contact with an infected horse or contaminated equipment. Genetically, S. equi strains are highly homogenous and differentiation of strains has proven difficult. However, the S. equi M-protein SeM contains a variable N-terminal region and has been proposed as a target gene to distinguish between different strains of S. equi and determine the source of an outbreak. In this study, strains of S. equi (n=60) from 32 strangles outbreaks in Sweden during 1998-2003 and 2008-2009 were genetically characterized by sequencing the SeM protein gene (seM), and by pulsed-field gel electrophoresis (PFGE). Swedish strains belonged to 10 different seM types, of which five have not previously been described. Most were identical or highly similar to allele types from strangles outbreaks in the UK. Outbreaks in 2008/2009 sharing the same seM type were associated by geographic location and/or type of usage of the horses (racing stables). Sequencing of the seM gene generally agreed with pulsed-field gel electrophoresis profiles. Our data suggest that seM sequencing as a epidemiological tool is supported by the agreement between seM and PFGE and that sequencing of the SeM protein gene is more sensitive than PFGE in discriminating strains of S. equi.

  17. Assessment of the yeast species composition of cocoa bean fermentations in different cocoa-producing regions using denaturing gradient gel electrophoresis.

    Science.gov (United States)

    Papalexandratou, Zoi; De Vuyst, Luc

    2011-11-01

    The yeast species composition of 12 cocoa bean fermentations carried out in Brazil, Ecuador, Ivory Coast and Malaysia was investigated culture-independently. Denaturing gradient gel electrophoresis of 26S rRNA gene fragments, obtained through polymerase chain reaction with universal eukaryotic primers, was carried out with two different commercial apparatus (the DCode and CBS systems). In general, this molecular method allowed a rapid monitoring of the yeast species prevailing during fermentation. Under similar and optimal denaturing gradient gel electrophoresis conditions, the CBS system allowed a better separated band pattern than the DCode system and an unambiguous detection of the prevailing species present in the fermentation samples. The most frequent yeast species were Hanseniaspora sp., followed by Pichia kudriavzevii and Saccharomyces cerevisiae, independent of the origin of the cocoa. This indicates a restricted yeast species composition of the cocoa bean fermentation process. Exceptionally, the Ivorian cocoa bean box fermentation samples showed a wider yeast species composition, with Hyphopichia burtonii and Meyerozyma caribbica among the main representatives. Yeasts were not detected in the samples when the temperature inside the fermenting cocoa pulp-bean mass reached values higher than 45 °C or under early acetic acid production conditions.

  18. Species identification of cooked fish by urea isoelectric focusing and sodium dodecylsulfate polyacrylamide gel electrophoresis : a collaborative study

    DEFF Research Database (Denmark)

    Rehbein, H.; Kundiger, R.; Yman, I.M.;

    1999-01-01

    The suitability and reliability of urea IEF and SDS-PAGE for the identification of cooked fish flesh was tested by a collaborative study among nine laboratories. Urea IEF was performed with CleanGels as well as with ImmobilineGels, and ExcelGels were used for SDS-PAGE, enabling all three types of...... was incorrect, and with SDS-PAGE a similar result was obtained. It was concluded that methods, as now developed, are suitable for checking the species declaration of fishery products. (C) 1999 Elsevier Science Ltd. All rights reserved...

  19. Assay of Histamine in Single Mast Cells by Capillary Zone Electrophoresis with Electrochemical Detection

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Capillary zone electrophoresis was employed for the analysis of histamine in single rat peritoneal mast cells using an amperometric detector. In this method, individual mast cells and then 0.02 mol/L NaOH as a lysing solution are injected into the front end of the separation capillary. A cell injector was constructed for easy injection of single cells. Histamine in single mast cells has been identified and quantified.

  20. Efficient extraction of proteins from recalcitrant plant tissue for subsequent analysis by two-dimensional gel electrophoresis.

    Science.gov (United States)

    Parkhey, Suruchi; Chandrakar, Vibhuti; Naithani, S C; Keshavkant, S

    2015-10-01

    Protein extraction for two-dimensional electrophoresis from tissues of recalcitrant species is quite problematic and challenging due to the low protein content and high abundance of contaminants. Proteomics in Shorea robusta is scarcely conducted due to the lack of a suitable protein preparation procedure. To establish an effective protein extraction protocol suitable for two-dimensional electrophoresis in Shorea robusta, four procedures (borate buffer/trichloroacetic acid extraction, organic solvent/trichloroacetic acid precipitation, sucrose/Tris/phenol, and organic solvent/phenol/sodium dodecyl sulfate) were evaluated. Following these, proteins were isolated from mature leaves and were analyzed for proteomics, and also for potential contaminants, widely reported to hinder proteomics. The borate buffer/trichloroacetic acid extraction had the lowest protein yield and did not result in any banding even in one-dimensional electrophoresis. In contrast, organic solvent/phenol/sodium dodecyl sulfate extraction allowed the highest protein yield. Moreover, during proteomics, organic solvent/phenol/sodium dodecyl sulfate extracted protein resolved the maximum number (144) of spots. Further, when proteins were evaluated for contaminants, significant (77-95%) reductions in the nucleic acids, phenol, and sugars were discernible with refinement in extraction procedure. Accumulated data suggested that the organic solvent/phenol/sodium dodecyl sulfate extraction was the most effective protocol for protein isolation for proteomics of Shorea robusta and can be used for plants that have a similar set of contaminants. PMID:26257211

  1. Comet-electrophoresis assay as a method for determining radiosensitivities of tumor cells

    International Nuclear Information System (INIS)

    Objective: To explore the feasibility of applying comet-electrophoresis to determining the radiosensitivity of tumor cells. Methods: The residual rates of DNA damage at 30 minute after 2 Gy gamma irradiation in four human tumor cell lines (WM9839, KB, LS-T-117, PC3M) were determined with the comet assay. The cell survival fraction of tumor cell after 2 Gy gamma ray-irradiation was determined with clonogenic assay. Results: There were good correlations between cell survival fraction (SF2 ) and residual rate of DNA damage at 30 minute after 2 Gy gamma ray-irradiation in these four human tumor cell lines, separately. Conclusion: The comet-electrophoresis assay may be used as a repaid and sensitive method for determining inherent radiosensitivities of tumor cells

  2. Serum proteins analysis by capillary electrophoresis

    OpenAIRE

    Uji, Yoshinori; Okabe, Hiroaki

    2001-01-01

    The purpose of this study was to evaluate the efficacy of multi-capillary electrophoresis instrument in clinical laboratory. An automated clinical capillary electrophoresis system was evaluated for performing serum proteins electrophoresis and immuno-fixation electrophoresis by subtraction. In this study the performance of capillary electrophoresis was compared with the cellulose acetate membrane electrophoresis and agarose gel immunofixation electrophoresis for serum proteins. The results of...

  3. Studies on middle silkgland proteins of cocoon colour sex-limited silkworm (Bombyx mori L.) using two-dimensional polyacrylamide gel electrophoresis

    Indian Academy of Sciences (India)

    Yuan-Xiang Jin; Yu-Yin Chen; Meng-Kui Xu; Yong-Huang Jiang

    2004-03-01

    Qualitative and quantitative differences in proteins expressed in the middle silkglands of male and female silkworm larvae that differ in silk colour were investigated by high resolution two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), followed by computer assisted image analysis. About 1000 protein spots were resolved in both the sexes and most proteins were shown to be distributed in the area from 15 kDa to 70 kDa and pH 4–8. It was found that some proteins displayed higher expression in yellow cocoon, while two proteins were only expressed in female silkworm silkgland tissue through the comparison and analysis by two-D software. These proteins especially existed in female silkworm middle silkgland tissue of yellow cocoon. Furthermore, these proteins might be involved in the expression of cocoon colour phenotype.

  4. Characterization of bacterial populations in Danish raw milk cheeses made with different starter cultures by denaturating gradient gel electrophoresis and pyrosequencing

    DEFF Research Database (Denmark)

    Masoud, Wafa Mahmoud Hasan; Takamiya, Monica K Wik; Vogensen, Finn Kvist;

    2011-01-01

    The bacterial populations in Danish raw milk cheeses were identified using denaturating gradient gel electrophoresis (DGGE) of PCR amplicons of the V3 region of the 16S rRNA gene and pyrosequencing of tagged amplicons of the V3 and V4 regions of the 16S rRNA gene. Both DNA and RNA extracted from...... cheeses were studied in order to determine the metabolically active bacteria. The main bacteria, which included Lactococcus, Lactobacillus and Streptococcus, were detected by pyrosequencing and DGGE in both 16S rDNA and cDNA obtained from cheeses indicating their viability and contribution to cheese...... ripening. Other bacteria like Corynebacterium, Halomonas, Pediococcus, Micrococcus and Staphylococcus, which were encountered in some cheese samples at low percentages compared with the total bacterial populations, were only detected by pyrosequencing. 16S rRNA gene pyrosequencing is an efficient method...

  5. Analysis of phosphate-accumulating organisms cultivated under different carbon sources with polymerase chain reaction-denaturing gradient gel electrophoresis assay

    Institute of Scientific and Technical Information of China (English)

    YU Shui-li; LIU Ya-nan; JING Guo-lin; ZHAO Bing-jie; GUO Si-yuan

    2005-01-01

    To investigate the microbial communities of microorganisms cultivated under different carbon sources, three sequencing batch reactors were operated. They were supplied with sewage, glucose and sodium acetate as carbon sources respectively and showed high phosphorus removal performance. The results of denaturing gradient gel electrophoresis(DGGE) of polymerase chain reaction-amplified (PCR) 16S rDNA fragments demonstrated that β-protebacteria, Actinomyces sp. and γ-protebacteria only exited in 1 # reactor. The microbiological diversity of 1 # reactor exceeded the other two reactors. Flavobacterium, Bacillales, Actinomyces, Actinobacteridae and uncultured bacteria(AF527584, AF502204, AY592749, AB076862, AJ619051, AF495454 and AY133070) could be detected in the biological phosphorus removal reactors.

  6. Characterization of Sm14 related components in different helminths by sodium dodecyl sulphate-polyacrylamide gel electrophoresis and Western blotting analysis

    Directory of Open Access Journals (Sweden)

    Nilton Thaumaturgo

    2002-10-01

    Full Text Available Sm14 was the first fatty acid-binding protein homologue identified in helminths. Thereafter, members of the same family were identified in several helminth species, with high aminoacid sequence homology between them. In addition, immune crossprotection was also reported against Fasciola hepatica infection, in animals previously immunized with the Schistosoma mansoni vaccine candidate, r-Sm14. In the present study, data on preliminary sodium dodecyl sulphate-polyacrylamide gel electrophoresis and Western blotting analysis of nine different helminth extracts focusing the identification of Sm14 related proteins, is reported. Out of these, three extracts - Ascaris suum (males and females, Echinostoma paraensei, and Taenia saginata - presented components that comigrated with Sm14 in SDS-PAGE, and that were recognized by anti-rSm14 policlonal serum, in Western blotting tests.

  7. Protein composition of wheat gluten polymer fractions determined by quantitative two-dimensional gel electrophoresis and tandem mass spectrometry

    Science.gov (United States)

    Flour proteins from the US bread wheat Butte 86 were extracted in 0.5% SDS using a two-step procedure with and without sonication and further separated by size exclusion chromatography into monomeric and polymeric fractions. Proteins in each fraction were analyzed by quantitative two-dimensional gel...

  8. Type I collagen gel protects murine fibrosarcoma L929 cells from TNFα-induced cell death

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Hong-Ju; He, Wen-Qi; Chen, Ling; Liu, Wei-Wei; Xu, Qian; Xia, Ming-Yu; Hayashi, Toshihiko [China-Japan Research Institute of Medical and Pharmaceutical Sciences, Shenyang Pharmaceutical University, Shenyang 110016 (China); Fujisaki, Hitomi; Hattori, Shunji [Nippi Research Institute of Biomatrix, Toride, Ibaraki 302-0017 (Japan); Tashiro, Shin-ichi [Institute for Clinical and Biomedical Sciences, Kyoto 603-8072 (Japan); Onodera, Satoshi [Department of Clinical and Pharmaceutical Sciences, Showa Pharmaceutical University, Tokyo 194-8543 (Japan); Ikejima, Takashi, E-mail: ikejimat@vip.sina.com [China-Japan Research Institute of Medical and Pharmaceutical Sciences, Shenyang Pharmaceutical University, Shenyang 110016 (China)

    2015-02-20

    Murine fibrosarcoma L929 cells have been used to test efficacy of proinflammatory cytokine TNFα. In the present study, we reported on protective effect of type I collagen gel used as L929 cell culture. L929 cell grew and proliferated well on collagen gel. However, the L929 cells exhibited cobblestone-like morphology which was much different from the spread fusiform shape when cultured on conventional cell dishes as well as the cells tended to aggregate. On conventional cell culture dishes, the cells treated with TNFα became round in shape and eventually died in a necroptotic manner. The cells cultured on collagen gel, however, were completely unaffected. TNFα treatment was reported to induce autophagy in L929 cells on the plastic dish, and therefore we investigated the effect of collagen gel on induction of autophagy. The results indicated that autophagy induced by TNFα treatment was much reduced when the cells were cultured on collagen gel. In conclusion, type I collagen gel protected L929 cell from TNFα-induced cell death. - Highlights: • Collagen gel culture changed the morphology of L929 cells. • L929 cell cultured on collagen gel were resistant to TNFα-induced cell death. • Collagen gel culture inhibited TNFα-induced autophagy in L929 cells.

  9. Polyclonal infections due to Mycobacterium avium complex in patients with AIDS detected by pulsed-field gel electrophoresis of sequential clinical isolates.

    Science.gov (United States)

    Slutsky, A M; Arbeit, R D; Barber, T W; Rich, J; von Reyn, C F; Pieciak, W; Barlow, M A; Maslow, J N

    1994-01-01

    Invasive infection with organisms of the Mycobacterium avium complex (MAC) is common among patients with advanced human immunodeficiency virus infection. In previous studies, we analyzed multiple individual colonies of MAC isolated from specimens obtained at the same time and observed that 14 to 20% of patients are simultaneously infected with more than one strain. In this study, we examined sequential isolates from 12 patients with AIDS who had two or more MAC isolates available from clinical specimens collected more than 1 week apart; the intervals between the first and last specimens ranged from 8 to 192 (median, 46) days. For each isolate, restriction digests of genomic DNA were analyzed by pulsed-field gel electrophoresis; DNA was prepared by using a protocol, described here in detail, which had been optimized for conditions of bacterial growth and lysis. The pulsed-field gel electrophoresis analysis identified four patients (33%) infected with two different MAC strains. Both M. avium and M. intracellulare were cultured from blood specimens from two patients. In each of the four patients, the second strain was identified from a culture taken within 14 days of the initial study isolate, and in three of these patients, the first strain was detected again in a subsequent culture. These observations suggest that the presence of two different strains among isolates from sequential cultures may reflect ongoing polyclonal infection. We conclude that polyclonal infection with MAC is common among patients with AIDS. The identification of such infections may be critical in the development of effective treatments. Images PMID:7929773

  10. [Urine protein analysis with the sodium-dodecyl-sulfate-polyacrylamide gel-electrophoresis (SDS-PAGE) in healthy cats and cats with kidney diseases].

    Science.gov (United States)

    Meyer-Lindenberg, A; Wohlsein, P; Trautwein, G; Nolte, I

    1997-03-01

    In this investigation, the value of urine protein analysis by means of molecular-weight related sodium dodecyl-polyacryl gradient gel electrophoresis (SDS-PAGE) was examined with regard to its applicability and diagnostic significance in nephropathy in the cat. A total of 87 cats was included in the study, 30 of them that were clinically healthy served as the control group. The urine protein pattern of this group had, besides the band representing the market albumin, and additional broad band within the size of the marker transferrin. In some cases, weak bands were present within the range of the Tamm-Horsfall-protein and immunoglobulin G. Micromolecular protein bands were not demonstrable. The remaining 57 animals had a histologically proven nephropathy. Thirty-eight cats had elevated urea and/or creatinine values in the plasma (group 1), and 19 animals had values within the reference range (group 2). The urine protein pattern as evidenced by SDS-urine electrophoresis was altered in all cats with histologically proven nephropathy, and it is thus concluded that with this technique a nephropathy can be diagnosed very early and prior to changes of plasma urea and creatinine (group 2). Moreover, in most of the cases, the nephrological changes can be classified as glomerular or tubulo-interstitial (group 1 and group 2). However, it is not possible to draw exact conclusions concerning the underlying morphological changes, nor can the severity of the disease be correctly assessed. PMID:9123982

  11. Identification of proteins of human colorectal carcinoma cell line SW480 by two-dimensional electrophoresis and MALDI-TOF mass spectrometry

    Institute of Scientific and Technical Information of China (English)

    Ying-Tao Zhang; Yi-Ping Geng; Le Zhou; Bao-Chang Lai; Lv-Sheng Si; Yi-Li Wang

    2005-01-01

    AIM: To conduct the proteomic analysis of human colorectal carcinoma cell line, SW480 by using two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption /ionization-time of flight mass spectrometry (MALDITOFMS).METHODS: The total proteins of human colorectal carcinoma cell line, SW480 were separated with 2-DE by using immobilized pH gradient strips and visualized by staining with silver nitrate. The gel images were acquired by scanner and 2-DE analysis software, Image Master 2D Elite. Nineteen distinct protein spots were excised from gel randomly and digested in gel by TPCK-trypsin. Mass analysis ofthe tryptic digest peptides mixture was performed by using MALDI-TOF MS. Peptide mass fingerprints (PMFs) obtained by the MALDI-TOF analysis were used to search NCBI,SWISS-PROT and MSDB databases by using Mascot software.RESULTS: PMF maps of all spots were obtained by MALDI-TOF MS and thirteen proteins were preliminarily identified.CONCLUSION: The methods of analysis and identification of protein spots of tumor cells in 2-DE gel with silver staining by MALDI-TOF MS derived PMF have been established.Protein expression profile of SW480 has been obtained.It is demonstrated that a combination of proteomics and cell culture is a useful approach to comprehend the process of colon carcinogenesis.

  12. Presence of a novel DNA methylation enzyme in methicillin-resistant Staphylococcus aureus isolates associated with pig farming leads to uninterpretable results in standard pulsed-field gel electrophoresis analysis.

    NARCIS (Netherlands)

    Bens, C.C.; Voss, A.; Klaassen, C.H.W.

    2006-01-01

    Genomic DNA from methicillin-resistant Staphylococcus aureus isolates recovered from pigs and their caretakers proved resistant to SmaI digestion, leading to uninterpretable results in standard pulsed-field gel electrophoresis. This is the result of a yet unknown restriction/methylation system in th

  13. Development of a sodium dodecyl sulfate-polyacrylamide gel electrophoresis reference method for the analysis and identification of fish species in raw and heat-processed samples : A collaborative study

    DEFF Research Database (Denmark)

    Pineiro, C.; Barros-Velazquez, J.; Perez-Martin, R.I.;

    1999-01-01

    A collaborative study was carried out in seven European labs with the aim of achieving a sodium dodecyl sulfate- polyacrylamide gel electrophoresis (SDS-PAGE) standard operation procedure to identify fish species in raw and cooked samples. Urea and SDS-containing solutions were evaluated as extra...

  14. Two distinct clones of methicillin-resistant Staphylococcus aureus (MRSA) with the same USA300 pulsed-field gel electrophoresis profile: a potential pitfall for identification of USA300 community-associated MRSA

    DEFF Research Database (Denmark)

    Larsen, Anders Rhod; Goering, Richard; Stegger, Marc;

    2009-01-01

    Analysis of methicillin-resistant Staphylococcus aureus (MRSA) characterized as USA300 by pulsed-field gel electrophoresis identified two distinct clones. One was similar to community-associated USA300 MRSA (ST8-IVa, t008, and Panton-Valentine leukocidin positive). The second (ST8-IVa, t024, and...

  15. Associated risk factors and pulsed field gel electrophoresis of nasal isolates of Staphylococcus aureus from medical students in a tertiary hospital in Lagos, Nigeria

    Directory of Open Access Journals (Sweden)

    Solayide A. Adesida

    2007-02-01

    Full Text Available Staphylococcus aureus infections are growing problems worldwide with important implications in hospitals. The organism is normally present in the nasal vestibule of about 35% of apparently healthy individuals and its carriage varies between different ethnic and age groups. Staphylococcal nasal carriage among health workers is particularly important to establish new clones and track origin of infections during outbreak situations. To determine the carriage rate and compare the pulsed field gel patterns of the strains, nasal swabs were collected from 185 medical students in a teaching hospital in Lagos, Nigeria. Isolates of S. aureus were tested for heamolysin production, methicillin sensitivity and Pulsed Field Gel Electrophoresis (PFGE was performed. The results showed S.aureus nasal carrier rate of 14% with significant rate among males compared to females. All the isolates produced heamolysin. Antibiotic susceptibility pattern revealed that majority of the isolates was susceptible. Five strains (19% harboured resistant determinants to penicillin and tetracycline. None of the strains was resistant to methicillin. 44% of the isolates typed by PFGE had type B, the most predominant pulsotype. PFGE A clone exhibited a single resistance phenotype suggesting a strong clonal relationship that could punctual an outbreak in the hospital. The results speculate that nasal carriage among medical personnel could be a function of various risk factors. Personal hygiene and behaviour may however be the means to reducing colonization and spread of S.aureus in our hospitals.

  16. Bacterial community structure in Apis florea larvae analyzed by denaturing gradient gel electrophoresis and 16S rRNA gene sequencing.

    Science.gov (United States)

    Saraithong, Prakaimuk; Li, Yihong; Saenphet, Kanokporn; Chen, Zhou; Chantawannakul, Panuwan

    2015-10-01

    This study characterizes the colonization and composition of bacterial flora in dwarf Asian honeybee (Apis florea) larvae and compares bacterial diversity and distribution among different sampling locations. A. florea larvae were collected from 3 locations in Chiang Mai province, Thailand. Bacterial DNA was extracted from each larva using the phenol-chloroform method. Denaturing gradient gel electrophoresis was performed, and the dominant bands were excised from the gels, cloned, and sequenced for bacterial species identification. The result revealed similarities of bacterial community profiles in each individual colony, but differences between colonies from the same and different locations. A. florea larvae harbor bacteria belonging to 2 phyla (Firmicutes and Proteobacteria), 5 classes (Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Bacilli, and Clostridia), 6 genera (Clostridium, Gilliamella, Melissococcus, Lactobacillus, Saccharibacter, and Snodgrassella), and an unknown genus from uncultured bacterial species. The classes with the highest abundance of bacteria were Alphaproteobacteria (34%), Bacilli (25%), Betaproteobacteria (11%), Gammaproteobacteria (10%), and Clostridia (8%), respectively. Similarly, uncultured bacterial species were identified (12%). Environmental bacterial species, such as Saccharibacter floricola, were also found. This is the first study in which sequences closely related to Melissococcus plutonius, the causal pathogen responsible for European foulbrood, have been identified in Thai A. florea larvae. PMID:25393530

  17. An Optimized Trichloroacetic Acid/Acetone Precipitation Method for Two-Dimensional Gel Electrophoresis Analysis of Qinchuan Cattle Longissimus Dorsi Muscle Containing High Proportion of Marbling.

    Directory of Open Access Journals (Sweden)

    Ruijie Hao

    Full Text Available Longissimus dorsi muscle (LD proteomics provides a novel opportunity to reveal the molecular mechanism behind intramuscular fat deposition. Unfortunately, the vast amounts of lipids and nucleic acids in this tissue hampered LD proteomics analysis. Trichloroacetic acid (TCA/acetone precipitation is a widely used method to remove contaminants from protein samples. However, the high speed centrifugation employed in this method produces hard precipitates, which restrict contaminant elimination and protein re-dissolution. To address the problem, the centrifugation precipitates were first grinded with a glass tissue grinder and then washed with 90% acetone (TCA/acetone-G-W in the present study. According to our result, the treatment for solid precipitate facilitated non-protein contaminant removal and protein re-dissolution, ultimately improving two-dimensional gel electrophoresis (2-DE analysis. Additionally, we also evaluated the effect of sample drying on 2-DE profile as well as protein yield. It was found that 30 min air-drying did not result in significant protein loss, but reduced horizontal streaking and smearing on 2-DE gel compared to 10 min. In summary, we developed an optimized TCA/acetone precipitation method for protein extraction of LD, in which the modifications improved the effectiveness of TCA/acetone method.

  18. Human cellular protein patterns and their link to genome DNA sequence data: usefulness of two-dimensional gel electrophoresis and microsequencing

    DEFF Research Database (Denmark)

    Celis, J E; Rasmussen, H H; Leffers, H;

    1991-01-01

    a global approach to the study of the cell. Using the integrated approach offered by 2-dimensional gel protein databases it is now possible to reveal phenotype specific protein (or proteins), to microsequence them, to search for homology with previously identified proteins, to clone the cDNAs, to assign...

  19. Scaffold architecture and fibrin gels promote meniscal cell proliferation

    International Nuclear Information System (INIS)

    Stability of the knee relies on the meniscus, a complex connective tissue with poor healing ability. Current meniscal tissue engineering is inadequate, as the signals for increasing meniscal cell proliferation have not been established. In this study, collagen scaffold structure, isotropic or aligned, and fibrin gel addition were tested. Metabolic activity was promoted by fibrin addition. Cellular proliferation, however, was significantly increased by both aligned architectures and fibrin addition. None of the constructs impaired collagen type I production or triggered adverse inflammatory responses. It was demonstrated that both fibrin gel addition and optimized scaffold architecture effectively promote meniscal cell proliferation

  20. Scaffold architecture and fibrin gels promote meniscal cell proliferation

    Energy Technology Data Exchange (ETDEWEB)

    Pawelec, K. M., E-mail: pawelec.km@gmail.com, E-mail: jw626@cam.ac.uk; Best, S. M.; Cameron, R. E. [Cambridge Centre for Medical Materials, Materials Science and Metallurgy Department, University of Cambridge, Cambridge CB3 0FS (United Kingdom); Wardale, R. J., E-mail: pawelec.km@gmail.com, E-mail: jw626@cam.ac.uk [Division of Trauma and Orthopaedic Surgery, Department of Surgery, University of Cambridge, Cambridge CB2 2QQ (United Kingdom)

    2015-01-01

    Stability of the knee relies on the meniscus, a complex connective tissue with poor healing ability. Current meniscal tissue engineering is inadequate, as the signals for increasing meniscal cell proliferation have not been established. In this study, collagen scaffold structure, isotropic or aligned, and fibrin gel addition were tested. Metabolic activity was promoted by fibrin addition. Cellular proliferation, however, was significantly increased by both aligned architectures and fibrin addition. None of the constructs impaired collagen type I production or triggered adverse inflammatory responses. It was demonstrated that both fibrin gel addition and optimized scaffold architecture effectively promote meniscal cell proliferation.

  1. [Modified Gedelisa test (electrophoresis in gradient of polyacrylamide gel combined with Elisa test). Applications to Toxoplasma gondii exo-antigens (author's transl)].

    Science.gov (United States)

    Desgeorges, P T; Ambroise-Thomas, P; Falanga, P; Renversez, J C

    1980-01-01

    The authors describe a modified Gedelisa test made up an electrophorese in gradient polyacrylamide gel plus an Elisa test. The gel gradient, after electrophoretic migration is cut longitudinaly. One half is stained with Coomassie blue and the second half is cut in slices of 1 mm thick. Each slice is placed in a well of a microtitration polystirene plate, filled up with carbonate buffer pH 9,6 and then scrached. Proteins diffuse out of the gel and coated on the polystirene. The antigenicity of the coated proteins is revealed by Elisa test. This technique was applied to the study of Toxoplasma gondii exo-antigens obtained from medium of in vitro culture on Vero cells. This antigen contains four fractions, three of them are stained with Coomassie blue, their molecular weights are 160 000, 830 000 and more than one million daltons. PMID:7212392

  2. [Microchips based on three dimensional gel cells: history and perspective].

    Science.gov (United States)

    Kolchinskiĭ, A M; Griadunov, D A; Lysov, Iu P; Mikhaĭlovich, V M; Nasedkina, T V; Turygin, A Iu; Rubina, A Iu; Barskiĭ, V E; Zasedatelev, A S

    2004-01-01

    The review describes the history of creation and development of the microchip technology and its role in the human genome project in Russia. The emphasis is placed on the three-dimensional gel-based microchips developed at the Center of Biological Microchips headed by A.D. Mirzabekov since 1988. The gel-based chips of the last generation, IMAGE chips (Immobilized Micro Array of Gel Elements), have a number of advantages over the previous versions. The microchips are manufactured by photo-initiated copolymerization of gel components and immobilized molecules (DNA, proteins, and ligands). This ensures an even distribution of the immobilized probe throughout the microchip gel element with a high yield (about 50% for oligonucleotides). The use of methacrylamide as a main component of the polymerization mixture resulted in a substantial increase of gel porosity without affecting its mechanical strength and stability, which allowed one to work with the DNA fragments of up to 500 nt in length, as well as with rather large protein molecules. At present, the gel-based microchips are widely applied to address different problems. The generic microchips containing a complete set of possible hexanucleotides are used to reveal the DNA motifs binding with different proteins and to study the DNA-protein interactions. The oligonucleotide microchips are a cheap and reliable tool of diagnostics designed for mass application. Biochips have been developed for identification of the tuberculosis pathogen and its antibiotic-resistant forms; for diagnostics of orthopoxviruses, including the smallpox virus; for diagnostics of the anthrax pathogen; and for identification of chromosomal rearrangements in leukemia patients. The protein microchips can be adapted for further use in proteomics. Bacterial and yeast cells were also immobilized in the gel, maintaining their viability, which open a wide potential for creation biosensors on the basis of microchips.

  3. Protein Electrophoresis/Immunofixation Electrophoresis

    Science.gov (United States)

    ... be limited. Home Visit Global Sites Search Help? Protein Electrophoresis Immunofixation Electrophoresis Share this page: Was this page helpful? Also known as: Serum Protein Electrophoresis; Protein ELP; SPE; SPEP; Urine Protein Electrophoresis; ...

  4. Development of a new method for the detection of vanadium complexes bound to DNA, using Agarose Gel Electrophoresis

    OpenAIRE

    Subedi, Prabal

    2012-01-01

    Existem apenas alguns métodos disponíveis para o estudo da ligação de metais ao ADN. Estes são baseados em técnicas espectroscópicas, que podem apenas ser utilizadas quando determinados cromóforos quer da molécula de ADN ou dos complexos metálicos estão directamente envolvidos na ligação de metais ao ADN. O objectivo deste projecto foi desenvolver um novo método que pode ser utilizado para detectar a ligação de um metal de transição ao ADN, utilizando Electroforese em gel de agarose (EGA)...

  5. Genetic Structure Change in Harvard Vaccine Strain of Clostridium Tetani for the Period of 1990 to 2010 by Pulsed-Field Gel Electrophoresis

    Directory of Open Access Journals (Sweden)

    Ahmad Sakhravi

    2013-07-01

    Full Text Available Background: PFGE facilitates the differential migration of large DNA fragments through agarose gel by constantly changing the direction of the electrical field during electrophoresis. Possibility of high difference between strains and repeatability make PFGE one of the strong molecular methods in study of bacterial strains in epidemiology. To identifying and DNA fingerprinting of vaccine strain of Clostridium tetani by PFGE technique. Also, possibility of genotyping profile changes in frequency of vaccine strain of C. tetani during the period of 1990 to 2011.Materials and Methods: The vaccine strain of C. tetani was provided by Razi Vaccine and Serum Research Institute in Karaj. The seeds were inoculated into Columbia blood agar and grown for 72 h. The cultures were incubated at 35°C in anaerobic conditions. The PFGE analyses were performed using genomic DNA digested with the restriction enzyme SmaI. The electrophoresis analyses were carried out on a CHEF DR III apparatus (Bio-Rad and band patterns obtained were then analyzed.Results: The PFGE profile obtained from vaccine strain during a period of more than two decades revealed no remarkable genetic changes and mutations. This type of analysis provides detailed data useful for surveillance of vaccine strains and isolates as well as for the selection of certain predominant profiles for further investigation.Conclusion: This study showed no considerable change in chromosomal genome of Harvard, the vaccine strain. It is therefore concluded that the vaccine produced by Razi Institute had evidently no alteration or modification in accordance to PFGE profile analysis during a period of more than two decades.

  6. Separation of intron 22 inversion type 1 and 2 of hemophilia A by modified inverse-shifting polymerase chain reaction and capillary gel electrophoresis.

    Science.gov (United States)

    Pan, Tzu-Yu; Chiou, Shyh-Shin; Wang, Chun-Chi; Wu, Shou-Mei

    2014-12-01

    An inverse-shifting polymerase chain reaction (IS-PCR) combined with short-end capillary gel electrophoresis (CGE) was developed for genotyping of intron 22 inversion Type 1 (Inv22-1) and Type 2 (Inv22-2) of hemophilia A (HA). Severe HA cases are affected by intron 22 inversion around 45-50%. Inv22-1 has higher frequency than Inv22-2. The aim of this study is to distinguish them by genotyping. In order to improve Inv22 genotyping efficiency, five primers were designed and applied to differentiate the wild type, Inv22-1, Inv22-2 and carrier. Three amplicons of 405, 457 and 512 bp were recognized for wild type; 333, 457 and 584 bp for Inv22-1; 385, 405 and 584 bp for Inv22-2. The Inv22-1 carrier has 5 amplicons including 333, 405, 457, 512, 584 bp and Inv22-2 carrier is differentiated by 385, 405, 457, 512 and 584 bp. The amplicons between Inv22-1 and Inv22-2 carriers are only different in 333 bp for Inv22-1 carrier and 385 bp for Inv22-2 carrier. Capillary gel electrophoresis (CGE) was used for separation within 5 min. The separation voltage was set at 8 kV (cathode at detector), and the temperature was kept at 25°C. The sieving matrix was 89 mM Tris, 89 mM boric acid, 2mM EDTA containing 0.4% (w/v) HPMC and 1 μM of YO-PRO(®)-1 Iodide. Total of 50 HA patients (including 35 non-Inv22, 14 Inv22-1, and one Inv22-2 patients) and 7 HA carriers were diagnosed in the application. Seven random samples (5 patients and 2 carriers) were subjected to comparison and gave identical results of DNA sequencing and this modified IS-PCR.

  7. Magnetization of microorganism cells by sol-gel method

    Institute of Scientific and Technical Information of China (English)

    CHEN Bo; ZHAN TianZhuo; LIAN ZhiYang; ZHANG DeYuan

    2008-01-01

    Microorganism cells could be used as templates during fabrication of magnetic or conductive microstructures in different standard shapes.In this paper,feasibility of magnetizing microorganism cells by sol-gel method,which is to coat cells of Spirulina (a type of natural micro-helical microorganism) with the ferrite (a kind of magnetic material),was discussed and investigated.Then the cell form,compo-nents and the phase structure were observed and analyzed using various tools including optical microscopy,scanning electron microscopy (SEM),energy dis-persive X-ray detector (EDX),transmission electron microscopy (TEM),and X-ray diffraction analysis (XRD).Results showed that spirulina cells could be coated with ferrite after the sol-gel process,with the shape of natural helixes well kept,that the components of different sampling points on the surface layer were consistent and the thickness of layer was uniform,and that the type of the surface ferrite layer formed was cubic Fe304.It was also observed that there were nano-parUcles yielded in the cells and certain deposit on the walls between cells.The kinetics of the cell magnetization technology by sol-gel was also discussed.

  8. Magnetization of microorganism cells by sol-gel method

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Microorganism cells could be used as templates during fabrication of magnetic or conductive microstructures in different standard shapes. In this paper, feasibility of magnetizing microorganism cells by sol-gel method, which is to coat cells of Spirulina (a type of natural micro-helical microorganism) with the ferrite (a kind of magnetic material), was discussed and investigated. Then the cell form, components and the phase structure were observed and analyzed using various tools including optical microscopy, scanning electron microscopy (SEM), energy dispersive X-ray detector (EDX), transmission electron microscopy (TEM), and X-ray diffraction analysis (XRD). Results showed that spirulina cells could be coated with ferrite after the sol-gel process, with the shape of natural helixes well kept, that the components of different sampling points on the surface layer were consistent and the thickness of layer was uniform, and that the type of the surface ferrite layer formed was cubic Fe3O4. It was also observed that there were nano-particles yielded in the cells and certain deposit on the walls between cells. The kinetics of the cell magnetization technology by sol-gel was also discussed.

  9. Application of nested PCR-DGGE (denaturing gradient gel electrophoresis) for the analysis of ciliate communities in soils.

    Science.gov (United States)

    Shimano, Satoshi; Sambe, Mitsuo; Kasahara, Yasuhiro

    2012-01-01

    Ciliates play important roles as prey and predators in ecosystems. Changes in the ciliate community can affect the composition and population of microfauna and microflora in ecosystems. To investigate the structure of ciliate communities, we developed a nested PCR-DGGE method, which combines a universal eukaryotic-specific primer set in the first PCR step with a ciliate-specific primer set in the second PCR step, to amplify 18S rRNA genes from ciliates. The 300 bp DGGE fragments generated more bands on the gel than the 600 bp DGGE fragments. Prior to bead beating, DNA extraction of ciliates from soil samples was optimized with a combination of freeze-thaw cycles and ultrasonication. We applied this nested PCR-DGGE method to agricultural soils amended with 0, 120, 300, and 600 t ha⁻¹ year⁻¹ of livestock slurry. The results from the DGGE profiles and principal component analysis (PCA) revealed that the supplement of slurry to soils influenced the ciliate communities. From phylogenetic analysis, 108 DGGE bands were assigned to six classes, which included Spirotrichea and Colpodea, of the subphylum Intramacronucleata, and one class of the subphylum Postciliodesmatophora. These results indicated that a wide variety of taxonomic groups were detected by DGGE profiling. Thus, the nested PCR-DGGE method described here could clearly differentiate between ciliate communities within soil samples and allowed for the phylogenetic identification of these ciliates at the class level.

  10. Association of diverse bacterial communities in human bile samples with biliary tract disorders: a survey using culture and polymerase chain reaction-denaturing gradient gel electrophoresis methods.

    Science.gov (United States)

    Tajeddin, E; Sherafat, S J; Majidi, M R S; Alebouyeh, M; Alizadeh, A H M; Zali, M R

    2016-08-01

    Bacterial infection is considered a predisposing factor for disorders of the biliary tract. This study aimed to determine the diversity of bacterial communities in bile samples and their involvement in the occurrence of biliary tract diseases. A total of 102 bile samples were collected during endoscopic retrograde cholangiopancreatography (ERCP). Characterization of bacteria was done using culture and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) methods. Antimicrobial susceptibility of the isolates was determined based on the Clinical and Laboratory Standards Institute (CLSI) guidelines and identity of the nucleotide sequences of differentiated bands from the DGGE gels was determined based on GenBank data. In total, 41.2 % (42/102) of the patients showed bacterial infection in their bile samples. This infection was detected in 21 % (4/19), 45.4 % (5/11), 53.5 % (15/28), and 54.5 % (24/44) of patients with common bile duct stone, microlithiasis, malignancy, and gallbladder stone, respectively. Escherichia coli showed a significant association with gallstones. Polymicrobial infection was detected in 48 % of the patients. While results of the culture method established coexistence of biofilm-forming bacteria (Pseudomonas aeruginosa, E. coli, Klebsiella pneumoniae, Enterococcus spp., and Acinetobacter spp.) in different combinations, the presence of Capnocytophaga spp., Lactococcus spp., Bacillus spp., Staphylococcus haemolyticus, Enterobacter or Citrobacter spp., Morganella spp., Salmonella spp., and Helicobacter pylori was also characterized in these samples by the PCR-DGGE method. Multidrug resistance phenotypes (87.5 %) and resistance to third- and fourth-generation cephalosporins and quinolones were common in these strains, which could evolve through their selection by bile components. Ability for biofilm formation seems to be a need for polymicrobial infection in this organ. PMID:27193890

  11. Protein identification from two-dimensional gel electrophoresis analysis of Klebsiella pneumoniae by combined use of mass spectrometry data and raw genome sequences

    Directory of Open Access Journals (Sweden)

    Zeng An-Ping

    2003-12-01

    Full Text Available Abstract Separation of proteins by two-dimensional gel electrophoresis (2-DE coupled with identification of proteins through peptide mass fingerprinting (PMF by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS is the widely used technique for proteomic analysis. This approach relies, however, on the presence of the proteins studied in public-accessible protein databases or the availability of annotated genome sequences of an organism. In this work, we investigated the reliability of using raw genome sequences for identifying proteins by PMF without the need of additional information such as amino acid sequences. The method is demonstrated for proteomic analysis of Klebsiella pneumoniae grown anaerobically on glycerol. For 197 spots excised from 2-DE gels and submitted for mass spectrometric analysis 164 spots were clearly identified as 122 individual proteins. 95% of the 164 spots can be successfully identified merely by using peptide mass fingerprints and a strain-specific protein database (ProtKpn constructed from the raw genome sequences of K. pneumoniae. Cross-species protein searching in the public databases mainly resulted in the identification of 57% of the 66 high expressed protein spots in comparison to 97% by using the ProtKpn database. 10 dha regulon related proteins that are essential for the initial enzymatic steps of anaerobic glycerol metabolism were successfully identified using the ProtKpn database, whereas none of them could be identified by cross-species searching. In conclusion, the use of strain-specific protein database constructed from raw genome sequences makes it possible to reliably identify most of the proteins from 2-DE analysis simply through peptide mass fingerprinting.

  12. Use of arbitrary DNA primers, polyacrylamide gel electrophoresis and silver staining for identity testing, gene discovery and analysis of gene expression

    International Nuclear Information System (INIS)

    To understand chemically-induced genomic differences in soybean mutants differing in their ability to enter the nitrogen-fixing symbiosis involving Bradyrhizobium japonicum, molecular techniques were developed to aid the map-based, or positional, cloning. DNA marker technology involving single arbitrary primers was used to enrich regional RFLP linkage data. Molecular techniques, including two-dimensional pulse field gel electrophoresis, were developed to ascertain the first physical mapping in soybean, leading to the conclusion that in the region of marker pA-36 on linkage group H, 1 cM equals about 500 cM. High molecular weight DNA was isolated and cloned into yeast or bacterial artificial chromosomes (YACs/ BACs). YACs were used to analyze soybean genome structure, revealing that over half of the genome contains repetitive DNA. Genetic and molecular tools are now available to facilitate the isolation of plant genes directly involved in symbiosis. The further characterization of these genes, along with the determination of the mechanisms that lead to the mutation, will be of value to other plants and induced mutation research. (author)

  13. Appropriate chicken sample size for identifying the composition of broiler intestinal microbiota affected by dietary antibiotics, using the polymerase chain reaction-denaturing gradient gel electrophoresis technique.

    Science.gov (United States)

    Zhou, H; Gong, J; Brisbin, J T; Yu, H; Sanei, B; Sabour, P; Sharif, S

    2007-12-01

    The bacterial microbiota in the broiler gastrointestinal tract are crucial for chicken health and growth. Their composition can vary among individual birds. To evaluate the composition of chicken microbiota in response to environmental disruption accurately, 4 different pools made up of 2, 5, 10, and 15 individuals were used to determine how many individuals in each pool were required to assess the degree of variation when using the PCR-denaturing gradient gel electrophoresis (DGGE) profiling technique. The correlation coefficients among 3 replicates within each pool group indicated that the optimal sample size for comparing PCR-DGGE bacterial profiles and downstream applications (such as identifying treatment effects) was 5 birds per pool for cecal microbiota. Subsequently, digesta from 5 birds was pooled to investigate the effects on the microbiota composition of the 2 most commonly used dietary antibiotics (virginiamycin and bacitracin methylene disalicylate) at 2 different doses by using PCR-DGGE, DNA sequencing, and quantitative PCR techniques. Thirteen DGGE DNA bands were identified, representing bacterial groups that had been affected by the antibiotics. Nine of them were validated. The effect of dietary antibiotics on the microbiota composition appeared to be dose and age dependent. These findings provide a working model for elucidating the mechanisms of antibiotic effects on the chicken intestinal microbiota and for developing alternatives to dietary antibiotics. PMID:18029800

  14. Development of an SDS-gel electrophoresis method on SU-8 microchips for protein separation with LIF detection: Application to the analysis of whey proteins.

    Science.gov (United States)

    Del Mar Barrios-Romero, Maria; Crevillén, Agustín G; Diez-Masa, José Carlos

    2013-08-01

    This work describes the development of an SDS-gel electrophoresis method for the analysis of major whey proteins (α-lactalbumin, β-lactoglobulin, and BSA) carried out in SU-8 microchips. The method uses a low-viscosity solution of dextran as a sieving polymer. A commercial coating agent (EOTrol LN) was added to the separation buffer to control the EOF of the chips. The potential of this coating agent to prevent protein adsorption on the walls of the SU-8 channels was also evaluated. Additionally, the fluorescence background of the SU-8 material was studied to improve the sensitivity of the method. By selecting an excitation wavelength of 532 nm at which the background fluorescence remains low and by replacing the mercury arc lamp by a laser in the detection system, an LOD in the nanomolar range was achieved for proteins derivatized with the fluorogenic reagent Chromeo P540. Finally, the method was applied to the analysis of milk samples, demonstrating the potential of SU-8 microchips for the analysis of proteins in complex food samples.

  15. Multiplex polymerase chain reaction-capillary gel electrophoresis: a promising tool for GMO screening--assay for simultaneous detection of five genetically modified cotton events and species.

    Science.gov (United States)

    Nadal, Anna; Esteve, Teresa; Pla, Maria

    2009-01-01

    A multiplex polymerase chain reaction assay coupled to capillary gel electrophoresis for amplicon identification by size and color (multiplex PCR-CGE-SC) was developed for simultaneous detection of cotton species and 5 events of genetically modified (GM) cotton. Validated real-time-PCR reactions targeting Bollgard, Bollgard II, Roundup Ready, 3006-210-23, and 281-24-236 junction sequences, and the cotton reference gene acp1 were adapted to detect more than half of the European Union-approved individual or stacked GM cotton events in one reaction. The assay was fully specific (PCR-CGE-SC assay to allow simultaneous detection of 6 cotton and 5 maize targets (two endogenous genes and 9 GM events) in two multiplex PCRs and a single CGE, making the approach more economic. Besides allowing simultaneous detection of many targets with adequate specificity and sensitivity, the multiplex PCR-CGE-SC approach has high throughput and automation capabilities, while keeping a very simple protocol, e.g., amplification and labeling in one step. Thus, it is an easy and inexpensive tool for initial screening, to be complemented with quantitative assays if necessary.

  16. Stage-specific analysis of plasma protein profiles in ovarian cancer: Difference in-gel electrophoresis analysis of pooled clinical samples

    Directory of Open Access Journals (Sweden)

    Mark J Bailey

    2013-01-01

    Full Text Available Introduction: Ovarian cancer is the leading cause of death from gynecological cancer. Non-specific symptoms early in disease and the lack of specific biomarkers hinder early diagnosis. Multi-marker blood screening tests have shown promise for improving identification of early stage disease; however, available tests lack sensitivity, and specificity. Materials and Methods: In this study, pooled deeply-depleted plasma from women with Stage 1, 2 or 3 ovarian cancer and healthy controls were used to compare the 2-dimensional gel electrophoresis (2-DE protein profiles and identify potential novel markers of ovarian cancer progression. Results/Discussion: Stage-specific variation in biomarker expression was observed. For example, apolipoprotein A1 expression is relatively low in control and Stage 1, but shows a substantial increase in Stage 2 and 3, thus, potential of utility for disease confirmation rather than early detection. A better marker for early stage disease was tropomyosin 4 (TPM4. The expression of TPM4 increased by 2-fold in Stage 2 before returning to "normal" levels in Stage 3 disease. Multiple isoforms were also identified for some proteins and in some cases, displayed stage-specific expression. An interesting example was fibrinogen alpha, for which 8 isoforms were identified. Four displayed a moderate increase at Stage 1 and a substantial increase for Stages 2 and 3 while the other 4 showed only moderate increases. Conclusion: Herein is provided an improved summary of blood protein profiles for women with ovarian cancer stratified by stage.

  17. Co-monitoring bacterial and dinoflagellates communities by denaturing gradient gel electrophoresis (DGGE) and SSU rRNA sequencing during a dinoflagellates bloom

    Institute of Scientific and Technical Information of China (English)

    KANJinjun; CHENFeng

    2004-01-01

    Dinoflagellates are unicellular eukaryotic protists that dominate in all coastal waters, and are also present in oceanic waters. Despite the central importance of dinoflagellates in global primary production, the relationship between dinoflagellates and bacteria are still poorly understood. In order to understand the ecological interaction between bacterial and dinoflageUates communities, denaturing gradient gel electrophoresis (DGGE) and SSU rRNA sequencing were applied to monitoring the population dynamics of bacteria and dinoflagellates from the onset to disappearance of a dinoflagellates bloom occurred in Baltimore Inner Harbor, from April 15 to 24, 2002. Although Prorocentrum minimum was the major bloom forming species under the light microscopy, DGGE method with dinoflagellate specific primers demonstrated that Prorocentrum micans, Gymnodinium galatheanum and Gyrodinium uncatenum were also present during the bloom. Population shifts among the minor dinoflagellate groups were observed. DGGE of PCR-amplified 16S rRNA gene fragments indicated that cyanobacteria, α, β, γ-proteobacteria, FlavobacteriumBacteroides-Cytophaga (FBC), and Planctomcetes were the major components of bacterial assemblages during the bloom. DGGE analysis showed that Cytophagales and α-proteobacteria played important roles at different stages of dinoflagellates bloom. DGGE can be used as a rapid tool to simultaneously monitor population dynamics of both bacterial and dinoflagellates communities in aquatic environments, which is demonstrated here.

  18. Molecular typing of enterohemorrhagic Escherichia coli O157:H7 isolated in Okayama Prefecture using pulsed field gel electrophoresis and random amplification of polymorphic DNA.

    Directory of Open Access Journals (Sweden)

    Funamori Y

    1999-08-01

    Full Text Available Three outbreaks and many isolated cases of enterohemorrhagic Escherichia coli O157:H7 occurred in 1996 and 1997 in Okayama Prefecture, Japan. In an attempt to investigate the route of these infections, the strains isolated from the 3 outbreaks (total 33 strains and 15 isolated cases (total 15 strains were investigated using random amplification of polymorphic DNA (RAPD and pulsed-field gel electrophoresis (PFGE. In addition, 10 strains from an outbreak in Tojo Cho, Hiroshima Prefecture (June 1996, 2 strains from the particular types of meat in Kochi Prefecture, and 42 strains isolated from bovine feces in a farm in Okayama Prefecture were also investigated in the same manner. PFGE was much more useful than RAPD for molecular typing of the clinical isolates, in that it allowed us to classify them into 10 PFGE groups. We noted that the strains differed according to the time and place of the outbreaks (or isolated cases. This indicates that O157:H7 infections in Okayama Prefecture were caused by different strains (although some cases were aggravated by the same strains as were found in other areas. The isolates from bovine feces were classified into 5 groups by PFGE profiles, but none of them were identical to those of the clinical isolates.

  19. PCR-denaturing gradient gel electrophoresis analysis of microbial community in soy-daddawa, a Nigerian fermented soybean (Glycine max (L.) Merr.) condiment.

    Science.gov (United States)

    Ezeokoli, Obinna T; Gupta, Arvind K; Mienie, Charlotte; Popoola, Temitope O S; Bezuidenhout, Cornelius C

    2016-03-01

    Soy-daddawa, a fermented soybean (Glycine max (L.) Merr.) condiment, plays a significant role in the culinary practice of West Africa. It is essential to understand the microbial community of soy-daddawa for a successful starter culture application. This study investigated the microbial community structure of soy-daddawa samples collected from Nigerian markets, by PCR-denaturing gradient gel electrophoresis (DGGE) targeting the V3-V5 region of the 16S rRNA gene of bacteria and internal transcribed spacer 2 (ITS2) region of fungi. Six bacterial and 16 fungal (nine yeasts and seven molds) operational taxonomic units (OTUs)/species were obtained at 97% sequence similarity. Taxonomic assignments revealed that bacterial OTUs belonged to the phyla Firmicutes and Actinobacteria, and included species from the genera Atopostipes, Bacillus, Brevibacterium and Nosocomiicoccus. Densitometric analysis of DGGE image/bands revealed that Bacillus spp. were the dominant OTU/species in terms of population numbers. Fungal OTUs belonged to the phyla Ascomycota and Zygomycota, and included species from the genera, Alternaria, Aspergillus, Candida, Cladosporium, Dokmaia, Issatchenkia, Kodamaea, Lecythophora, Phoma, Pichia, Rhizopus, Saccharomyces and Starmerella. The majority of fungal species have not been previously reported in soy-daddawa. Potential opportunistic human pathogens such as Atopostipes suicloacalis, Candida rugosa, Candida tropicalis, and Kodamaea ohmeri were detected. Variation in soy-daddawa microbial communities amongst samples and presence of potential opportunistic pathogens emphasises the need for starter culture employment and good handling practices in soy-daddawa processing. PMID:26796580

  20. Combined Use of a Solid-Phase Hexapeptide Ligand Library with Liquid Chromatography and Two-Dimensional Difference Gel Electrophoresis for Intact Plasma Proteomics

    Directory of Open Access Journals (Sweden)

    Tatsuo Hagiwara

    2011-01-01

    Full Text Available The intact plasma proteome is of great interest in biomarker studies because intact proteins reflect posttranslational protein processing such as phosphorylation that may correspond to disease status. We examined the utility of a solid-phase hexapeptide ligand library in combination with conventional plasma proteomics modalities for comprehensive profiling of intact plasma proteins. Plasma proteins were sequentially fractionated using depletion columns for albumin and immunoglobulin, and separated using an anion-exchange column. Proteins in each fraction were treated with a solid-phase hexapeptide ligand library and compared to those without treatment. Two-dimensional difference gel electrophoresis demonstrated an increased number of protein spots in the treated samples. Mass spectrometric studies of these protein spots with unique intensity in the treated samples resulted in the identification of high- and medium-abundance proteins. Our results demonstrated the possible utility of a solid-phase hexapeptide ligand library to reveal greater number of intact plasma proteins. The characteristics of proteins with unique affinity to the library remain to be clarified by more extensive mass spectrometric protein identification, and optimized protocols should be established for large-scale plasma biomarker studies.

  1. Molecular characterization of Salmonella paratyphi B dT+ and Salmonella Heidelberg from poultry and retail chicken meat in Colombia by pulsed-field gel electrophoresis.

    Science.gov (United States)

    Donado-Godoy, Pilar; Byrne, Barbara A; Hume, Michael; León, Maribel; Pérez-Gutiérrez, Enriqué; Vives Flores, Martha J; Clavijo, Viviana; Holguin, Ángela; Romero-Zuñiga, Juan J; Castellanos, Ricardo; Tafur, McAllister; Smith, Woutrina A

    2015-04-01

    Salmonella Paratyphi B dT+ variant (also termed Salmonella Java) and Salmonella Heidelberg are pathogens of public health importance that are frequently isolated from poultry. As a step toward implementing the Colombian Integrated Program for Antimicrobial Resistant Surveillance, this study characterized molecular patterns of Salmonella Paratyphi B dT+ and Salmonella Heidelberg isolated from poultry farms, fecal samples, and retail chicken meat using pulsed-field gel electrophoresis (PFGE). The objective of this study was to determine the genetic relationship among isolates and to determine potential geographically predominant genotypes. Based on PFGE analysis, both serovars exhibited high heterogeneity: the chromosomal DNA fingerprints of 82 Salmonella Paratyphi B dT+ isolates revealed 42 PFGE patterns, whereas the 21 isolates of Salmonella Heidelberg revealed 10 patterns. Similar genotypes of both serovars were demonstrated to be present on farms and in retail outlets. For Salmonella Paratyphi B dT+, closely genetically related strains were found among isolates coming from different farms and different integrated poultry companies within two departments (Santander and Cundinamarca) and also from farms located in the two geographically distant departments. For Salmonella Heidelberg, there were fewer farms with genetically related isolates than for Salmonella Paratyphi B dT+. A possible dissemination of similar genotypes of both serovars along the poultry production chain is hypothesized, and some facilitating factors existing in Colombia are reviewed.

  2. Soil clone library analyses to evaluate specificity and selectivity of PCR primers targeting fungal 18S rDNA for denaturing-gradient gel electrophoresis (DGGE).

    Science.gov (United States)

    Takada Hoshino, Yuko; Morimoto, Sho

    2010-01-01

    We evaluated the fungal specificity and detection bias of four fungal 18S rRNA gene (18S rDNA) primer sets for denaturing-gradient gel electrophoresis (DGGE). We constructed and compared clone libraries amplified from upland and paddy field soils with each primer set (1, NS1/GCFung; 2, FF390/FR1-GC; 3, NS1/FR1-GC; and 4, NS1/EF3 for the first PCR and NS1/FR1-GC for the second PCR). Primer set 4 (for nested PCR) showed the highest specificity for fungi but biased specific sequences. Sets 1, 2, and 3 (for single PCR) amplified non-fungal eukaryotic sequences (from 7 to 16% for upland soil and from 20 to 31% for paddy field soil) and produced libraries with similar distributions of fungal 18S rDNA sequences at both the phylum and the class level. Set 2 tended to amplify more diverse fungal sequences, maintaining higher specificity for fungi. In addition, clone analyses revealed differences among primer sets in the frequency of chimeras. In upland field soil, the libraries amplified with primer sets 3 and 4, which targeted long fragments, contained many chimeric 18S rDNA sequences (18% and 48%, respectively), while the libraries obtained with sets 1 and 2, which targeted short fragments, contained fewer chimeras (5% and 10%, respectively).

  3. Separation of native allophycocyanin and R-phycocyanin from marine red macroalga Polysiphonia urceolata by the polyacrylamide gel electrophoresis performed in novel buffer systems.

    Directory of Open Access Journals (Sweden)

    Yu Wang

    Full Text Available Three buffer systems of Imidazole-Acetic acid, HEPES-Imidazole/Bis-tris and Bis-tris-HEPES-MES were designed based on the principle of discontinuous polyacrylamide gel electrophoresis (PAGE for the native PAGE which could be performed in pH 7.0 and 6.5 in order to analyze and prepare the minor components of allophycocyanin (AP and R-phycocyanin (R-PC from marine red macroalga Polysiphonia urceolata. These AP and R-PC phycobiliproteins are easily denatured in alkaline environments. The obtained results demonstrated that the PAGE modes performed in the buffer systems of HEPES-Imidazole/Bis-tris and Bis-tris-HEPES-MES gave the satisfactory resolution and separation of AP and R-PC proteins. The absorption and fluorescence spectra of the AP and R-PC proteins which were prepared by the established PAGE modes proved that they maintained natural spectroscopic characteristics. The established PAGE modes may also provide useful references and selections for some other proteins that are sensitive to alkaline environments or are not effectively separated by the classical PAGE modes performed normally in alkaline buffer systems.

  4. Parallel characterization of anaerobic toluene- and ethylbenzene-degrading microbial consortia by PCR-denaturing gradient gel electrophoresis, RNA-DNA membrane hybridization, and DNA microarray technology

    Science.gov (United States)

    Koizumi, Yoshikazu; Kelly, John J.; Nakagawa, Tatsunori; Urakawa, Hidetoshi; El-Fantroussi, Said; Al-Muzaini, Saleh; Fukui, Manabu; Urushigawa, Yoshikuni; Stahl, David A.

    2002-01-01

    A mesophilic toluene-degrading consortium (TDC) and an ethylbenzene-degrading consortium (EDC) were established under sulfate-reducing conditions. These consortia were first characterized by denaturing gradient gel electrophoresis (DGGE) fingerprinting of PCR-amplified 16S rRNA gene fragments, followed by sequencing. The sequences of the major bands (T-1 and E-2) belonging to TDC and EDC, respectively, were affiliated with the family Desulfobacteriaceae. Another major band from EDC (E-1) was related to an uncultured non-sulfate-reducing soil bacterium. Oligonucleotide probes specific for the 16S rRNAs of target organisms corresponding to T-1, E-1, and E-2 were designed, and hybridization conditions were optimized for two analytical formats, membrane and DNA microarray hybridization. Both formats were used to characterize the TDC and EDC, and the results of both were consistent with DGGE analysis. In order to assess the utility of the microarray format for analysis of environmental samples, oil-contaminated sediments from the coast of Kuwait were analyzed. The DNA microarray successfully detected bacterial nucleic acids from these samples, but probes targeting specific groups of sulfate-reducing bacteria did not give positive signals. The results of this study demonstrate the limitations and the potential utility of DNA microarrays for microbial community analysis.

  5. Multilocus sequence typing reveals a lack of diversity among Escherichia coli O157:H7 isolates that are distinct by pulsed-field gel electrophoresis.

    Science.gov (United States)

    Noller, Anna C; McEllistrem, M Catherine; Stine, O Colin; Morris, J Glenn; Boxrud, David J; Dixon, Bruce; Harrison, Lee H

    2003-02-01

    Escherichia coli O157:H7 is a major cause of foodborne illness in the United States. Pulsed-field gel electrophoresis (PFGE) is the molecular epidemiologic method mostly commonly used to identify food-borne outbreaks. Although PFGE is a powerful epidemiologic tool, it has disadvantages that make a DNA sequence-based approach potentially attractive. Multilocus sequence typing (MLST) analyzes the internal fragments of housekeeping genes to establish genetic relatedness between isolates. We sequenced selected portions of seven housekeeping genes and two membrane protein genes (ompA and espA) of 77 isolates that were diverse by PFGE to determine whether there was sufficient sequence variation to be useful as an epidemiologic tool. There was no DNA sequence diversity in the sequenced portions of the seven housekeeping genes and espA. For ompA, all but five isolates had sequence identical to that of the reference strains. E. coli O157:H7 has a striking lack of genetic diversity in the genes we explored, even among isolates that are clearly distinct by PFGE. Other approaches to identify improved molecular subtyping methods for E. coli 0157:H7 are needed.

  6. Approach to analyze the diversity of myxobacteria in soil by semi-nested PCR-denaturing gradient gel electrophoresis (DGGE based on taxon-specific gene.

    Directory of Open Access Journals (Sweden)

    Baiyuan Li

    Full Text Available The genotypic diversity of insoluble macromolecules degraded myxobacteria, provided an opportunity to discover new bacterial resources and find new ecological functions. In this study, we developed a semi-nested-PCR-denaturing gradient gel electrophoresis (DGGE strategy to determine the presence and genotypic diversity of myxobacteria in soil. After two rounds of PCR with myxobacteria-specific primers, an 194 bp fragment of mglA, a key gene involved in gliding motility, suitable for DGGE was obtained. A large number of bands were observed in DGGE patterns, indicating diverse myxobacteria inhabiting in soils. Furthermore, sequencing and BLAST revealed that most of the bands belonged to the myxobacteria-group, and only three of the twenty-eight bands belonged to other group, i.e., Deinococcus maricopensis. The results verified that myxobacterial strains with discrepant sequence compositions of gene mglA could be discriminated by DGGE with myxobacteria-specific primers. Collectively, the developed semi-nested-PCR-DGGE strategy is a useful tool for studying the diversity of myxobacteria.

  7. Comparison of Fecal Methanogenic Archaeal Community Between Erhualian and Landrace Pigs Using Denaturing Gradient Gel Electrophoresis and Real-Time PCR Analysis

    Institute of Scientific and Technical Information of China (English)

    SU Yong; Hauke Smidt; ZHU Wei-Yun

    2014-01-01

    Erhualian and Landrace breeds are typical genetically obese and lean pigs, respectively. To compare the fecal methanogenic Archaeal community between these two pig breeds, fecal samples from different growth phase pigs were collected and used for PCR-denaturing gradient gel electrophoresis (DGGE) with two primer pairs (344fGC/519r and 519f/915rGC) and real-time PCR analysis. Results showed that a better separation and higher quality of bands pattern were obtained in DGGE proifles using primers 344fGC/519r as compared with primers 519f/915rGC. Sequencing of DGGE bands showed that the predominant methanogens in the feces of Erhualian and Landrace pigs belonged to Methanobrevibacter spp. and Methanosphaera spp. Real-time PCR analysis revealed that there was no signiifcant difference in the numbers of fecal total methanogens between Erhualian and Landrace pigs;however, pig growth phase affected the numbers of 16S rRNA genes of total methanogens and Methanobrevibacter smithii. Dissociation curves of methyl coenzyme-M reductase subunit A (mcrA) gene fragments ampliifed with real-time PCR showed all samples possessed a single peak at 82°C, which might be associated with M. smithii. Samples from the same growth phase of each breed showed good replicative dissociation curves. The results suggest that the growth phase (including diet factor) other than genotype of pig may affect the fecal methanogenic Archaeal community of pigs.

  8. Combining two-dimensional gel electrophoresis and metabolomic data in support of dry-season survival in the two main species of the malarial mosquito Anopheles gambiae

    Directory of Open Access Journals (Sweden)

    Hidalgo K.

    2015-12-01

    Full Text Available In dry savannahs of West-Africa, the malarial mosquitoes of the Anopheles gambiae sensu stricto complex annually survive the harsh desiccating conditions of the dry season. However, the physiological and biochemical mechanisms underlying how these mosquitoes survive such desiccating conditions are still undefined, and controversial. In this context, we provide the first work examining both proteomic and metabolomic changes in the two molecular forms of A. gambiae s.s (M and S forms experimentally exposed to the rainy and dry season conditions as they experience in the field. Protein abundances of the mosquitoes were measured using a two-dimensional fluorescence difference gel electrophoresis (2D DIGE coupled with a matrix-assisted laser desorption/ionisation-time of flight (MALDI-TOF and tandem mass spectrometry (MS for protein identification. These assays were conducted by Applied Biomics (http://www.appliedbiomics.com, Applied Biomics, Inc. Hayward, CA, USA, and the mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org via the PRIDE partner repository with the dataset identifier PXD000294. The metabolomic analysis was conducted using both Acquity UPLC® system (for amino acid identification, and a gas-chromatography-mass spectrometry platform (for sugars identification. Metabolomic fingerprintings were assessed in the University of Rennes 1, UMR CNRS 6553 EcoBio (France. A detailed interpretation of the obtained data can be found in Hidalgo et al. (2014 [1] (Journal of Insect Physiology (2014.

  9. Molecular characterization of Salmonella paratyphi B dT+ and Salmonella Heidelberg from poultry and retail chicken meat in Colombia by pulsed-field gel electrophoresis.

    Science.gov (United States)

    Donado-Godoy, Pilar; Byrne, Barbara A; Hume, Michael; León, Maribel; Pérez-Gutiérrez, Enriqué; Vives Flores, Martha J; Clavijo, Viviana; Holguin, Ángela; Romero-Zuñiga, Juan J; Castellanos, Ricardo; Tafur, McAllister; Smith, Woutrina A

    2015-04-01

    Salmonella Paratyphi B dT+ variant (also termed Salmonella Java) and Salmonella Heidelberg are pathogens of public health importance that are frequently isolated from poultry. As a step toward implementing the Colombian Integrated Program for Antimicrobial Resistant Surveillance, this study characterized molecular patterns of Salmonella Paratyphi B dT+ and Salmonella Heidelberg isolated from poultry farms, fecal samples, and retail chicken meat using pulsed-field gel electrophoresis (PFGE). The objective of this study was to determine the genetic relationship among isolates and to determine potential geographically predominant genotypes. Based on PFGE analysis, both serovars exhibited high heterogeneity: the chromosomal DNA fingerprints of 82 Salmonella Paratyphi B dT+ isolates revealed 42 PFGE patterns, whereas the 21 isolates of Salmonella Heidelberg revealed 10 patterns. Similar genotypes of both serovars were demonstrated to be present on farms and in retail outlets. For Salmonella Paratyphi B dT+, closely genetically related strains were found among isolates coming from different farms and different integrated poultry companies within two departments (Santander and Cundinamarca) and also from farms located in the two geographically distant departments. For Salmonella Heidelberg, there were fewer farms with genetically related isolates than for Salmonella Paratyphi B dT+. A possible dissemination of similar genotypes of both serovars along the poultry production chain is hypothesized, and some facilitating factors existing in Colombia are reviewed. PMID:25836408

  10. DNA gel electrophoretic and microaut oradiographic studies on apoptosisin bone tumor cells after exposure with 153Sm-EDTMP

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    The apoptosis in bone tumor cells is studied after 153Sm-EDTMP irradiation.Fragmented DNA is analyzed by agarose gel electrophoresis.Experimental observations show that 153Sm-EDTMP exposureinduces the internucleosomal DNA damage in bone tumor cells the DNAladder pattern formation in bone tumor cells is shown.At the same time,the microautoradiographic study indicates that 153153Sm-EDTMP could permeate through cell membrane and displays membrane-seeking condensation in bone tumor cells.Soon afterwards 153Sm-EDTMP could be phagocytized by the tumor cells and distributed in cytoplasm as well as nucleus in the form of phagosome.With the prolongation of observing time, the membrane-bounded apoptotic bodies are observed.

  11. Self-Polarization of Cells in Elastic Gels

    Science.gov (United States)

    Zemel, Assaf; Safran, Samuel

    2008-03-01

    The shape of a cell as well as the rigidity and geometry of its surroundings play an important role in vital cellular processes. The contractile activity of cells provides a generic means by which cells may sense and respond to mechanical features. The matrix stresses, that depend on the elasticity and geometry of cells, feedback on the cells and influence their activity. This suggests a mechanical mechanism by which cells control their shape and forces. We present a quantitative, mechanical model that predicts that cells in an elastic medium can self-polarize to form well ordered stress fibers. We focus on both single cells in a gel, as well as on an ensemble of cells that is confined to some region within the gel. While the magnitude of the cellular forces is found to increase monotonically with the matrix rigidity the anisotropy of the forces, and thus the ability of the cells to polarize, is predicted to depend non-monotonically on the medium's rigidity. We discuss these results with experimental findings and with the observation of an optimal medium elasticity for cell function and differentiation.

  12. Analysis of Two-Dimensional Gel Electrophoresis Images of Protein from Posterior Silk Gland of Silkworm (Bombyx mori) on Day 1 and Day 4 in the 5th Instar Stage

    Institute of Scientific and Technical Information of China (English)

    WU Wei-cheng; ZHONG Bo-xiong; GAO Qi-kang; CHEN Jin-e; YE Jian; QIAN Yang-wen; LI Jian-ying; LU Hua-yun; MENG Zhi-qi; NI Chun-xiao

    2007-01-01

    The posterior silk gland (PSG) of silkworm is an important organ where fibroin is synthesized and secreted exclusively.Because fibroin constitutes 75-80% of the silk filament, the mechanism governing fibroin secretion, quality and yield of cocoon can be elucidated by the study on the PSG. Using two-dimensional gel electrophoresis (2-DE) and image analysis system, the changes in the protein composition in the PSG cell were investigated on the day 1 (D1) and day 4 (D4) in the 5th instar stage from five different strains of silkworm (Bombyx mori). While differences at protein level between days and strains were far less than those observed at the gene level using EST analysis. The change trends in protein composition from D1 to D4 were diverse among the different strains. The results suggest that the secretion of fibroin is regulated by multiple proteins. The site of regulation and the proteins responsible for the regulation vary with the strain, which leads to differences between strains in the capacity of fibroin secretion in the PSG cell.

  13. Investigation of interaction between the drug and cell membrane by capillary electrophoresis

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    By introducing cell membrane into electrophoretic buffer as pseudo-stationary phase,a novel capillary electrophoresis method was established to explore the interaction between drugs and cell membrane,where the interaction between citalopram and rabbit red blood cell membrane was used as an example. A series of concentrations of cell membrane were suspended into the running buffer by peak-shift method. The binding constant of citalopram to rabbit red blood cell membrane of 0.977 g-1·L was obtained after treatment of Scatchard plot. This method could provide not only a new way for the investigation on the interactions between drugs and cell membrane,but also a new approach for high throughput screening of the drug membrane permeability,biological activity,and evaluating drugs in vivo.

  14. Changes in protein abundance between tender and tough meat from bovine Longissimus thoracis muscle assessed by isobaric Tag for Relative and Absolute Quantitation (iTRAQ) and 2-dimensional gel electrophoresis analysis

    DEFF Research Database (Denmark)

    Bjarnadóttir, S G; Hollung, K; Høy, M;

    2012-01-01

    The aim of this study was to find potential biomarkers for meat tenderness in bovine Longissimus thoracis muscle and to compare results from isobaric Tag for Relative and Absolute Quantitation (iTRAQ) and 2-dimensional gel electrophoresis (2-DE) analysis. The experiment included 4 tender and 4......-DE analysis (P meat samples in the present study. These include proteins related to control of flux through the tricarboxylate cycle [2...

  15. P187-S Differential Proteome Analysis of the Cerebrospinal Fluid of Normal and Equine Protozoal Myeloencephalitis Affected Horses Using Two-Dimensional Fluorescence Difference Gel Electrophoresis and Mass Spectrometry

    OpenAIRE

    Terry, D. E.; Levy, M.; Isaac, I.; Sharma, N

    2007-01-01

    Equine protozoal myeloencephalitis (EPM) is a common and costly neurologic disease of horses caused by Sarcocystis neurona, protozoa that parasitize the nervous system. Confirmation of the clinical diagnosis is a challenge for veterinarians because the current immunologic tests lack specificity. Multiplexing strategy approaches including two-dimensional fluorescence difference gel electrophoresis (2D DIGE) and mass spectrometry were employed to identify differential protein expression associa...

  16. Protective effects of Brussels sprouts towards B[a]P-induced DNA damage: a model study with the single-cell gel electrophpresis (SCGE)/Hep G2 assay

    NARCIS (Netherlands)

    Laky, B.; Knasmuller, S.; Gminski, R.; Mersch-Sundermann, V.; Scharf, G.; Verkerk, R.; Freywald, C.; Uhl, M.; Kassie, F.

    2002-01-01

    The aim of this study was to investigate the chemoprotective effects of Brussels sprouts juice towards benzo[a]pyrene (B(a)P)-induced DNA damage in the single-cell gel electrophoresis (SCGE)/Hep G2 test system. This assay combines the advantages of the SCGE assay with that of the use of human-derive

  17. Identification and comparative proteomic study of quail and duck egg white protein using 2-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry analysis.

    Science.gov (United States)

    Hu, S; Qiu, N; Liu, Y; Zhao, H; Gao, D; Song, R; Ma, M

    2016-05-01

    A proteomic study of egg white proteins from 2 major poultry species, namely quail (Coturnix coturnix) and duck (Anas platyrhynchos), was performed with comparison to those of chicken (Gallus gallus) through 2-dimensional polyacrylamide gel electrophoresis (2-DE) analysis. By using matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI-TOF MS/MS), 29 protein spots representing 10 different kinds of proteins as well as 17 protein spots designating 9 proteins were successfully identified in quail and duck egg white, respectively. This report suggested a closer relationship between quail and chicken egg white proteome patterns, whereas the duck egg white protein distribution on the 2-DE map was more distinct. In duck egg white, some well-known major proteins, such as ovomucoid, clusterin, extracellular fatty acid-binding protein precursor (ex-FABP), and prostaglandin D2 synthase (PG D2 synthase), were not detected, while two major protein spots identified as "deleted in malignant brain tumors 1" protein (DMBT1) and vitellogenin-2 were found specific to duck in the corresponding range on the 2-DE gel map. These interspecies diversities may be associated with the egg white protein functions in cell defense or regulating/supporting the embryonic development to adapt to the inhabiting environment or reproduction demand during long-term evolution. The findings of this work will give insight into the advantages involved in the application on egg white proteins from various egg sources, which may present novel beneficial properties in the food industry or related to human health.

  18. Analysis of bacterial diversity during the fermentation of inyu, a high-temperature fermented soy sauce, using nested PCR-denaturing gradient gel electrophoresis and the plate count method.

    Science.gov (United States)

    Wei, Chia-Li; Chao, Shiou-Huei; Tsai, Wen-Bin; Lee, Pei-Shan; Tsau, Nai-Hung; Chen, Jhih-Shan; Lai, Wen-Lin; Tu, James Ching-Yueh; Tsai, Ying-Chieh

    2013-04-01

    The diversity of bacteria associated with the fermentation of inyu, also known as black soy sauce, was studied through the nested PCR-denaturing gradient gel electrophoresis (DGGE) of samples collected from the fermentation stages of the inyu production process. The DGGE profiles targeted the bacterial 16S rDNA and revealed the presence of Citrobacter farmeri, Enterobacter cloacae, Enterobacter hormaechei, Enterococcus faecium, Klebsiella pneumoniae, Pantoea agglomerans, Salmonella enterica, Serratia marcescens, Staphylococcus sciuri and Weissella confusa. The bacterial compositions of 4 fermented samples were further elucidated using the plate count method. The bacteria isolated from the koji-making stage exhibited the highest diversity; Brachybacterium rhamnosum, E. hormaechei, K. pneumoniae, Kurthia gibsonii, Pantoea dispersa, Staphylococcus gallinarum, Staphylococcus kloosii and S. sciuri were identified. Koji collected during the preincubation stage presented the largest cell counts, and E. hormaechei, K. pneumoniae, E. cloacae and Enterobacter pulveris were identified. In brine samples aged for 7 and 31 days, the majority of the bacteria isolated belonged to 4 Bacillus species, but 4 Staphylococcus species and Delftia tsuruhatensis were also detected. This study demonstrates the benefits of using a combined approach to obtain a more complete picture of microbial populations and provides useful information for the control or development of bacterial flora during inyu fermentation.

  19. Comparative assessment of irradiated proteins in potato tuber with untreated control by high performance liquid chromatography (HPLC) and gel electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Ghojaie, M.; Sayhoon, M. [Atomic Energy Organization of Iran, Tehran (Iran, Islamic Republic of). Gamma Irradiation Center

    1995-10-01

    About 2% of the weight of potato tuber is composed of proteins. In spite of their low quantity the proteins play a key role in the physiological activities leading to the break of the dormancy period and start of the cell division. This causes sprouting and also greening due to chlorophyll formation. This in turn is always accompanied by the production of the glycoalkaloid solanine in the flesh of tuber. For evaluation of radiation effect (dose range 50-250 Gy) and probable structural changes (amino acid release), analysis of selected proteins (molecular range 5 x 10{sup 4} - 2 x 10{sup 5} Dalton) of potato tuber in both irradiated and control type by HPLC showed no considerable changes in retention times, but qualitative assessment of amino acids by Pico-TagTM Pre-derivatizing method had some changes in quantity of amino acids like lysine which was increased 1 month after irradiation while Glutamic acid had considerable decreasment after the same time of irradiation. (Author).

  20. Application of PCR-denaturing-gradient gel electrophoresis (DGGE) method to examine microbial community structure in asparagus fields with growth inhibition due to continuous cropping.

    Science.gov (United States)

    Urashima, Yasufumi; Sonoda, Takahiro; Fujita, Yuko; Uragami, Atsuko

    2012-01-01

    Growth inhibition due to continuous cropping of asparagus is a major problem; the yield of asparagus in replanted fields is low compared to that in new fields, and missing plants occur among young seedlings. Although soil-borne disease and allelochemicals are considered to be involved in this effect, this is still controversial. We aimed to develop a technique for the biological field diagnosis of growth inhibition due to continuous cropping. Therefore, in this study, fungal community structure and Fusarium community structure in continuously cropped fields of asparagus were analyzed by polymerase chain reaction/denaturing-gradient gel electrophoresis (PCR-DGGE). Soil samples were collected from the Aizu region of Fukushima Prefecture, Japan. Soil samples were taken from both continuously cropped fields of asparagus with growth inhibition and healthy neighboring fields of asparagus. The soil samples were collected from the fields of 5 sets in 2008 and 4 sets in 2009. We were able to distinguish between pathogenic and non-pathogenic Fusarium by using Alfie1 and Alfie2GC as the second PCR primers and PCR-DGGE. Fungal community structure was not greatly involved in the growth inhibition of asparagus due to continuous cropping. By contrast, the band ratios of Fusarium oxysporum f. sp. asparagi in growth-inhibited fields were higher than those in neighboring healthy fields. In addition, there was a positive correlation between the band ratios of Fusarium oxysporum f. sp. asparagi and the ratios of missing asparagus plants. We showed the potential of biological field diagnosis of growth inhibition due to continuous cropping of asparagus using PCR-DGGE.

  1. Antimicrobial resistance, genotypic characterization and pulsed-field gel electrophoresis typing of extended spectrum β-lactamases-producing clinical Escherichia coli strains in Macao, China

    Institute of Scientific and Technical Information of China (English)

    YE Qian-hong; LAU Ying; LIANG Bin; TIAN Su-fei

    2011-01-01

    Background The rise of the production of CTX-M class extended spectrum β-lactamases (ESBLs) has been well documented in traveling countries but no data are found for Macao,an international travel city.The objectives of this study were to identify the antimicrobial resistance pattern,and determine the prevalence,genotype and clonal relationship of ESBLs in 209 clinical Escherichia coli strains from Macao,China.Methods Antimicrobial susceptibility test was performed to determine the resistance patterns of the isolates using the disk diffusion method with 17 antimicrobial agents.Phenotypic detection was screened and confirmed according to the Clinical and Laboratory Standards Institute.Genotypic characterization was detected by isoelectric focusing analysis,polymerase chain reaction and sequencing.The clonal relationship between the different ESBL isolates was studied by pulsed-field gel electrophoresis (PFGE).Results Imipenem and meropenem exhibited 100% susceptible among 209 strains.Overall,82.3%,67.3%,52.9%,51.2% and 51.0% of the isolates displayed resistance to ampicillin,tetracylcline,ciprofloxacin,sulfamethoxazole trimethoprin and gentamycin.The prevalence rate of ESBLs was 30.1%.Antibiotic resistances were found to be significantly higher among the ESBL producing group compared to non-ESBL producing group.We detected CTX-M-14 to be the major genotypic characterization of ESBLs (76.2%).Two strains showed indistinguishable patterns by PFGE.Conclusions The prevalence of antimicrobial resistance is alarming high in Macao.Antimicrobial resistance is significantly higher among the ESBL producing group.This study documented CTX-M-14 as the predominant ESBL type.Although indistinguishable pattern was found between two strains,it was too small to decide whether any of the investigated strains was epidemic.Our findings may be also pertinent for other geographic areas undergoing similar travel characteristics to understand the corresponding effects on bacterial

  2. Diversity of pulsed-field gel electrophoresis pulsotypes, serovars, and antibiotic resistance among Salmonella isolates from wild amphibians and reptiles in the California Central Coast.

    Science.gov (United States)

    Gorski, Lisa; Jay-Russell, Michele T; Liang, Anita S; Walker, Samarpita; Bengson, Yingjia; Govoni, Jessica; Mandrell, Robert E

    2013-06-01

    A survey of cold-blooded vertebrates and associated surface waters in a produce-growing region on the Central California Coast was done between May and September 2011 to determine the diversity of Salmonella. Samples from 460 amphibians and reptiles and 119 water samples were collected and cultured for Salmonella. Animals sampled were frogs (n=331), lizards (n=59), newts (n=5), salamanders (n=6), snakes (n=39), and toads (n=20). Salmonella was isolated from 37 individual animals, including frogs, lizards, snakes, and toads. Snakes were the most likely to contain Salmonella, with 59% testing positive followed by 15.3% of lizards, 5% of toads, and 1.2% of frogs. Fifteen water samples (12.6%) were positive. Twenty-two different serovars were identified, and the majority of isolates were S. enterica subsp. IIIb, with subsp. I, II, and IIIa also found. The serovar isolated most frequently was S. enterica subsp. IIIb 16:z₁₀:e,n,x,z₁₅, from snakes and frogs in five different locations. S. enterica subsp. I serovar Typhimurium and the monophasic I 6,8:d:- were isolated from water, and subspecies I Duisburg and its variants were found in animals and water. Some samples contained more than one type of Salmonella. Analysis of pulsed-field gel electrophoresis pulsotypes indicated that some strains persisted in animals and water collected from the same location. Sixty-six isolates displayed antibiotic resistance, with 27 isolates resistant to more than one antibiotic, including a subspecies IIIb isolate from snake having resistance to five different antibiotics. Twenty-three isolates were resistant to more than one class of antibiotic, and six isolates were resistant to three classes. While these subspecies of IIIa and IIIb cause fewer instances of human illness, they may serve as reservoirs of antibiotic resistance, determinants in the environment, and be sources of contamination of leafy greens associated with product recalls.

  3. Transmission of endemic ST22-MRSA-IV on four acute hospital wards investigated using a combination of spa, dru and pulsed-field gel electrophoresis typing.

    LENUS (Irish Health Repository)

    Creamer, E

    2012-11-01

    The transmission of meticillin-resistant Staphylococcus aureus (MRSA) between individual patients is difficult to track in institutions where MRSA is endemic. We investigated the transmission of MRSA where ST22-MRSA-IV is endemic on four wards using demographic data, patient and environmental screening, and molecular typing of isolates. A total of 939 patients were screened, 636 within 72 h of admission (on admission) and 303 >72 h after admission, and 1,252 environmental samples were obtained. Isolates were typed by spa, dru and pulsed-field gel electrophoresis (PFGE) typing. A composite dendrogram generated from the three sets of typing data was used to divide isolates into \\'dendrogram groups\\' (DGs). Ten percent of patients (92\\/939) were MRSA-positive; 7 % (44\\/636) on admission and 16 % (48\\/303) >72 h after admission (p = 0.0007). MRSA was recovered from 5 % of environmental specimens (65\\/1,252). Most isolates from patients (97 %, 85\\/88) and the environment (97 %, 63\\/65) exhibited the ST22-MRSA-IV genotype. Four DGs (DG1, DG4, DG16 and DG17) accounted for 58 % of ST22-MRSA-IV isolates from patients. Epidemiological evidence suggested cross-transmission among 44\\/92 patients (48 %) but molecular typing confirmed probable cross-transmission in only 11 instances (13 %, 11\\/88), with the majority of cross-transmission (64 %; 7\\/11) occurring on one ward. In the setting of highly clonal endemic MRSA, the combination of local epidemiology, PFGE, spa and dru typing provided valuable insights into MRSA transmission.

  4. Enhanced discrimination of highly clonal ST22-methicillin-resistant Staphylococcus aureus IV isolates achieved by combining spa, dru, and pulsed-field gel electrophoresis typing data.

    LENUS (Irish Health Repository)

    Shore, Anna C

    2010-05-01

    ST22-methicillin-resistant Staphylococcus aureus type IV (ST22-MRSA-IV) is endemic in Irish hospitals and is designated antibiogram-resistogram type-pulsed-field group (AR-PFG) 06-01. Isolates of this highly clonal strain exhibit limited numbers of pulsed-field gel electrophoresis (PFGE) patterns and spa types. This study investigated whether combining PFGE and spa typing with DNA sequencing of the staphylococcal cassette chromosome mec element (SCCmec)-associated direct repeat unit (dru typing) would improve isolate discrimination. A total of 173 MRSA isolates recovered in one Irish hospital during periods in 2007 and 2008 were investigated using antibiogram-resistogram (AR), PFGE, spa, dru, and SCCmec typing. Isolates representative of each of the 17 pulsed-field group 01 (PFG-01) spa types identified underwent multilocus sequence typing, and all isolates were ST22. Ninety-seven percent of isolates (168 of 173) exhibited AR-PFG 06-01 or closely related AR patterns, and 163 of these isolates harbored SCCmec type IVh. The combination of PFGE, spa, and dru typing methods significantly improved discrimination of the 168 PFG-01 isolates, yielding 65 type combinations with a Simpson\\'s index of diversity (SID) of 96.53, compared to (i) pairwise combinations of spa and dru typing, spa and PFGE typing, and dru and PFGE typing, which yielded 37, 44, and 43 type combinations with SIDs of 90.84, 91.00, and 93.57, respectively, or (ii) individual spa, dru, and PFGE typing methods, which yielded 17, 17, and 21 types with SIDs of 66.9, 77.83, and 81.34, respectively. Analysis of epidemiological information for a subset of PFG-01 isolates validated the relationships inferred using combined PFGE, spa, and dru typing data. This approach significantly enhances discrimination of ST22-MRSA-IV isolates and could be applied to epidemiological investigations of other highly clonal MRSA strains.

  5. Quantification of PEGylated proteases with varying degree of conjugation in mixtures: An analytical protocol combining protein precipitation and capillary gel electrophoresis.

    Science.gov (United States)

    Morgenstern, Josefine; Busch, Markus; Baumann, Pascal; Hubbuch, Jürgen

    2016-09-01

    PEGylation, i.e. the covalent attachment of chemically activated polyethylene glycol (PEG) to proteins, is a technique commonly used in biopharmaceutical industry to improve protein stability, pharmacokinetics and resistance to proteolytic degradation. Therefore, PEGylation represents a valuable strategy to reduce autocatalysis of biopharmaceutical relevant proteases during production, purification and storage. In case of non-specific random conjugation the existence of more than one accessible binding site results in conjugates which vary in position and number of attached PEG molecules. These conjugates may differ considerably in their physicochemical properties. Optimizing the reaction conditions with respect to the degree of PEGylation (number of linked PEG molecules) using high-throughput screening (HTS) technologies requires a fast and reliable analytical method which allows stopping the reaction at defined times. In this study an analytical protocol for PEGylated proteases is proposed combining preservation of sample composition by trichloroacetic acid (TCA) precipitation with high-throughput capillary gel electrophoresis (HT-CGE). The well-studied protein hen egg-white lysozyme served as a model system for validating the newly developed analytical protocol for 10kDa mPEG-aldehyde conjugates. PEGamer species were purified by chromatographic separation for calibrating the HT-CGE system. In a case study, the serine protease Savinase(®) which is highly sensitive to autocatalysis was randomly modified with 5kDa and 10kDa mPEG-aldehyde and analyzed. Using the presented TCA protocol baseline separation between PEGamer species was achieved allowing for the analysis of heterogeneous PEGamer mixtures while preventing protease autocatalysis. PMID:27521256

  6. Proteome changes of lungs artificially infected with H-PRRSV and N-PRRSV by two-dimensional fluorescence difference gel electrophoresis

    Directory of Open Access Journals (Sweden)

    Zhu Kongju

    2010-05-01

    Full Text Available Abstract Background Porcine reproductive and respiratory syndrome with PRRS virus (PRRSV infection, which causes significant economic losses annually, is one of the most economically important diseases affecting swine industry worldwide. In 2006 and 2007, a large-scale outbreak of highly pathogenic porcine reproductive and respiratory syndrome (PRRS happened in China and Vietnam. However little data is available on global host response to PRRSV infection at the protein level, and similar approaches looking at mRNA is problematic since mRNA levels do not necessarily predict protein levels. In order to improve the knowledge of host response and viral pathogenesis of highly virulent Chinese-type PRRSV (H-PRRSV and Non-high-pathogenic North American-type PRRSV strains (N-PRRSV, we analyzed the protein expression changes of H-PRRSV and N-PRRSV infected lungs compared with those of uninfected negative control, and identified a series of proteins related to host response and viral pathogenesis. Results According to differential proteomes of porcine lungs infected with H-PRRSV, N-PRRSV and uninfected negative control at different time points using two-dimensional fluorescence difference gel electrophoresis (2D-DIGE and mass spectrometry identification, 45 differentially expressed proteins (DEPs were identified. These proteins were mostly related to cytoskeleton, stress response and oxidation reduction or metabolism. In the protein interaction network constructed based on DEPs from lungs infected with H-PRRSV, HSPA8, ARHGAP29 and NDUFS1 belonged to the most central proteins, whereas DDAH2, HSPB1 and FLNA corresponded to the most central proteins in those of N-PRRSV infected. Conclusions Our study is the first attempt to provide the complex picture of pulmonary protein expression during H-PRRSV and N-PRRSV infection under the in vivo environment using 2D-DIGE technology and bioinformatics tools, provides large scale valuable information for better

  7. A comparison of the sensitivity of three gel electrophoresis methods for the RFLP analysis of mycobacterial heat shock protein 65 gene%三种凝胶电泳分析分枝杆菌热休克蛋白65基因酶切片段的灵敏度比较

    Institute of Scientific and Technical Information of China (English)

    张彩萍; 王洪生; 冯雨苗; 林麟; 崔盘根; 陈敏; 吴勤学

    2013-01-01

    Objective To compare the performance of 2% (w/v) agarose gel,2% (w/v) Metaphor agarose gel and 10%(w/v) nondenaturating polyacrylamide gel in the PCR-restriction fragment length polymorphism (RFLP) analysis of mycobacterial heat shock protein 65 (hsp65) gene.Methods This study included 8 Mycobacteria strains,including clinical isolates and standard strains of Mycobacteria tuberculosis and Mycobacterium intracellulare.Bacterialsuspension of these strains was prepared with the concentration of bacterial cells varying from 10 to 106per milliliter.PCR was performed to amplify the hsp65 gene with a pair of universal primers followed by the digestion of amplicons with two restriction endonucleases,BstE Ⅱ and Hae Ⅲ.Then,the restriction enzyme-digested fragments were subjected to electrophoresis in 2% agarose gel,2% Metaphor agarose gel and 10% nondenaturating polyacrylamide gel respectively.Results As analysis of variance showed,the three gel electrophoresis methods were statistically different in sensitivity for the RFLP analysis of mycobacterial hsp65 gene (F =36.379,P < 0.01).Least significance difference (LSD) procedure revealed that the 2% agarose gel-based electrophoresis was less sensitive than the 2% Metaphor agarose gel-and 10% non-denaturing polyacrylamide gel-based electrophoresis (both P < 0.01),and no significant differences were observed between the 2% Metaphor agarose gel-and 10% non-denaturing polyacrylamide gel-based electrophoresis (P > 0.05).Conclusion The 2% Metaphor agarose gel-and 10%nondenaturating polyacrylamide gel-based electrophoresis methods appear to be more sensitive than the 2% agarose gel-based electrophoresis method for the PCR-RFLP analysis of mycobacterial hsp65 gene.%目的 比较2%(w/v)琼脂糖凝胶、2% (w/v)Metaphor琼脂糖凝胶和10%(w/v)非变性聚丙烯酰胺凝胶分析分枝杆菌热休克蛋白65(hsp65)基因酶切片段的灵敏度.方法 分枝杆菌8株,分别制成106~101

  8. A microchip electrophoresis-mass spectrometric platform with double cell lysis nano-electrodes for automated single cell analysis.

    Science.gov (United States)

    Li, Xiangtang; Zhao, Shulin; Hu, Hankun; Liu, Yi-Ming

    2016-06-17

    Capillary electrophoresis-based single cell analysis has become an essential approach in researches at the cellular level. However, automation of single cell analysis has been a challenge due to the difficulty to control the number of cells injected and the irreproducibility associated with cell aggregation. Herein we report the development of a new microfluidic platform deploying the double nano-electrode cell lysis technique for automated analysis of single cells with mass spectrometric detection. The proposed microfluidic chip features integration of a cell-sized high voltage zone for quick single cell lysis, a microfluidic channel for electrophoretic separation, and a nanoelectrospray emitter for ionization in MS detection. Built upon this platform, a microchip electrophoresis-mass spectrometric method (MCE-MS) has been developed for automated single cell analysis. In the method, cell introduction, cell lysis, and MCE-MS separation are computer controlled and integrated as a cycle into consecutive assays. Analysis of large numbers of individual PC-12 neuronal cells (both intact and exposed to 25mM KCl) was carried out to determine intracellular levels of dopamine (DA) and glutamic acid (Glu). It was found that DA content in PC-12 cells was higher than Glu content, and both varied from cell to cell. The ratio of intracellular DA to Glu was 4.20±0.8 (n=150). Interestingly, the ratio drastically decreased to 0.38±0.20 (n=150) after the cells are exposed to 25mM KCl for 8min, suggesting the cells released DA promptly and heavily while they released Glu at a much slower pace in response to KCl-induced depolarization. These results indicate that the proposed MCE-MS analytical platform may have a great potential in researches at the cellular level. PMID:27207575

  9. Electrochemical Detection of Alkaline Phosphatase in BALB/c Mouse Fetal Liver Stromal Cells with Capillary Electrophoresis

    Institute of Scientific and Technical Information of China (English)

    Xue Mei SUN; Dong LI; Zeng Liang BAI; Wen Rui JIN

    2004-01-01

    A method for determination of alkaline phosphatase (ALP) in BALB/c mouse fetal liver stromal cells has been described based on the catalytic reaction. After the cell extract is incubated with the substrate disodium phenyl phosphate, the reaction product phenol generated by ALP is determined by capillary electrophoresis with electrochemical detection.

  10. Establishment of Two-Dimensional Gel Electrophoresis System for Rat Cortex Mitochondria%大鼠皮层线粒体双向凝胶电泳体系的建立

    Institute of Scientific and Technical Information of China (English)

    杨涌涛; 谢鹏; 陈康宁; 黄河清; 贺伟峰

    2013-01-01

    Objective To establish two-dimensional gel electrophoresis system for rat cortex mitochondria. Methods The adult male SD rats were sacrificed by cervical dislocation , the brain tissues quickly harvested and thecortex isolated on ice. The mitochondria were extracted and purified twice by density gradient centrifugation. Two-dimensional gel electrophoresis was performed. Immobilized pH gradient isoelectric focusing (IPG-IEF) was modified and carried out. The gels were focused at 3500 V for a total of 14000Vh and then subjected to SDS-PAGE and silver staining. Results Electrophoregram of rat cerebral cortex mitochondria was obtained with high resolu -tion by using the established two -dimensional gel electrophoresis system. Conclusion The two-dimensional gel electrophoresis system for rat cortex mitochondria was successfully established , which provides a theoretical basis and a technical support for research of cerebral cortex mitochondrion pro -teins in diseases.%目的 构建稳定的大鼠皮层线粒体双向凝胶电泳体系.方法 SD大鼠在规定的时间内快速断头取脑,冰上分离大脑皮层组织,两次密度梯度离心纯化线粒体.利用双向凝胶电泳技术改良等电聚焦的电压在3 500V聚焦,总伏小时固定为14 000 Vh.以12%的SDS-PAGE进行第二向电泳,银染显色.结果得到了分辨率较高的皮层线粒体蛋白双向凝胶电泳图谱.结论 利用改进的方法构建了高质量的双向电泳图谱,为各种疾病状态下皮层线粒体差异蛋白的研究提供了实验基础.

  11. Correlation of acidic and basic carrier ampholyte and immobilized pH gradient two-dimensional gel electrophoresis patterns based on mass spectrometric protein identification

    DEFF Research Database (Denmark)

    Nawrocki, A; Larsen, Martin Røssel; Podtelejnikov, A V;

    1998-01-01

    -MS) to determine the identities of 335 protein spots in these two 2-D gel systems, including a substantial number of basic proteins which had never been identified before. Proteins that were identified in both gel systems allowed us to cross-reference the gel patterns. Vector analysis of these cross......-references demonstrated that there is no obvious pattern by which the mobility of a protein in one gel system can be used to predict its mobility in the other. Thus, as laboratories adopt the immobilized pH gradient-based 2-D gel systems, the only reliable means of translating the data gained with the carrier ampholyte...

  12. Analysis of pulsed-field gel electrophoresis molecular subtyping of Shigella strains in Shenzhen%深圳市志贺菌脉冲场电泳分子分型分析

    Institute of Scientific and Technical Information of China (English)

    兰全学; 扈庆华; 石晓路; 王冰; 林一曼; 程锦泉; 张顺祥

    2008-01-01

    目的 分析深圳市2001-2006年分离志贺菌菌株之间的相关性,初步建立志贺菌的脉冲场电泳(pulsed-field gel electrophoresis,PFGE)分子分型监测网络.方法 55株志贺菌基因组DNA经Xba Ⅰ酶切,通过PFGE获得电泳图谱,利用BioNumerics软件对图谱进行聚类分析.结果 55株志贺菌被分为41种PFGE图谱,聚类分析显示32株细菌谱型属于同一个群,其余菌株谱型差异较大.结论 深圳地区存在遗传紧密相关的志贺菌流行克隆,也存在遗传不相关克隆.PFGE分子分型监测网络的建立,有助于细菌性痢疾的主动监测、暴发调查和传染源追踪.%Objective To analyze the genetic relations of Shigella isolated from Shenzhen in 2001-2006 and develop primary molecular subtyping surveillance network of Shigella. Methods Chromosomal DNAs from 55 isolated in agarose were digested with the restriction enzyme Xba Ⅰ , and then were analyzed by pulsed-field gel electrophoresis. Pulsed-field gel electrophoresis (PFGE) patterns were clustered using BioNumerics software. Results All 41 distinctive PFGE patterns were identified among 55 strains. 32 strains belonged to one cluster. Differences were observed in other strains. Conclusion Both genetic-related clones and non-related clones of Shigella existed in Shenzhen. The development of PFGE molecular subtyping surveillance network would contribute to the active surveillance, outbreak investigation and source tracking for Shigellosis.

  13. Pulsed-Field Gel Electrophoresis Typing of Escherichia coli Strains from Samples Collected before and after Pivmecillinam or Placebo Treatment of Uncomplicated Community-Acquired Urinary Tract Infection in Women

    OpenAIRE

    Ejrnaes, Karen; Sandvang, Dorthe; Lundgren, Bettina; Ferry, Sven; Holm, Stig; Monsen, Tor; Lundholm, Rolf; Frimodt-Moller, Niels

    2006-01-01

    The primary infecting Escherichia coli strains from 156 women with community-acquired uncomplicated urinary tract infection (UTI) randomized to pivmecillinam or placebo and the E. coli strains causing UTI at two follow-up visits were typed using pulsed-field gel electrophoresis (PFGE). In the pivmecillinam treatment group PFGE showed that among patients having a negative urine culture at the first follow-up 77% (46/60) had a relapse with the primary infecting E. coli strain and 23% (14/60) ha...

  14. Evaluation of diffusion in gel entrapment cell culture within hollow fibers

    Institute of Scientific and Technical Information of China (English)

    Dan-Qing Wu; Guo-Liang Zhang; Chong Shen; Qian Zhao; Hui Li; Qin Meng

    2005-01-01

    AIM: To investigate diffusion in mammalian cell culture by gel entrapment within hollow fibers.METHODS: Freshly isolated rat hepatocytes or human oral epidermoid carcinoma (KB) cells were entrapped in type Ⅰ collagen solutions and statically cultured inside microporous and ultrafiltration hollow fibers. During the culture time collagen gel contraction, cell viability and specific function were assessed. Effective diffusion coefficients of glucose in cell-matrix gels were determined by lag time analysis in a diffusion cell.R ESULTS: Significant gel contractions occurred in the collagen gels by entrapment of either viable hepatocytes or KB cells. And the gel contraction caused a significant reduction on effective diffusion coefficient of glucose. The cell viability assay of both hepatocytes and KB cells statically cultured in hollow fibers by collagen entrapment further confirmed the existence of the inhibited mass transfer by diffusion. Urea was secreted about 50% more by hepatocytes entrapped in hollow fibers with pore size of 0.1 pm than that in hollow fibers with MWCO of 100 ku.CONCLUSION: Cell-matrix gel and membrane pore size are the two factors relevant to the limited mass transfer by diffusion in such gel entrapment of mammalian cell culture.

  15. Performance enhancement of phosphoric acid fuel cell using phosphosilicate gel based electrolyte

    Institute of Scientific and Technical Information of China (English)

    Kajari Kargupta; Swati Saha; Dipali Banerjee; Mrinal Seal; Saibal Ganguly

    2012-01-01

    Replacement of phosphoric acid electrolyte by phosphosilicate gel based electrolytes is proposed for performance enhancement of phosphoric acid fuel cell (PAFG).Phosphosilicate gel in paste form and in powder form is synthesized from tetraethoxysilane and orthophosphoric acid using sol-gel method for two different P/Si ratio of 5 and 1.5 respectively.Replacement of phosphoric acid electrolyte by phosphosilicate gel paste enhances the peak power generation of the fuel cell by 133% at 120 ℃ cell temperature; increases the voltage generation in the ohmic regime and extends the maximum possible load current.Polyinyl alcohol (PVA) is used to bind the phosphosilicate gel powder and to form the hybrid crosslinked gel polymer electrolyte membrane.Soaking the membrane with phosphoric acid solution,instead of that with water improves the proton conductivity of the membrane,enhances the voltage and power generation by the fuel cell and extends the maximum possible operating temperature.At lower operating temperature of 70 ℃,peak power produced by phosphosilicate gel polymer electrolyte membrane fuel cell ( PGMFC ) is increased by 40% compared to that generated by phosphoric acid fuel cell ( PAFC ).However,the performance of composite membrane diminishes as the cell temperature increases.Thus phosphosilicate gel in paste form is found to be a good alternative of phosphoric acid electrolyte at medium operating temperature range while phosphosilicate gel-PVA composite offers performance enhancement at low operating temperatures.

  16. On-line wall-free cell for laser-induced fluorescence detection in capillary electrophoresis.

    Science.gov (United States)

    Yu, Chang-Zhu; He, You-Zhao; Xie, Hai-Yang; Gao, Yong; Gan, Wu-Er; Li, Jun

    2009-05-15

    A wall-free detection method based on liquid junction in a capillary gap was proposed for laser-induced fluorescence (LIF) of capillary electrophoresis (CE). The capillary gap of the wall-free cell was fabricated by etching a 10-mm x 50-microm I.D. fused-silica capillary to obtain a polyimide coating sleeve, decoating about 6mm at one end of both 50 microm I.D. separation and liquid junction capillary, inserting the treated capillary ends into the coating sleeve oppositely, fixing the capillaries with a gap distance of 140 microm by epoxy glue and removing the coating sleeve by burning. The theoretical model, experimental results and wall-free cell images indicated that the gap distance and applied voltage were main influence factors on the wall-free detection. Since the wall-free cell increased the absorption light path and avoided the stray light from the capillary wall, it improved the ratio of signal to noise and limit of detection (LOD) of CE-LIF. Three flavin compounds of riboflavin (RF), flavin mononucleotide sodium (FMN) and flavin adenine dinucleotide disodium (FAD) were used to evaluate the wall-free detection method. Compared with on-column cell, the LODs of the wall-free cell were improved 15-, 6- and 9-fold for RF, FMN and FAD, respectively. The linear calibration concentrations of the flavins ranged from 0.005 to 5.0 micromol/L. The column efficiency was in the range from 1.0 x 10(5) to 2.5 x 10(5) plates. The wall-free detection of CE-LIF was applied to the analysis of the flavins in spinach and lettuce leaves. PMID:19329123

  17. Comparative two-dimensional gel analysis and microsequencing identifies gelsolin as one of the most prominent downregulated markers of transformed human fibroblast and epithelial cells

    DEFF Research Database (Denmark)

    Vandekerckhove, J; Bauw, G; Vancompernolle, K;

    1990-01-01

    A systematic comparison of the protein synthesis patterns of cultured normal and transformed human fibroblasts and epithelial cells, using two-dimensional gel protein analysis combined with computerized imaging and data acquisition, identified a 90-kD protein (SSP 5714) as one of the most striking...... downregulated markers typical of the transformed state. Using the information stored in the comprehensive human cellular protein database, we found this protein strongly expressed in several fetal tissues and one of them, epidermis, served as a source for preparative two-dimensional gel electrophoresis. Partial...... coelectrophoresis with purified human gelsolin. These results suggest that an important regulatory protein of the microfilament system may play a role in defining the phenotype of transformed human fibroblast and epithelial cells in culture. Udgivelsesdato: 1990-Jul...

  18. Modelling of conditions for the enantiomeric separation of beta(2)-adrenergic sympathicomimetics by capillary electrophoresis using cyclodextrins as chiral selectors in a polyethylene glycol gel

    NARCIS (Netherlands)

    de Boer, T; Bijma, R; Ensing, K

    1999-01-01

    A two-factor central composite design was used to determine a mathematical model for prediction of the optimal conditions for the separation of the enantiomers of some widely used beta(2)-sympathicomimetic drugs (beta(2)-agonists) by capillary electrophoresis using cyclodextrins (CD) as a chiral sel

  19. Apparatus for electrophoresis separation

    Science.gov (United States)

    Anderson, Norman L.

    1978-01-01

    An apparatus is disclosed for simultaneously performing electrophoresis separations on a plurality of slab gels containing samples of protein, protein subunits or nucleic acids. A reservoir of buffer solution is divided into three compartments by two parallel partitions having vertical slots spaced along their length. A sheet of flexible, electrically insulative material is attached to each partition and is provided with vertical slits aligned with the slots. Slab-gel holders are received within the slots with the flexible material folded outwardly as flaps from the slits to overlay portions of the holder surfaces and thereby act as electrical and liquid seals. An elongated, spaghetti-like gel containing a sample of specimen that was previously separated by isoelectric focusing techniques is vertically positioned along a marginal edge portion of the slab gel. On application of an electrical potential between the two outer chambers of buffer solution, a second dimensional electrophoresis separation in accordance with molecular weight occurs as the specimen molecules migrate across the slab gel.

  20. GJB2全序列长链PCR和琼脂糖凝胶电泳方法研究%Long-chain PCR Method and Agarose Gel Electrophoresis for Full Sequence of GJB2 Gene

    Institute of Scientific and Technical Information of China (English)

    王辉兵; 于飞; 戴朴; 单希征; 袁永一; 张昕; 康东洋; 韩东一

    2014-01-01

    目的:探讨GJB2全序列长链PCR方法和琼脂糖凝胶电泳方法,以及影响长链PCR和电泳结果的可能因素。方法应用Primer Premier 5.0软件和Oligo 6 Demo软件针对GJB2全序列设计引物,应用DNA聚合酶KOD FX Neo试剂盒进行两步法长链PCR扩增,调整加入DNA模板量、PCR延伸时间、循环次数等影响PCR产物量,通过0.8%琼脂糖凝胶电泳检测PCR产物长度和量,调整加样槽的宽度、加样量、电泳电压、电流、电泳时间得到清晰条带,若PCR产物存在大片段碱基插入或缺失,用限制性内切酶BamHI进行内切酶反应,初步判断插入或缺失的大致位置。结果正向引物F:5’-AGATCGGGACCTCGAAGGGGACTTG-3’;反向引物R:5’-AGGTGGGCACGGGGTTAGGTAGAAA-3’,扩增片段长5887 bp。长链PCR条件为:50μl的反应体系中加入2μl(约40 ng)的基因组DNA,预变性94℃2分钟,变性98℃10秒,68℃延伸5分钟,共32个循环。电泳条件为:加样槽5 mm宽,每槽加样0.8μl PCR产物,电泳电压50 V,电流50 mA,电泳时间140分钟。结论应用DNA聚合酶KOD FX Neo试剂盒进行两步法长链PCR,可进行GJB2全序列扩增,影响PCR的可能因素为引物、DNA模板的质和量、延伸时间、循环次数等。0.8%琼脂糖凝胶电泳可获得较好的分离效果,影响电泳可能的因素为加样槽宽度、加样量、电泳电压、电流、电泳时间等。%Objective To explore the long-chain PCR method and agarose gel electrophoresis for the full sequence of GJB2 gene and to discuss the possible factors affecting the long-chain PCR and electrophoresis results. Methods The primers for the full sequence of GJB2 gene were designed by Primer Premier 5.0 software and Oligo 6 Demo software and the sequence were amplified using DNA polymerase of KOD FX Neo kit by the two-step PCR method. The product amount of PCR was controlled by the amount of the DNA template, the extension time and the

  1. A chip-type thin-layer electrochemical cell coupled with capillary electrophoresis for online separation of electrode reaction products

    Energy Technology Data Exchange (ETDEWEB)

    He, Jian-Bo, E-mail: jbhe@hfut.edu.cn; Cui, Ting; Zhang, Wen-Wen; Deng, Ning

    2013-07-05

    Graphical abstract: -- Highlights: •A new coupling of thin-layer electrolysis with capillary electrophoresis (CE). •Rapid electrolysis, direct sampling followed by online CE separation. •At least 13 products of quercetin oxidation were separated. •Thermodynamic and kinetic parameters were determined from CE peak areas. -- Abstract: A coupling technique of thin-layer electrolysis with high-performance capillary electrophoresis/UV–vis technique(EC/HPCE/UV–vis) is developed for online separation and determination of electrode reaction products. A chip-type thin-layer electrolytic (CTE) cell was designed and fabricated, which contains a capillary channel and a background electrolyte reservoir, allowing rapid electrolysis, direct sampling and online electrophoretic separation. This chip-type setup was characterized based on an electrophoresis expression of Nernst equation that was applied to the redox equilibrium of o-tolidine at different potentials. The utility of the method was demonstrated by separating and determining the electro-oxidation products of quercetin in different pH media. Two main products were always found in the studied time, potential and pH ranges. The variety of products increased not only with increasing potential but also with increasing pH value, and in total, at least 13 products were observed in the electropherograms. This work illustrates a novel example of capillary electrophoresis used online with thin-layer electrolysis to separate and detect electrode reaction products.

  2. The application of methylation specific electrophoresis (MSE to DNA methylation analysis of the 5' CpG island of mucin in cancer cells

    Directory of Open Access Journals (Sweden)

    Yokoyama Seiya

    2012-02-01

    Full Text Available Abstract Background Methylation of CpG sites in genomic DNA plays an important role in gene regulation and especially in gene silencing. We have reported mechanisms of epigenetic regulation for expression of mucins, which are markers of malignancy potential and early detection of human neoplasms. Epigenetic changes in promoter regions appear to be the first step in expression of mucins. Thus, detection of promoter methylation status is important for early diagnosis of cancer, monitoring of tumor behavior, and evaluating the response of tumors to targeted therapy. However, conventional analytical methods for DNA methylation require a large amount of DNA and have low sensitivity. Methods Here, we report a modified version of the bisulfite-DGGE (denaturing gradient gel electrophoresis using a nested PCR approach. We designated this method as methylation specific electrophoresis (MSE. The MSE method is comprised of the following steps: (a bisulfite treatment of genomic DNA, (b amplification of the target DNA by a nested PCR approach and (c applying to DGGE. To examine whether the MSE method is able to analyze DNA methylation of mucin genes in various samples, we apply it to DNA obtained from state cell lines, ethanol-fixed colonic crypts and human pancreatic juices. Result The MSE method greatly decreases the amount of input DNA. The lower detection limit for distinguishing different methylation status is Conclusions The MSE method can provide a qualitative information of methylated sequence profile. The MSE method allows sensitive and specific analysis of the DNA methylation pattern of almost any block of multiple CpG sites. The MSE method can be applied to analysis of DNA methylation status in many different clinical samples, and this may facilitate identification of new risk markers.

  3. Controlling Gel Structure to Modulate Cell Adhesion and Spreading on the Surface of Microcapsules.

    Science.gov (United States)

    Zheng, Huizhen; Gao, Meng; Ren, Ying; Lou, Ruyun; Xie, Hongguo; Yu, Weiting; Liu, Xiudong; Ma, Xiaojun

    2016-08-01

    The surface properties of implanted materials or devices play critical roles in modulating cell behavior. However, the surface properties usually affect cell behaviors synergetically so that it is still difficult to separately investigate the influence of a single property on cell behavior in practical applications. In this study, alginate-chitosan (AC) microcapsules with a dense or loose gel structure were fabricated to understand the effect of gel structure on cell behavior. Cells preferentially adhered and spread on the loose gel structure microcapsules rather than on the dense ones. The two types of microcapsules exhibited nearly identical surface positive charges, roughness, stiffness, and hydrophilicity; thus, the result suggested that the gel structure was the principal factor affecting cell behavior. X-ray photoelectron spectroscopy analyses demonstrated that the overall percentage of positively charged amino groups was similar on both microcapsules. The different gel structures led to different states and distributions of the positively charged amino groups of chitosan, so we conclude that the loose gel structure facilitated greater cell adhesion and spreading mainly because more protonated amino groups remained unbound and exposed on the surface of these microcapsules. PMID:27404911

  4. Microchip-based Integration of Cell Immobilization, Electrophoresis, Post-column Derivatization, and Fluorescence Detection for Monitoring the Release of Dopamine from PC 12 Cells

    OpenAIRE

    Li, Michelle W.; Martin, R. Scott

    2008-01-01

    In this paper, we describe the fabrication and evaluation of a multilayer microchip device that can be used to quantitatively measure the amount of catecholamines released from PC 12 cells immobilized within the same device. This approach allows immobilized cells to be stimulated on-chip and, through rapid actuation of integrated microvalves, the products released from the cells are repeatedly injected into the electrophoresis portion of the microchip, where the analytes are separated based u...

  5. Calcium alginate gels as stem cell matrix-making paracrine stem cell activity available for enhanced healing after surgery.

    Directory of Open Access Journals (Sweden)

    Andreas Schmitt

    Full Text Available Regeneration after surgery can be improved by the administration of anabolic growth factors. However, to locally maintain these factors at the site of regeneration is problematic. The aim of this study was to develop a matrix system containing human mesenchymal stem cells (MSCs which can be applied to the surgical site and allows the secretion of endogenous healing factors from the cells. Calcium alginate gels were prepared by a combination of internal and external gelation. The gelling behaviour, mechanical stability, surface adhesive properties and injectability of the gels were investigated. The permeability of the gels for growth factors was analysed using bovine serum albumin and lysozyme as model proteins. Human MSCs were isolated, cultivated and seeded into the alginate gels. Cell viability was determined by AlamarBlue assay and fluorescence microscopy. The release of human VEGF and bFGF from the cells was determined using an enzyme-linked immunoassay. Gels with sufficient mechanical properties were prepared which remained injectable through a syringe and solidified in a sufficient time frame after application. Surface adhesion was improved by the addition of polyethylene glycol 300,000 and hyaluronic acid. Humans MSCs remained viable for the duration of 6 weeks within the gels. Human VEGF and bFGF was found in quantifiable concentrations in cell culture supernatants of gels loaded with MSCs and incubated for a period of 6 weeks. This work shows that calcium alginate gels can function as immobilization matrices for human MSCs.

  6. Hydroponics gel as a new electrolyte gelling agent for alkaline zinc-air cells

    Science.gov (United States)

    Othman, R.; Basirun, W. J.; Yahaya, A. H.; Arof, A. K.

    The viability of hydroponics gel as a new alkaline electrolyte gelling agent is investigated. Zinc-air cells are fabricated employing 12 wt.% KOH electrolyte immobilised with hydroponics gel. The cells are discharged at constant currents of 5, 50 and 100 mA. XRD and SEM analysis of the anode plates after discharge show that the failure mode is due to the formation of zinc oxide insulating layers and not due to any side reactions between the gel and the plate or the electrolyte.

  7. An accurate radioimmunoassay of human growth hormone with separation on polyacrylamide gel electrophoresis of free antigen, antigen-antibody complex and damaged labelled antigen. Further study of damaged labelled antigen to obtain long-lasting labelled products

    International Nuclear Information System (INIS)

    The purpose of this work was to obtain a radioimmunoassay that would be sufficiently accurate and precise to provide a suitable means of determining human growth hormone (hGH) in both extracts and physiological fluids for specific research purposes rather than for routine clinical assays where the labelled products could be used as long as possible. The only technique found that could satisfy these requirements was polyacrylamide gel electrophoresis (PAGE), though in some respects it is more laborious than other techniques. By introducing some modifications to the original method of Davis it was possible, with 11-cm tubes, to separate the free, the antibody-bound, and the damaged labelled antigen on the same gel. The method, being able to detect separately and independently these three components and to give a better control of the analytically dangerous ''damaged'' antigens, furnished accurate and reproducible curves. An example of a determination is the one on KABI-Crescormon which compares the results obtained with the present technique with those presented by another laboratory. Thanks to this method, the labelled antigen could be used for up to one month, after which re-purification on Sephadex enabled the same labelled product to be used profitably for two more months. Parallel to this work, a study has been performed on the various components originating in this so-called process of ''damaging'', and particular importance has been given to a more precise knowledge of the amount of antigen, in terms of mass, present in an assay. (author)

  8. Initial research of screening for the differentially expressed proteins in beagles irradiated with 4.5 Gy 60Co γ-rays by two-dimensional gel electrophoresis and mass spectrometry

    International Nuclear Information System (INIS)

    Objective: To explore the mechanisms of cytokines on acute radiation disease in irradiation beagles. Methods: The sera of beagles irradiated with 4.5 Gy γ-rays with cytokines treatment was collected at different time points post irradiation. The two-dimensional gel electrophoresis (2-DE) was differentially expressed proteins with significance, and the amino acid sequences should be determined. Results: High resolution 2-DE gel map was obtained. There were six differentially expressed proteins in sera of irradiated beagles at different time points. Four protein spots were successfully identified by MS. A significant spot was identified as serum amyloid A (SAA) by HD-MS, with relative molecular mass of 13 077 and isoelectric point of 6.26. Expression of SAA was not found 1 d pre-irradiation and 36 d post-irradiation, but increased slightly 1 d (0.2166) and significantly 14 d post-irradiation (0.4577). Conclusions: The expression of serum amyloid A was consistent with the process of acute radiation injury, which might indicate the turnover of the disease. (authors)

  9. Comprehensive two-dimensional gel protein databases offer a global approach to the analysis of human cells: the transformed amnion cells (AMA) master database and its link to genome DNA sequence data

    DEFF Research Database (Denmark)

    Celis, J E; Gesser, B; Rasmussen, H H;

    1990-01-01

    A total of 3430 polypeptides (2592 cellular; 838 secreted) from transformed human amnion cells (AMA) labeled with [35S]methionine were separated and recorded using computer-aided two-dimensional (2-D) gel electrophoresis. A master 2-D gel database of cellular protein information that includes both......, mitochondria, Golgi, ribosomes, intermediate filaments, microfilaments and microtubules), levels in fetal human tissues, partial protein sequences (containing information on 48 human proteins microsequenced so far), cell cycle-regulated proteins, proteins sensitive to interferons alpha, beta, and gamma, heat......-specific proteins, to microsequence them and store the information in the database, to identify the corresponding genes, to search for homology with previously characterized proteins and to study the function of groups of proteins (pathways, organelles, etc.) that exhibit interesting regulatory properties...

  10. Effects of estrogen on collagen gel contraction by human retinal glial cells

    Institute of Scientific and Technical Information of China (English)

    QIU Qing-hua; CHEN Zhi-Yi; YIN Li-li; ZHENG Zhi; WU Xing-wei

    2012-01-01

    Background There are definite gender differences in patients with macular holes.Menopausal women over 50 years are most affected.We aimed to observe the effect of estrogen on collagen gel contraction by cultured human retinal glial cells.It is speculated that estrogen could strengthen the tensile stress of the macula by maintaining the correct morphology and contraction.Methods Estrogen was used to determine its effects on collagen gel contraction,and its function was measured using morphological changes in cells.Human retinal glial cells were cultured in collagen solution.The cells were then exposed to collagen gels and the degree of contraction of the gel was determined.Results Estrogen at differing concentrations had no effect on the growth of human retinal glial cells.However,after exposed to collagen gel block,less contraction was noted in the estrogen-treated group than in the control group.Conclusions Estrogen can inhibit collagen gel contraction by glial cells.These results suggest a mechanism for macular hole formation,which is observed in menopausal females.

  11. Two-dimensional electrophoresis analysis of proteomics based on image feature and mathematical morphology

    Institute of Scientific and Technical Information of China (English)

    SHEN; Peng; FAN; Xiaohui; ZENG; Zhen

    2005-01-01

    In this paper, a novel method to automatically detect protein spots on a two-dimensional (2-D) electrophoresis gel image is proposed to implement proteomics analysis of complex analyte.On the basis of the identifying spots results based on color variation and spot size features, morphological feature is introduced as a new criterion to distinguish protein spots from non-protein spots.Image-sharpening, edge-detecting and morphological feature extraction methods were consequently combined to detect protein spots on a 2-D electrophoresis gel image subject to strong disturbance.The proposed method was applied to detect the protein spots of proteomic gel images from E.coli cell, human kidney tissue and human serum.The results demonstrated that this method is more accurate and reliable than previous methods such as PDQuest 7.2 and ImageMaster 5.0 software for detecting protein spots on gel images with strong interferences.

  12. Simian virus 40 large T antigen oligomers: analysis of electrophoresis in the absence of detergent.

    OpenAIRE

    Stedman, D; Whittaker, L.; Hand, R

    1985-01-01

    Large T antigen of simian virus 40 is found as monomeric and oligomeric species in transformed cells. These can be demonstrated in cell extracts by velocity centrifugation in sucrose gradients. We analyzed them further in a transformed human line cell (SV80) and a transformed mouse line cell (SVT2). Individual fractions from sucrose gradients were subjected to polyacrylamide gel electrophoresis in the absence of detergent. T-antigen species were then detected by protein blotting and antibody ...

  13. Comparison of two label-free global quantitation methods, APEX and 2D gel electrophoresis, applied to the Shigella dysenteriae proteome

    Directory of Open Access Journals (Sweden)

    Fleischmann Robert D

    2009-06-01

    Full Text Available Abstract The in vitro stationary phase proteome of the human pathogen Shigella dysenteriae serotype 1 (SD1 was quantitatively analyzed in Coomassie Blue G250 (CBB-stained 2D gels. More than four hundred and fifty proteins, of which 271 were associated with distinct gel spots, were identified. In parallel, we employed 2D-LC-MS/MS followed by the label-free computationally modified spectral counting method APEX for absolute protein expression measurements. Of the 4502 genome-predicted SD1 proteins, 1148 proteins were identified with a false positive discovery rate of 5% and quantitated using 2D-LC-MS/MS and APEX. The dynamic range of the APEX method was approximately one order of magnitude higher than that of CBB-stained spot intensity quantitation. A squared Pearson correlation analysis revealed a reasonably good correlation (R2 = 0.67 for protein quantities surveyed by both methods. The correlation was decreased for protein subsets with specific physicochemical properties, such as low Mr values and high hydropathy scores. Stoichiometric ratios of subunits of protein complexes characterized in E. coli were compared with APEX quantitative ratios of orthologous SD1 protein complexes. A high correlation was observed for subunits of soluble cellular protein complexes in several cases, demonstrating versatile applications of the APEX method in quantitative proteomics.

  14. CSE-MECC two-dimensional capillary electrophoresis analysis of proteins in the mouse tumor cell (AtT-20) homogenate

    OpenAIRE

    Chen, Xingguo; Fazal, Md. Abul; Dovichi, Norman J.

    2007-01-01

    Two-dimensional capillary electrophoresis was used for the separation of proteins and biogenic amines from the mouse AtT-20 cell line. The first-dimension capillary contained a TRIS-CHES-SDS-dextran buffer to perform capillary sieving electrophoresis, which is based on molecular weight of proteins. The second-dimension capillary contained a TRIS-CHES-SDS buffer for micel1ar electrokinetic capillary chromatography. After a 61 seconds preliminary separation, fractions from the first-dimension c...

  15. Growth and differentiation of neural stem cells in a three-dimensional collagen gel scaffold

    Institute of Scientific and Technical Information of China (English)

    Fei Huang; Qiang Shen; Jitong Zhao

    2013-01-01

    Collagen protein is an ideal scaffold material for the transplantation of neural stem cells. In this study, rat neural stem cells were seeded into a three-dimensional collagen gel scaffold, with suspension cultured neural stem cells being used as a control group. Neural stem cells, which were cultured in medium containing epidermal growth factor and basic fibroblast growth factor, actively expanded and formed neurospheres in both culture groups. In serum-free medium conditions, the processes extended from neurospheres in the collagen gel group were much longer than those in the suspension culture group. Immunofluorescence staining showed that neurospheres cultured in collagen gels were stained positive for nestin and differentiated cells were stained positive for the neuronal marker βIII-tubulin, the astrocytic marker glial fibrillary acidic protein and the oligodendrocytic marker 2',3'-cyclic nucleotide 3'-phosphodiesterase. Compared with neurospheres cultured in suspension, the differentiation potential of neural stem cells cultured in collagen gels increased, with the formation of neurons at an early stage. Our results show that the three-dimensional collagen gel culture system is superior to suspension culture in the proliferation, differentiation and process outgrowth of neural stem cells.

  16. Combination of 768-well microplate array diagonal gel electrophoresis with duplex PCR of X and Y chromosome markers for quality control of epidemiological DNA banks.

    Science.gov (United States)

    Huang, Shuwen; Chen, Xiao-he; Day, Ian N M

    2006-08-01

    Large DNA banks for human epidemiological studies have become an increasingly important research tool. The power of genotype-phenotype studies is dependent both on the quality of phenotyping and of genotyping and of correct linking of phenotypes to genotypes. Samples must be tracked through numerous steps between subject or patient and post-genotypic data. Only one phenotype, sex, has a perfect and binary correlation with genotype. In mixed sex studies, it may be advantageous for purposes of quality control to keep sexes mixed during the steps from acquisition to DNA bank, in order to be able to check later for sample swaps. We have designed a duplex PCR combining an amplicon from MAOA marking the X chromosome and an amplicon from DDX3Y marking the Y chromosome. We combined this with a simple economical palmtop sized 768-well microplate compatible electrophoresis system developed in-house for examination of duplex PCR products. We applied this quality control test in the validation of two DNA banks.

  17. Enhancing the performance of dye-sensitized solar cells by incorporating nanosilicate platelets in gel electrolyte

    KAUST Repository

    Lai, Yi-Hsuan

    2009-10-01

    Two kinds of gel-type dye-sensitized solar cells (DSSCs), composed of two types of electrolytes, were constructed and the respective cell performance was evaluated in this study. One electrolyte, TEOS-Triton X-100 gel, was based on a hybrid organic/inorganic gel electrolyte made by the sol-gel method and the other was based on poly(vinyidene fluoride-co-hexafluoro propylene) (PVDF-HFP) copolymer. TEOS-Triton X-100 gel was based on the reticulate structure of silica, formed by hydrolysis, and condensation of tetraethoxysilane (TEOS), while its organic subphase was a mixture of surfactant (Triton X-100) and ionic liquid electrolytes. Both DSSC gel-type electrolytes were composed of iodine, 1-propy-3-methyl-imidazolium iodide, and 3-methoxypropionitrile to create the redox couple of I3 -/I-. Based on the results obtained from the I-V characteristics, it was found that the optimal iodine concentrations for the TEOS-Triton X-100 gel electrolyte and PVDF-HFP gel electrolyte are 0.05 M and 0.1 M, respectively. Although the increase in the iodine concentration could enhance the short-circuit current density (JSC), a further increase in the iodine concentration would reduce the JSC due to increased dark current. Therefore, the concentration of I2 is a significant factor in determining the performance of DSSCs. In order to enhance cell performance, the addition of nanosilicate platelets (NSPs) in the above-mentioned gel electrolytes was investigated. By incorporating NSP-Triton X-100 into the electrolytes, the JSC of the cells increased due to the decrease of diffusion resistance, while the open circuit voltage (VOC) remained almost the same. As the loading of the NSP-Triton X-100 in the TEOS-Triton X-100 gel electrolyte increased to 0.5 wt%, the JSC and the conversion efficiency increased from 8.5 to 12 mA/cm2 and from 3.6% to 4.7%, respectively. However, the JSC decreased as the loading of NSP-Triton X-100 exceeded 0.5 wt%. At higher NSP-Triton X-100 loading, NSPs acted as

  18. A flexible Li polymer primary cell with a novel gel electrolyte based on poly(acrylonitrile)

    Science.gov (United States)

    Akashi, Hiroyuki; Tanaka, Ko-ichi; Sekai, Koji

    The performance of a Li polymer primary cell with fire-retardant poly(acrylonitrile) (PAN)-based gel electrolytes is reported. By optimizing electrodes, electrolytes, the packaging material, and the structural design of the polymer cell, we succeeded in developing a "film-like" Li polymer primary cell with sufficient performance for practical use. The cell is flexible and less than 0.5 mm thick, which makes it suitable for a power source for some smart devices, such as an IC card. Fast cation conduction in the gel electrolyte minimizes the drop of the discharge capacity even at -20 °C. The high chemical stability of the gel electrolytes and the new packaging material allow the self-discharge rate to be limited to under 4.3%, which is equivalent to that of conventional coin-shaped or cylindrical Li-MnO 2 cells.

  19. Analysis of Amino Acids in a Single Human Red Blood Cell by Capillary Zone Electrophoresis with Intracellular NDA derivatization and Electrochemical Detection

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    A novel method for detcrmination of amino acids in individual human red blood cells has been dcveloped. In this method, the derivatization reagents (NDA and CN-) are introduced into living cells by clcctroporation. After completion of derivatization, the amino acids in a single cell is determined by capillary zone electrophoresis with end-column ampcrometric detection.

  20. Analysis of Amino Acids in a Single Human Red Blood Cell by Capillary Zone Electrophoresis with Intracellular NDA—derivatization and Electrochemical Detection

    Institute of Scientific and Technical Information of China (English)

    QianDONG; XiaoLeiWANG; 等

    2002-01-01

    A novel method for determination of amino acids in individual red blood cells has been developed. In this method, the derivatization reagents (NDA and CN-) are introduced into living cells by electroporation. After completion of derivatization,the amino acids in a single cell is determined by capillary zone electrophoresis with end-column amperometric detection.

  1. Phenotyping breast cancer cell lines EM-G3, HCC1937, MCF7 and MDA-MB-231 using 2-D electrophoresis and affinity chromatography for glutathione-binding proteins

    Directory of Open Access Journals (Sweden)

    Mladkova Jana

    2010-08-01

    Full Text Available Abstract Background Transformed phenotypes are common to cell lines derived from various cancers. Proteome profiling is a valuable tool that may reveal uncharacteristic cell phenotypes in transformed cells. Changes in expression of glutathione S-transferases (GSTs and other proteins interacting with glutathione (GSH in model cell lines could be of particular interest. Methods We compared the phenotypes of breast cell lines EM-G3, HCC1937, MCF7 and MDA-MB-231 using 2-D electrophoresis (2-DE. We further separated GSH-binding proteins from the cell lines using affinity chromatography with GSH-Sepharose 4B, performed 2-DE analysis and identified the main protein spots. Results Correlation coefficients among 2-DE gels from the cell lines were lower than 0.65, pointing to dissimilarity among the cell lines. Differences in primary constituents of the cytoskeleton were shown by the 2-D protein maps and western blots. The spot patterns in gels of GSH-binding fractions from primary carcinoma-derived cell lines HCC1937 and EM-G3 were similar to each other, and they differed from the spot patterns of cell lines MCF7 and MDA-MB-231 that were derived from pleural effusions of metastatic mammary carcinoma patients. Major differences in the expression of GST P1-1 and carbonyl reductase [NADPH] 1 were observed among the cell lines, indicating differential abilities of the cell lines to metabolize xenobiotics. Conclusions Our results confirmed the applicability of targeted affinity chromatography to proteome profiling and allowed us to characterize the phenotypes of four breast cancer cell lines.

  2. The effect of spirulina gel on fibroblast cell number after wound healing

    Directory of Open Access Journals (Sweden)

    Fitria Rahmitasari

    2011-12-01

    Full Text Available Background: Wound healing treatment after tooth extraction should be an important consideration due to mouth discomfort and pain. Spirulina (blue green algae consists of C-phycocyanin, b–carotenoids, vitamin E, zinc, some other trace elements and natural phytochemical which are believed to act as antioxidant and takes part in wound healing process. Purpose: The purpose of this study was to examine the effect of spirulina gel on fibroblast cell number after wound healing process. Methods: Twenty eight males guinea pig are devided into four group, 7 guinea pig each. They are control group and treatment group which is given 0%, 3%, 6%, and 12% spirulina gel. After tooth extraction, histopathological evaluation was done to count fibroblast cell. The data was analyzed by One-Way ANOVA and Tukey HSD. Results: The research has proven the relation between the increased growth of fibroblast cell and spirulina gel application. The higher the doses, the more cell growth. Hence, there has been significant different (p < 0.05 among groups. Conclusion: Spirulina gel increases the number of fibroblast in wound after tooth extraction and 12% spirulina gel has the most potential ability.Latar Belakang: Proses penyembuhan luka pasca pencabutan gigi merupakan salah satu hal yang penting karena akan menimbulkan rasa nyeri dan tidak nyaman dalam rongga mulut. Spirulina (Blue green Algae mengandung C-phycocyanin, b-carotenoids, vitamin E, seng, beberapa trace elemen lainnya, dan phytochemical alami yang terbukti dapat berperan sebagai antioksidan dalam proses penyembuhan luka. Tujuan: Tujuan dari penelitian ini adalah untuk mengetahui efek pemberian gel spirulina terhadap jumlah sel fibroblas pada proses penyembuhan luka pasca pencabutan gigi. Metode: Dua puluh delapan ekor guinea pig jantan dibagi dalam 7 kelompok, masing-masing terdiri dari 4 ekor. Kelompok tersebut adalah kelompok kontrol dan kelompok perlakuan yang diberikan gel spirulina dengan konsentrasi 0

  3. Estimating the DNA strand breakage using a fuzzy inference system and agarose gel electrophoresis, a case study with toothed carp Aphanius sophiae exposed to cypermethrin.

    Science.gov (United States)

    Poorbagher, Hadi; Moghaddam, Maryam Nasrollahpour; Eagderi, Soheil; Farahmand, Hamid

    2016-07-01

    The DNA breakage has been widely used in ecotoxicological studies to investigate effects of pesticides in fishes. The present study used a fuzzy inference system to quantify the breakage of DNA double strand in Aphanius sophiae exposed to the cypermethrin. The specimens were adapted to different temperatures and salinity for 14 days and then exposed to cypermethrin. DNA of each specimens were extracted, electrophoresed and photographed. A fuzzy system with three input variables and 27 rules were defined. The pixel value curve of DNA on each gel lane was obtained using ImageJ. The DNA breakage was quantified using the pixel value curve and fuzzy system. The defuzzified values were analyzed using a three-way analysis of variance. Cypermethrin had significant effects on DNA breakage. Fuzzy inference systems can be used as a tool to quantify the breakage of double strand DNA. DNA double strand of the gill of A. sophiae is sensitive enough to be used to detect cypermethrin in surface waters in concentrations much lower than those reported in previous studies. PMID:27000282

  4. Identification of vaginal bacteria diversity and it's association with clinically diagnosed bacterial vaginosis by denaturing gradient gel electrophoresis and correspondence analysis.

    Science.gov (United States)

    Xia, Qing; Cheng, Lijuan; Zhang, Hua; Sun, Shangwen; Liu, Fang; Li, Hao; Yuan, Jing; Liu, Zhendong; Diao, Yutao

    2016-10-01

    Bacterial vaginosis (BV) is a common complex associated with numerous adverse health outcomes, affecting women of different ages throughout the world. The etiology of BV remains poorly understood due to the difficulty of establishing a molecular genetic criterion to recognize the vaginal microbiota of BV-positive women from that of the normal women. We used techniques of broad-range PCR-DGGE and gel imaging analysis system cooperated with 16S rRNA gene sequencing and statistical analysis to investigate the community structure of the healthy and BV-affected vaginal microbial ecosystems. The community of vaginal bacteria detected in subjects with BV was far more luxuriant and diverse than in subjects without BV. The mean number of microbial species in 128 BV-positive women was nearly two times greater than in 68 subjects without BV(4.05±1.96 versus 2.59±1.14). Our sequencing efforts yielded many novel phylotypes (198 of our sequences represented 59 species), including several novel BV-associated bacteria (BVAB) and many belonging to opportunistic infections, which remain inexplicable for their roles in determining the health condition of vaginal microflora. This study identifies Algoriphagus aquatilis, Atopobium vaginae, Burkholderia fungorum, Megasphaera genomosp species as indicators to BV and subjects with BV harbor particularly taxon-rich and diverse bacterial communities. Maybe Bifidobacterium, Staphylococcus or even more alien species are commensal creatures in normal vaginal microbiota. PMID:27503595

  5. Fibrin Gel as an Injectable Biodegradable Scaffold and Cell Carrier for Tissue Engineering

    Directory of Open Access Journals (Sweden)

    Yuting Li

    2015-01-01

    Full Text Available Due to the increasing needs for organ transplantation and a universal shortage of donated tissues, tissue engineering emerges as a useful approach to engineer functional tissues. Although different synthetic materials have been used to fabricate tissue engineering scaffolds, they have many limitations such as the biocompatibility concerns, the inability to support cell attachment, and undesirable degradation rate. Fibrin gel, a biopolymeric material, provides numerous advantages over synthetic materials in functioning as a tissue engineering scaffold and a cell carrier. Fibrin gel exhibits excellent biocompatibility, promotes cell attachment, and can degrade in a controllable manner. Additionally, fibrin gel mimics the natural blood-clotting process and self-assembles into a polymer network. The ability for fibrin to cure in situ has been exploited to develop injectable scaffolds for the repair of damaged cardiac and cartilage tissues. Additionally, fibrin gel has been utilized as a cell carrier to protect cells from the forces during the application and cell delivery processes while enhancing the cell viability and tissue regeneration. Here, we review the recent advancement in developing fibrin-based biomaterials for the development of injectable tissue engineering scaffold and cell carriers.

  6. Gel de plaquetas: arcabouço 3D para cultura celular Platelet gel: 3D scaffold for cell culture

    Directory of Open Access Journals (Sweden)

    Andrei Moroz

    2009-01-01

    Full Text Available INTRODUÇÃO: O reparo tissular é o objetivo final da cirurgia. A cultura celular requer arcabouço mecânico que dê suporte ao crescimento celular e difusão dos nutrientes. O uso do plasma rico em plaquetas (PRP como um arcabouço 3D possui diversas vantagens: é material biológico, de fácil absorção pós-transplante, rico em fatores de crescimento, em especial PDGF- ββ e TGF-β que estimula síntese de matriz extracelular na cartilagem. OBJETIVO: Desenvolver arcabouço 3D à base de PRP. MATERIAIS E MÉTODOS: Duas formas foram idealizadas: Sphere e Carpet. Condições estéreis foram utilizadas. O gel de plaquetas permaneceu em cultura celular, observado diariamente em microscópio invertido. RESULTADOS: Ambos arcabouços obtiveram sucesso, com aspectos positivos e negativos. DISCUSSÃO: A forma Sphere não aderiu ao plástico. Observou-se retração do gel e investigação ao microscópio dificultada devido às áreas opacas no campo visual. A forma Carpet não aderiu ao plástico e apresentou-se translúcida. O tempo de estudo foi de 20 dias. CONCLUSÕES: A produção de um arcabouço 3D PRP foi um sucesso, e trata-se de uma alternativa que necessita ser mais utilizado e investigado para que se consolide em uma rota eficiente e confiável na tecnologia de engenharia tissular, particularmente em cultura de tecido cartilaginoso.INTRODUCTION: Tissue repair has been the ultimate goal of surgery. Cell culture requires a mechanical scaffold that supports cell growth and nutrient diffusion. Using platelet-rich plasma (PRP as a 3D scaffold presents various advantages: it is a biological material, easily absorbed after transplantation, rich in growth factors, in particular, PDGF-ββ and TGF-β that stimulate extracellular matrix synthesis in cartilage culture. OBJECTIVE: To develop a PRP 3D scaffold. Material and METHODS: Two forms were idealized: Sphere and Carpet. Sterile conditions were used. The platelet gel remained in culture

  7. Polymorphic Amplified Typing Sequences and Pulsed-Field Gel Electrophoresis Yield Comparable Results in the Strain Typing of a Diverse Set of Bovine Escherichia coli O157:H7 Isolates

    Directory of Open Access Journals (Sweden)

    Indira T. Kudva

    2012-01-01

    Full Text Available Polymorphic amplified typing sequences (PATS, a PCR-based Escherichia coli O157:H7 (O157 strain typing system, targets insertions-deletions and single nucleotide polymorphisms at XbaI and AvrII restriction enzyme sites, respectively, and the virulence genes (stx1, stx2, eae, hlyA in the O157 genome. In this study, the ability of PATS to discriminate O157 isolates associated with cattle was evaluated. An in-depth comparison of 25 bovine O157 isolates, from different geographic locations across Northwest United States, showed that about 85% of these isolates shared the same dendogram clade by PATS and pulsed-field gel electrophoresis (PFGE, irrespective of the restriction enzyme sites targeted. The Pearson’s correlation coefficient, r, calculated at about 0.4, 0.3, and 0.4 for XbaI-based, AvrII-based and combined-enzymes PATS and PFGE similarities, respectively, indicating that these profiles shared a good but not high correlation, an expected inference given that the two techniques discriminate differently. Isolates that grouped differently were better matched to their locations using PATS. Overall, PATS discriminated the bovine O157 isolates without interpretive biases or sophisticated analytical software, and effectively complemented while not duplicating PFGE. With its quick turnaround time, PATS has excellent potential as a convenient tool for early epidemiological or food safety investigations, enabling rapid notification/implementation of quarantine measures.

  8. Identification of DNA-binding proteins that interact with the 5'-flanking region of the human D-amino acid oxidase gene by pull-down assay coupled with two-dimensional gel electrophoresis and mass spectrometry.

    Science.gov (United States)

    Tran, Diem Hong; Shishido, Yuji; Chung, Seong Pil; Trinh, Huong Thi Thanh; Yorita, Kazuko; Sakai, Takashi; Fukui, Kiyoshi

    2015-12-10

    D-Amino acid oxidase (DAO) is a flavoenzyme that metabolizes D-amino acids and is expected to be a promising therapeutic target of schizophrenia and glioblastoma. The study of DNA-binding proteins has yielded much information in the regulation of transcription and other biological processes. However, proteins interacting with DAO gene have not been elucidated. Our assessment of human DAO promoter activity using luciferase reporter system indicated the 5'-flanking region of this gene (-4289 bp from transcription initiation site) has a regulatory sequence for gene expression, which is regulated by multi-protein complexes interacting with this region. By using pull-down assay coupled with two-dimensional gel electrophoresis and mass spectrometry, we identified six proteins binding to the 5'-flanking region of the human DAO gene (zinc finger C2HC domain-containing protein 1A; histidine-tRNA ligase, cytoplasmic; molybdenum cofactor biosynthesis protein; 60S ribosomal protein L37; calponin-1; calmodulin binding protein and heterogeneous nuclear ribonucleoprotein A2/B1). These preliminary results will contribute to the advance in the understanding of the potential factors associated with the regulatory mechanism of DAO expression.

  9. Speciation and subcellular location of Se-containing proteins in human liver studied by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and hydride generation-atomic fluorescence spectrometric detection

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Chunying; Zhao, Jiujiang; Zhang, Peiqun; Chai, Zhifang [Institute of High Energy Physics and Laboratory of Nuclear Analytical Techniques, Chinese Academy of Sciences, Beijing (China)

    2002-02-01

    Speciation of Se-containing proteins in the subcellular fractions of human liver was studied by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) followed by hydride generation-atomic fluorescence spectrometric (HG-AFS) detection. It was found that about 24 kinds of Se-containing proteins existed in subcellular fractions of normal human liver. The molecular weights (MW) of the subunits were mostly in the range 20-30 kDa and 50-80 kDa. Major Se-containing protein fractions at 61 kDa and 21 kDa are probably selenoprotein P and glutathione peroxidase, respectively. The 54 kDa protein is probably a thioredoxin reductase, which is presented in nuclei, mitochondria, lysosome, microsome and cytosol. We noticed that the Se-containing protein with the lowest MW of 9.3 kDa only existed in lysosome. Most of the proteins have not been identified and would require further investigation to characterize them. The specific subcellular distributions of different Se-containing proteins suggest that they could play important biological roles in each organelle. (orig.)

  10. 脉冲场凝胶电泳技术在致病菌分型技术的应用%Pulsed-field Gel Electrophoresis and its Application in Pathogen Molecular Typing

    Institute of Scientific and Technical Information of China (English)

    王宇

    2015-01-01

    Pulsed Field Gel Electrophoresis (PFGE) is a new technique of gelelectrophoresis developed in1980's. It can be used to separate large DNA molecules ranging from 35 to10 Mb. It has been widely applied to the pathogen molecular typ-ing , identification of species groups ,Source-tracking of pathogen and nosocomial infection surveillance.%脉冲场凝胶电泳(pulse-field gelelectrophoresis,PFGE),又称脉冲式交变电场电泳,该技术是将电泳电场方向交替性改变,并优化脉冲时间和其他条件,可以分辨凝胶中35~10 000 kb的DNA分子.该方法应用于分子流行病学中,通过观察电泳条带的差异,为确定菌株之间的亲缘关系提供了可靠的技术手段.该技术在致病菌溯源(细菌性传染性疾病溯源、细菌性食源性疾病溯源)、医院内感染流行监测等方面都有广泛的应用.

  11. Microbiota during fermentation of chum salmon (Oncorhynchus keta) sauce mash inoculated with halotolerant microbial starters: analyses using the plate count method and PCR-denaturing gradient gel electrophoresis (DGGE).

    Science.gov (United States)

    Yoshikawa, Shuji; Yasokawa, Daisuke; Nagashima, Koji; Yamazaki, Koji; Kurihara, Hideyuki; Ohta, Tomoki; Kawai, Yuji

    2010-06-01

    Nine different combinations of mugi koji (barley steamed and molded with Aspergillus oryzae) and halotolerant microorganisms (HTMs), Zygosaccharomyces rouxii, Candida versatilis, and Tetragenococcus halophilus, were inoculated into chum salmon sauce mash under a non-aseptic condition used in industrial fish sauce production and fermented at 35 +/- 2.5 degrees C for 84 days to elucidate the microbial dynamics (i.e., microbial count and microbiota) during fermentation. The viable count of halotolerant yeast (HTY) in fermented chum salmon sauce (FCSS) mash showed various time courses dependent on the combination of the starter microorganisms. Halotolerant lactic acid bacteria (HTL) were detected morphologically and physiologically only from FCSS mash inoculated with T. halophilus alone or with T. halophilus and C. versatilis during the first 28 days of fermentation. Only four fungal species, Z. rouxii, C. versatilis, Pichia guilliermondii, and A. oryzae, were detected throughout the fermentation by PCR-denaturing gradient gel electrophoresis (PCR-DGGE). In FCSS mash, dominant HTMs, especially eumycetes, were nonexistent. However, under the non-aseptic conditions, undesirable wild yeast such as P. guilliermondii grew fortuitously. Therefore, HTY inoculation into FCSS mash at the beginning of fermentation is effective in preventing the growth of wild yeast and the resultant unfavorable flavor. PMID:20417400

  12. Post-factum detection of radiation treatment of meat and fish by means of DNA alterations identified by gas chromatography-mass spectrometry or pulsed-field gel electrophoresis

    International Nuclear Information System (INIS)

    The doctoral thesis explains methods and experiments for post-factum detection of radiation-induced alterations of DNA. There are various manifestations of such alterations. Ionizing radiation can directly alter the bases and/or sugar component, or can indirectly induce DNA damage by way of forming water radicals. Both mechanisms result in base derivatives, released for some part from the DNA strand, or formed by alterations of the 2-deoxyribose, inducing strand breaks ( single and double strand breaks). The first part of the thesis explains the approach applying GC-MS for detection of radiation-induced base derivatives, using herring sperm DNA as a model DNA. Some typical types of base derivatives were identified (thymine glycol, 5-hydroxycytosine).Some base derivatives were also found in DNA samples derived from poultry meat. These base derivatives are known to be indicators of food processing with ionizing radiation, but surprisingly were also found in non-irradiated controls, although in minor amounts. The second part discusses the identification of strand breaks applying the pused-field gel electrophoresis. This method is capable of producing evidence that irradiation markedly enhances the short-chain DNA molecules as compared to non-irradiated controls. DNA molecules of a size of approx. 2.2 million base pairs are almost completely broken into short-chain fragments. The method reliably detects radiation treatments down to 1500 Gy, even if applied long ago. (orig./MG)

  13. Proteomic Analysis of Xuanwei Ham by Two-Dimensional Gel Electrophoresis%双向电泳分析宣威火腿蛋白质组方法的建立

    Institute of Scientific and Technical Information of China (English)

    廖国周; 王桂瑛; 程志斌; 施忠芬; 曹锦轩

    2012-01-01

    以宣威火腿为对象,采用三氯乙酸-丙酮沉淀法提取宣威火腿肌肉蛋白,对蛋白定量后,进行一向等电聚焦电泳和二向聚丙烯酰胺凝胶电泳,电泳后的凝胶以考马斯亮蓝染色,ImageMaster 2D Platinum软件分析凝胶上的蛋白质点,切取1个蛋白质点,经胰蛋白酶消化后使用基质辅助激光解析电离-串联飞行时间质谱(MALDI-TOF/TOFMS)获取肽质量指纹图谱,并用Mascot软件分析,以建立宣威火腿的蛋白质组学研究方法。结果表明:经双向电泳图谱分析所获得的宣威火腿蛋白点分布于pH4.0~7.0之间,共发现1749个蛋白点,蛋白点清晰,图谱分辨率较好;切取的蛋白质点经鉴定为Gamma-2-肌动蛋白,Mascot检索分值为129分(阈值为67分)。可见,成功建立双向电泳分析宣威火腿蛋白质组的方法。%In the present study,a method for the proteomic analysis of Xuanwei ham was established using two-dimensional gel electrophoresis(2-DE).Muscle protein from Xuanwei ham was extracted with trichloroacetic acid-acetone,quantified,and analyzed by isoelectric focusing electrophoresis and SDS-PAGE.After electrophoresis,the gels were stained with coomassie brilliant blue,and the observed protein spots were analyzed using imageMaster 2D platinum software and one of them was selected and analyzed by matrix-assisted laser desorption ionization-time of flight-time of flight-mass spectrometry(MALDI-TOF/TOF MS) after tripsin digestion.The obtained peptide mapping fingerprint was analyzed using Mascot software.A total of 1749 clear protein spots were observed in the 2-DE pattern of Xuanwei ham,which were mainly distributed over a pH range of 4.0-7.0.The tested protein spot was identified as gamma-2-actin protein and found to have a Mascot score of 129(threshold was 67).These results demonstrate the successful establishment of a 2-DE method for the proteomic analysis of Xuanwei ham.

  14. A large-scale electrophoresis- and chromatography-based determination of gene expression profiles in bovine brain capillary endothelial cells after the re-induction of blood-brain barrier properties

    Directory of Open Access Journals (Sweden)

    Duban-Deweer Sophie

    2010-11-01

    Full Text Available Abstract Background Brain capillary endothelial cells (BCECs form the physiological basis of the blood-brain barrier (BBB. The barrier function is (at least in part due to well-known proteins such as transporters, tight junctions and metabolic barrier proteins (e.g. monoamine oxidase, gamma glutamyltranspeptidase and P-glycoprotein. Our previous 2-dimensional gel proteome analysis had identified a large number of proteins and revealed the major role of dynamic cytoskeletal remodelling in the differentiation of bovine BCECs. The aim of the present study was to elaborate a reference proteome of Triton X-100-soluble species from bovine BCECs cultured in the well-established in vitro BBB model developed in our laboratory. Results A total of 215 protein spots (corresponding to 130 distinct proteins were identified by 2-dimensional gel electrophoresis, whereas over 350 proteins were identified by a shotgun approach. We classified around 430 distinct proteins expressed by bovine BCECs. Our large-scale gene expression analysis enabled the correction of mistakes referenced into protein databases (e.g. bovine vinculin and constitutes valuable evidence for predictions based on genome annotation. Conclusions Elaboration of a reference proteome constitutes the first step in creating a gene expression database dedicated to capillary endothelial cells displaying BBB characteristics. It improves of our knowledge of the BBB and the key proteins in cell structures, cytoskeleton organization, metabolism, detoxification and drug resistance. Moreover, our results emphasize the need for both appropriate experimental design and correct interpretation of proteome datasets.

  15. Comparative investigations of T cell receptor gamma gene rearrangements in frozen and formalin-fixed paraffin wax-embedded tissues by capillary electrophoresis

    DEFF Research Database (Denmark)

    Christensen, M; Funder, A D; Bendix, K;

    2006-01-01

    AIM: To compare clonal T cell receptor gamma (TCRgamma) gene rearrangements in frozen and formalin-fixed paraffin wax-embedded (FFPE) tissue, using capillary electrophoresis for use in diagnostics, as T cell lymphomas may be difficult to diagnose by conventional methods. METHODS: The DNA for PCR...

  16. Combining blue native polyacrylamide gel electrophoresis with liquid chromatography tandem mass spectrometry as an effective strategy for analyzing potential membrane protein complexes of Mycobacterium bovis bacillus Calmette-Guérin

    Directory of Open Access Journals (Sweden)

    Li Weijun

    2011-01-01

    Full Text Available Abstract Background Tuberculosis is an infectious bacterial disease in humans caused primarily by Mycobacterium tuberculosis, and infects one-third of the world's total population. Mycobacterium bovis bacillus Calmette-Guérin (BCG vaccine has been widely used to prevent tuberculosis worldwide since 1921. Membrane proteins play important roles in various cellular processes, and the protein-protein interactions involved in these processes may provide further information about molecular organization and cellular pathways. However, membrane proteins are notoriously under-represented by traditional two-dimensional polyacrylamide gel electrophoresis (2-D PAGE and little is known about mycobacterial membrane and membrane-associated protein complexes. Here we investigated M. bovis BCG by an alternative proteomic strategy coupling blue native PAGE to liquid chromatography tandem mass spectrometry (LC-MS/MS to characterize potential protein-protein interactions in membrane fractions. Results Using this approach, we analyzed native molecular composition of protein complexes in BCG membrane fractions. As a result, 40 proteins (including 12 integral membrane proteins, which were organized in 9 different gel bands, were unambiguous identified. The proteins identified have been experimentally confirmed using 2-D SDS PAGE. We identified MmpL8 and four neighboring proteins that were involved in lipid transport complexes, and all subunits of ATP synthase complex in their monomeric states. Two phenolpthiocerol synthases and three arabinosyltransferases belonging to individual operons were obtained in different gel bands. Furthermore, two giant multifunctional enzymes, Pks7 and Pks8, and four mycobacterial Hsp family members were determined. Additionally, seven ribosomal proteins involved in polyribosome complex and two subunits of the succinate dehydrogenase complex were also found. Notablely, some proteins with high hydrophobicity or multiple transmembrane

  17. Design and experimental verification of low-voltage two-dimensional CMOS electrophoresis platform with 32 × 32 sample/hold cell array

    Science.gov (United States)

    Yamaji, Yuuki; Niitsu, Kiichi; Nakazato, Kazuo

    2016-03-01

    Electrophoresis is widely used in biomedical applications. However, conventional (centimeter-order) electrophoresis requires a high-voltage power supply, which is not suitable for point-of-care testing (POCT). Electrophoresis is driven by electric fields, and miniaturization (from the centimeter order to the micrometer order) is effective for low-voltage operation. A CMOS platform is a cost-competitive and promising candidate for miniaturization and enables the integration of biomolecule manipulation by electrophoresis and its electrochemical sensing. These features will contribute to the development of a biochemical analyzer called the micro-total analysis system (µ-TAS). To realize a truly portable electrophoresis system, we present the design and experimental verification of a low-voltage (<1 V), two-dimensional CMOS electrophoresis platform with 32 × 32 sample/hold cell array. Experimental results showed successful constant voltage outputs to each electrode. By miniaturizing the electrode structure to a 60 µm pitch, we achieved sufficient electric field strength even at low voltages.

  18. Effect of controlled release of brain-derived neurotrophic factor and neurotrophin-3 from collagen gel on neural stem cells.

    Science.gov (United States)

    Huang, Fei; Wu, Yunfeng; Wang, Hao; Chang, Jun; Ma, Guangwen; Yin, Zongsheng

    2016-01-20

    This study aimed to examine the effect of controlled release of brain-derived neurotrophic factor (BDNF) and neurotrophin-3 (NT-3) from collagen gel on rat neural stem cells (NSCs). With three groups of collagen gel, BDNF/collagen gel, and NT-3/collagen gel as controls, BDNF and NT-3 were tested in the BDNF-NT-3/collagen gel group at different time points. The enzyme-linked immunosorbent assay results showed that BDNF and NT-3 were steadily released from collagen gels for 10 days. The cell viability test and the bromodeoxyuridine incorporation assay showed that BDNF-NT-3/collagen gel supported the survival and proliferation of NSCs. The results also showed that the length of processes was markedly longer and differentiation percentage from NSCs into neurons was much higher in the BDNF-NT-3/collagen gel group than those in the collagen gel, BDNF/collagen gel, and NT-3/collagen gel groups. These findings suggest that BDNF-NT-3/collagen gel could significantly improve the ability of NSCs proliferation and differentiation.

  19. Detection of Molecular Weight of PMCA Isoform with 20 cm SDS PAGE Electrophoresis:Compared with 8 cm SDS PAGE

    Institute of Scientific and Technical Information of China (English)

    Hui Yang; Junwen Zeng

    2005-01-01

    Purpose: To compare the effect of 20 cm SDS-PAGE electrophoresis, which is most widely used in proteomic research, in identifying human lens epithelium B3 (HLE B3) cells plasma membrane calcium ATPase (PMCA) isoform's apparent molecular weight (MW), with that of 8 cm SDS-PAGE electrophoresis.Method: HLE B-3 cells were cultured and membrane protein sample was collected. Part of the sample is electrophoresised with 20 cm gel, 16 mA/gel for 1.5 hrs and then 24 mA/gel for 4~5 hrs. The same sample is electrophoresised with 8cm mini gel, 200V for 2 hrs. Protein marker of known MW was run with the sample in the same gel. The resulting separated proteins were transferred to polyvinylidene difluoride (PVDF) membrane and Western blot were used to identify the PMCA isoform with specific antibody against PMCA 1, 2, 4. The apparent MW was calculated in reference to the known protein marker that was electrophoresised in the same gel.Result: In 8 cm gel the distance between 208 kDa and 126 kDa band was about 6.1 mm,while that of 20 cm gel was 32.8 mm. The distance between 126 kDa and 97 kDa was about 5.2 mm, while that of 20 cm gel was 20.2 mm. The migration distance differences of protein bands were significantly much longer in 20 cm gel than in 8 cm gel (P < 0.005).But the bands were generally more condensed in 8 cm gel. The apparent MW of PMCA1,2, 4 were 153.8, 153.5 and 152.9 kDa respectively. In the 20 cm gel, the apparent MW for PMCA1, 2, 4 was 153.1, 125.5 and 147.4 kDa respectively.Conclusion: Both the 20 cm gel and 8 cm gel successful identified PMCA 1,2, 4 in HLE B-3 cells. The apparent MW for PMCA1, 2, 4 was 153.8, 153.5 and 152.9 kDa respectively in 8 cm gel,and 153.1,125.5 and 147.4 kDa respectively in 20 cm gel.PMCA2 probably had some kinds of degradation during the long electrophoresis time in 20 cm gel.

  20. Investigation of different cell types and gel carriers for cell-based intervertebral disc therapy, in vitro and in vivo studies.

    Science.gov (United States)

    Henriksson, H B; Hagman, M; Horn, M; Lindahl, A; Brisby, H

    2012-10-01

    Biological treatment options for the repair of intervertebral disc damage have been suggested for patients with chronic low back pain. The aim of this study was to investigate possible cell types and gel carriers for use in the regenerative treatment of degenerative intervertebral discs (IVD). In vitro: human mesenchymal cells (hMSCs), IVD cells (hDCs), and chondrocytes (hCs) were cultivated in three gel types: hyaluronan gel (Durolane®), hydrogel (Puramatrix®), and tissue-glue gel (TISSEEL®) in chondrogenic differentiation media for 9 days. Cell proliferation and proteoglycan accumulation were evaluated with microscopy and histology. In vivo: hMSCs or hCs and hyaluronan gel were co-injected into injured IVDs of six minipigs. Animals were sacrificed at 3 or 6 months. Transplanted cells were traced with anti-human antibodies. IVD appearance was visualized by MRI, immunohistochemistry, and histology. Hyaluronan gel induced the highest cell proliferation in vitro for all cell types. Xenotransplanted hMSCs and hCs survived in porcine IVDs for 6 months and produced collagen II in all six animals. Six months after transplantation of cell/gel, pronounced endplate changes indicating severe IVD degeneration were observed at MRI in 1/3 hC/gel, 1/3 hMSCs/gel and 1/3 gel only injected IVDs at MRI and 1/3 hMSC/gel, 3/3 hC/gel, 2/3 gel and 1/3 injured IVDs showed positive staining for bone mineralization. In 1 of 3 discs receiving hC/gel, in 1 of 3 receiving hMSCs/gel, and in 1 of 3 discs receiving gel alone. Injected IVDs on MRI results in 1 of 3 hMSC/gel, in 3 of 3 hC/gel, in 2 of 3 gel, and in 1 of 3 injured IVDs animals showed positive staining for bone mineralization. The investigated hyaluronan gel carrier is not suitable for use in cell therapy of injured/degenerated IVDs. The high cell proliferation observed in vitro in the hyaluronan could have been a negative factor in vivo, since most cell/gel transplanted IVDs showed degenerative changes at MRI and

  1. Fabricating neuromast-inspired gel structures for membrane-based hair cell sensing

    Science.gov (United States)

    Tamaddoni, Nima J.; Stephens, Christopher P.; Sarles, S. A.

    2012-04-01

    Recent research has shown that a new class of mechanical sensor, assembled from biomolecules and which features an artificial cell membrane as the sensing element, can be used to mimic basic hair cell mechanotransduction in vertebrates. The work presented in this paper is motivated by the need to increase sensor performance and stability by refining the methods used to fabricate and connect lipid-encapsulated hydrogels. Inspired by superficial neuromasts found on fish, three hydrogel materials are compared for their ability to be readily shaped into neuromast-inspired geometries and enable lipid bilayer formation using self-assembly at an oil/water interface. Agarose, polyethylene glycol (PEG, 6kg/mole), and hydroxyethyl methacrylate (HEMA) gel materials are compared. The results of this initial study determined that UV-curable gel materials such as PEG and HEMA enable more accurate shaping of the gel-needed for developing a sensor that uses a gel material both for mechanical support and membrane formation-compared to agarose. However, the lower hydrophobicity of agarose and PEG materials provide a more fluid, water-like environment for membrane formation-unlike HEMA. In working toward a neuromast-inspired design, a final experiment demonstrates that a bilayer can also be formed directly between two lipid-covered PEG surfaces. These initial results suggest that candidate gel materials with a low hydrophobicity, high fluidity, and a low modulus can be used to provide membrane support.

  2. Motion of an Adhesive Gel in a Swelling Gradient a Mechanism for Cell Locomotion

    CERN Document Server

    Joanny, J F; Prost, J; Joanny, Jean-Francois; Julicher, Frank; Prost, Jacques

    2003-01-01

    Motivated by the motion of nematode sperm cells, we present a model for the motion of an adhesive gel on a solid substrate. The gel polymerizes at the leading edge and depolymerizes at the rear. The motion results from a competition between a self-generated swelling gradient and the adhesion on the substrate. The resulting stress provokes the rupture of the adhesion points and allows for the motion. The model predicts an unusual force-velocity relation which depends in significant ways on the point of application of the force.

  3. Cytotoxicity of Aloe vera gel extracts on Allium cepa root tip cells

    OpenAIRE

    İLBAŞ, Ali İrfan; GÖNEN, Umut; YILMAZ, Semih; DADANDI, Mehmet Yaşar

    2012-01-01

    Aloe vera L. is a valuable medicinal plant and is currently used in pharmaceutical, cosmetic, and food industries worldwide. In the present study, the effect of various concentrations of Aloe vera leaf gel extracts was investigated on mitotic and phase indexes of Allium cepa L. root tip cells for 24 and 48 h durations. The EC50 value of gel extracts was found to be 20% and was used to determine the experimental concentrations. The results indicated that the mitotic index and root growth rate ...

  4. Antibiotic resistance and pulsed-field gel electrophoresis patterns of Shigella sonnei isolates%宋内志贺菌耐药性及脉冲场凝胶电泳分子分型分析

    Institute of Scientific and Technical Information of China (English)

    章红红; 连伟刚; 王闻卿; 杨玲凤; 陈敏; 陈洪友; 张曦; 朱林英; 苏靖华; 傅慧琴; 黄红; 张勇琪

    2012-01-01

    目的 通过对宋内志贺菌菌株耐药性及脉冲场凝胶电泳(pulse-field gel electrophoresis,PFGE)分子分型分析,了解上海市浦东新区宋内志贺菌的耐药谱,并建立宋内志贺菌DNA指纹图谱数据库.方法 运用K-B法对34株宋内志贺菌株进行12种抗生素药敏试验,同时对菌株基因组DNA经限制性内切酶XbaⅠ酶切后进行PFGE分子分型,利用BioNumerics Version 5.10分析软件对图谱进行聚类分析.结果 34株宋内志贺菌菌株对链霉素、萘啶酸、甲氧嘧啶、复方新诺明耐药率为100%,对氨苄西林、庆大霉素、四环素耐药率分别为94.1%、91.2%和88.2%,对头孢他啶、头孢吡肟耐药率均为2.9%,对阿莫西林/克拉维酸、氯霉素、氧氟沙星为100%敏感.共获得13个PFGE带型,各带型间相似性系数在90%以上.相同PFGE带型内各菌株间药敏结果完全一致.J16X01.sh011为优势带型,不同时间、不同腹泻监测点之间存在完全相同PFCE条带.结论 宋内志贺菌多重耐药现象日趋严重,浦东新区存在遗传谱紧密相关的宋内志贺菌流行克隆系.%Objective To understand antibiotic resistance of Shigella sonnei and establish its DNA fingerprint database in Pudong district by conducting drug resistance test and pulsed-field gel electrophoresis (PFGE) molecular subtyping. Methods The drug resistance of 34 5. sonnei isolates to 12 antibiotics was conducted by K-B method, and the molecular subtyping of the isolates was done by PFGE after the digestion of restriction enzyme Xba I . Results The resistant rates of isolates to streptomycin, nalidixic acid, trimethoprim and sulfamethoxazole were 100% , and the resistant rate was 94. 1% to ampicillin, 91.2% to gentamicin, 88.2% to tetracycline and 2.9% to ceftazidime and cefepime, but they were all sensitive to amoxicillin, clavulanic acid, chloramphenicol and ofloxacin. All the isolates showed 13 PFGE patterns and similarity was more than 90%. The

  5. Bacterial communities in Agaricus bisporus compost analysed by denatu-ring gradient gel electrophoresis%双孢蘑菇培养料发酵过程中细菌群落结构分析

    Institute of Scientific and Technical Information of China (English)

    王琳; 李敏; 魏启舜; 张洪海; 周影; 赵荷娟

    2015-01-01

    PCR-denaturing gradient gel electrophoresis ( DGGE) was emloyed to analyze the V3 regions of bacterial 16S ribosomal DNA collected from the compost for Agaricus bisporus cultivation in spring and winter. The dominant DNA were cloned, sequenced and analyzed. Bacillus sp, Flavobacterium sp. , Lysinibacillus sp. , Thermus thermophilus,Pseudomonas fragi, Solibacillus silvestris,Thermobifida fusca, and two kinds of uncultured bacteria were identified in the compost. The bac-teria in spring and winter showed similar changing trend during phase I composting and similar community at the end of com-posting. The bacterial community structure differed at initial composting, phase I composting and phase II composting. The community diversity was environmental temperature-dependant. The bacteria existing in the compost all through the process of composting shared high sequence similarity with that of the bacteria degrading lignocellulose, which was favorable for the com-post to be applied as culture matrix.%为探明双孢蘑菇培养料发酵过程中细菌群落多样性和组成的演变,获得相关优势菌落的信息,本研究利用变性梯度凝胶电泳( Denaturing gradient gel electrophoresis,DGGE)对不同季节不同发酵阶段样品的的细菌进行特异性扩增,并选取主要DNA条带进行克隆、测序和生物信息学分析。结果显示,不同发酵时期带谱差异明显。发酵过程中,培养料中主要有芽孢杆菌属、黄杆菌属、杆菌属、假单胞菌属、Solibacillus、嗜热裂孢菌属、高温双歧菌属和未知分类地位的不可培养细菌。不同季节(春季、冬季)的培养料一次发酵过程中细菌多样性变化趋势相似,且发酵结束时细菌菌落结构相似。双孢蘑菇培养料在发酵过程中细菌群落结构至少经历了3个阶段的演替,即建堆初期、一次发酵阶段和二次发酵阶段。双孢蘑菇培养料发酵过程中细菌种群丰富,并随着发酵的不同阶段发生演

  6. Comparative Study of Early Cold-Regulated Proteins by Two-Dimensional Difference Gel Electrophoresis Reveals a Key Role for Phospholipase Dα1 in Mediating Cold Acclimation Signaling Pathway in Rice.

    Science.gov (United States)

    Huo, Chenmin; Zhang, Baowen; Wang, Hui; Wang, Fawei; Liu, Meng; Gao, Yingjie; Zhang, Wenhua; Deng, Zhiping; Sun, Daye; Tang, Wenqiang

    2016-04-01

    To understand the early signaling steps that regulate cold responses in rice, two-dimensional difference gel electrophoresis (2-D DIGE)(1)was used to study early cold-regulated proteins in rice seedlings. Using mass spectrometry, 32 spots, which represent 26 unique proteins that showed an altered expression level within 5 min of cold treatment were identified. Among these proteins, Western blot analyses confirmed that the cellular phospholipase D α1 (OsPLDα1) protein level was increased as early as 1 min after cold treatment. Genetic studies showed that reducing the expression ofOsPLDα1makes rice plants more sensitive to chilling stress as well as cold acclimation increased freezing tolerance. Correspondingly, cold-regulated proteomic changes and the expression of the cold-responsive C repeat/dehydration-responsive element binding 1 (OsDREB1) family of transcription factors were inhibited in thepldα1mutant. We also found that the expression ofOsPLDα1is directly regulated by OsDREB1A. This transcriptional regulation ofOsPLDα1could provide positive feedback regulation of the cold signal transduction pathway in rice. OsPLDα1 hydrolyzes phosphatidylcholine to produce the signal molecule phosphatidic acid (PA). By lipid-overlay assay, we demonstrated that the rice cold signaling proteins, MAP kinase 6 (OsMPK6) and OsSIZ1, bind directly to PA. Taken together, our results suggest that OsPLDα1 plays a key role in transducing cold signaling in rice by producing PA and regulatingOsDREB1s' expression by OsMPK6, OsSIZ1, and possibly other PA-binding proteins. PMID:26747563

  7. Multilocus Variable-Number Tandem-Repeat Analysis, Pulsed-Field Gel Electrophoresis, and Antimicrobial Susceptibility Patterns in Discrimination of Sporadic and Outbreak-Related Strains of Yersinia enterocolitica

    Directory of Open Access Journals (Sweden)

    Skurnik Mikael

    2011-02-01

    Full Text Available Abstract Background We assessed the potential of multilocus variable-number tandem-repeat analysis (MLVA, pulsed-field gel electrophoresis (PFGE, and antimicrobial susceptibility testing for discriminating 104 sporadic and outbreak-related Yersinia enterocolitica (YE bio/serotype 3-4/O:3 and 2/O:9 isolates. MLVA using six VNTR markers was performed in two separate multiplex PCRs, and the fluorescently labeled PCR products were accurately sized on an automated DNA sequencer. Results MLVA discriminated 82 sporadic YE 3-4/O:3 and 2/O:9 strains into 77 types, whereas PFGE with the restriction enzyme NotI discriminated the strains into 23 different PFGE pulsotypes. The discriminatory index for a sporadic strain was 0.862 for PFGE and 0.999 for MLVA. MLVA confirmed that a foodborne outbreak in the city of Kotka, Finland in 2003 had been caused by a multiresistant YE 4/O:3 strain that was distinctly different from those of epidemiologically unrelated strains with an identical PFGE pulsotype. The multiresistance of Y. enterocolitica strains (19% of the sporadic strains correlated significantly (p = 0.002 with travel abroad. All of the multiresistant Y. enterocolitica strains belonged to four PFGE pulsotypes that did not contain any susceptible strains. Resistance to nalidixic acid was related to changes in codons 83 or 87 that stemmed from mutations in the gyrA gene. The conjugation experiments demonstrated that resistance to CHL, STR, and SUL was carried by a conjugative plasmid. Conclusions MLVA using six loci had better discriminatory power than PFGE with the NotI enzyme. MLVA was also a less labor-intensive method than PFGE and the results were easier to analyze. The conjugation experiments demonstrated that a resistance plasmid can easily be transferred between Y. enterocolitica strains. Antimicrobial multiresistance of Y. enterocolitica strains was significantly associated with travel abroad.

  8. 16S-23S Internal Transcribed Spacer Region PCR and Sequencer-Based Capillary Gel Electrophoresis has Potential as an Alternative to High Performance Liquid Chromatography for Identification of Slowly Growing Nontuberculous Mycobacteria

    Science.gov (United States)

    Subedi, Shradha; Kong, Fanrong; Jelfs, Peter; Gray, Timothy J.; Xiao, Meng; Sintchenko, Vitali; Chen, Sharon C-A

    2016-01-01

    Accurate identification of slowly growing nontuberculous mycobacteria (SG-NTM) of clinical significance remains problematic. This study evaluated a novel method of SG-NTM identification by amplification of the mycobacterial 16S-23S rRNA internal transcribed spacer (ITS) region followed by resolution of amplified fragments by sequencer-based capillary gel electrophoresis (SCGE). Fourteen American Type Culture Collection (ATCC) strains and 103 clinical/environmental isolates (total n = 24 species) of SG-NTM were included. Identification was compared with that achieved by high performance liquid chromatography (HPLC), in-house PCR and 16S/ITS sequencing. Isolates of all species yielded a SCGE profile comprising a single fragment length (or peak) except for M. scrofulaceum (two peaks). SCGE peaks of ATCC strains were distinct except for peak overlap between Mycobacterium kansasii and M. marinum. Of clinical/environmental strains, unique peaks were seen for 7/17 (41%) species (M. haemophilum, M. kubicae, M. lentiflavum, M. terrae, M. kansasii, M. asiaticum and M. triplex); 3/17 (18%) species were identified by HPLC. There were five SCGE fragment length types (I–V) each of M. avium, M. intracellulare and M. gordonae. Overlap of fragment lengths was seen between M. marinum and M. ulcerans; for M. gordonae SCGE type III and M. paragordonae; M. avium SCGE types III and IV, and M. intracellulare SCGE type I; M. chimaera, M. parascrofulaceum and M. intracellulare SCGE types III and IV; M. branderi and M. avium type V; and M. vulneris and M. intracellulare type V. The ITS-SCGE method was able to provide the first line rapid and reproducible species identification/screening of SG-NTM and was more discriminatory than HPLC. PMID:27749897

  9. Softness of the bacterial cell wall of Streptococcus mitis as probed by micro-electrophoresis

    NARCIS (Netherlands)

    Vadillo-Rodriguez, V.; Busscher, H.J.; Norde, W.; Mei, van der H.C.

    2002-01-01

    Chemical and structural complexity of bacterial cell surfaces complicate accurate quantification of cell surfaces properties. The presence of fibrils, fimbriae or other surface appendages on bacterial cell surfaces largely influence those properties and would therefore play a major function in inter

  10. Pharmacological effect of carvacrol on D: -galactosamine-induced mitochondrial enzymes and DNA damage by single-cell gel electrophoresis.

    Science.gov (United States)

    Aristatile, Balakrishnan; Al-Numair, Khalid S; Al-Assaf, Abdullah H; Pugalendi, Kodukkur Viswanathan

    2011-07-01

    The present study aimed at investigating the effect of carvacrol on hepatic mitochondrial enzyme activities and DNA damage in D: -galactosamine (D: -GalN)-induced hepatotoxicity in male albino Wistar rats. The activities of hepatic mitochondrial enzymes such as isocitrate dehydrogenase, α-ketoglutarate dehydrogenase, succinate dehydrogenase, malate dehydrogenase, NADPH dehydrogenase and cytochrome c oxidase significantly decreased in D: -GalN-hepatotoxic rats, and administration of carvacrol brought these parameters towards normality. In D: -GalN-hepatotoxic rats, the hepatic mitochondrial concentration of thiobarbituric acid reactive substances significantly increased, and administration of carvacrol significantly reduced them towards normality. Furthermore, the activities of enzymatic antioxidants such as superoxide dismutase and glutathione peroxidase and the levels of non-enzymatic antioxidants such as vitamin C, vitamin E and reduced glutathione decreased significantly in the liver mitochondria. Administration of carvacrol returned the enzymatic and non-enzymatic antioxidants towards normality. D: -GalN-hepatotoxic rats had increased DNA damage, which administration of carvacrol significantly decreased. These results suggest that carvacrol has liver mitochondrial antioxidant properties and possesses a defensive effect against mitochondrial enzymes and DNA damage in D: -GalN-induced rats.

  11. Chlorination-induced genotoxicity in the mussel Perna viridis: assessment by single cell gel electrophoresis (comet) assay.

    Science.gov (United States)

    Chavan, Pooja; Kumar, Rajesh; Kirubagaran, Ramalingam; Venugopalan, Vayalam P

    2016-08-01

    Mussels are important fouling organisms in the cooling water systems of coastal power plants. Continuous low-dose chlorination (CLDC) is being practiced as an effective method to control mussel biofouling in power plant cooling water systems. CLDC effectively controls mussel fouling by discouraging larval settlement rather than by killing the larvae or adults. Mussels are an integral part of the natural benthic community in the receiving water body where the coolant water is discharged. Hence, from a toxicological point of view, they can serve as both target and non-target organisms. Previous researchers have indicated that chlorine residual, rather than elevated temperature, can be the major stress factor in the effluents released from coastal power plants. However, very little data are available on the sub-lethal effects of low level chlorination on representative benthic fauna. In this study, we used native and transplanted mussels (Perna viridis) to study lethal and sub-lethal effects of chlorination in the cooling water circuit of an operating power plant. Experiments involving comet assay suggested that CLDC can cause DNA damage in treated mussels. However, activation of DNA repair appeared to get initiated after the accrued damage reached a threshold. The results indicate that, at chlorine residual levels observed at the discharge point, exposure to chlorinated effluents is unlikely to cause significant genetic damage to mussels in the recipient water body. PMID:27155389

  12. 人Ⅰ期肺腺癌及癌旁组织蛋白质双向电泳图谱的差异分析%Identification of differentially expressed proteins in human stage I lung adenocarcinoma and tumor-adjacent tissues with two-dimension gel electrophoresis profiling

    Institute of Scientific and Technical Information of China (English)

    Feifei Feng; Guizhi Liu; Yiming Wu

    2009-01-01

    Objective: The aim of this study was to establish reproducible two-dimensional electrophoretic assay used for profiling and identification of differentially expressed proteins in human stage I lung adenocarcinoma and paired normal tu- mor-adjacent tissue. Methods: The proteins from 12 human stage I lung adenocarcinoma tissues and normal tumor-adjacent tissues were separated using isoelectric focusing electrophoresis (the first dimension) and the subsequent homogeneous SDS-polyacrylamide gel electrophoresis (SDS-PAGE) (the second dimension). The differentially expressed proteins were determined with PDQuest image analysis software, and identified using matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) and database searching. Results: The well-reproducible 2-DE gel patterns of human stage I lung adenocarcinoma and normal tumor-adjacent tissues were profiled and 26 differentially expressed proteins uncovered. Nine of these 26 protein spots were cut out from the preparation gels and determined with MALDI-TOF-MS. Searching against the protein database, four candidate proteins were identified. They were 60S acidic ribosomal protein P2, Cathepsin B1, Apolipoprotein A-I precursor, and La 4.1 protein. Conclusion: In this study, high reproducible 2-DE gel protein images of human stage I lung adenocarcinoma and paired normal tumor-adjacent tissues were achieved successfully, and 4 differentially expressed proteins were revealed. These data will be helpful for screen of early biomarker and study of molecular mechanisms of human lung adenocarcinoma.

  13. Self-Assembled Peptide Gels for 3D Cell Culture

    OpenAIRE

    Tang, Claire

    2010-01-01

    Under specific conditions short peptides modified with an N-terminal fluorenyl-9-methoxycarbonyl (Fmoc) group can self-assemble into hydrogel scaffolds similar in properties to the natural extracellular matrix. Fmoc-diphenylalanine (Fmoc-FF) for instance, has been shown to form hydrogels at physiological pH that have the ability to support 2D and 3D cell culture. The aim of this investigation is to provide further understanding of the self-assembly mechanism of such systems in order to progre...

  14. The alkaline single cell electrophoresis assay with eight mouse organs: results with 22 mono-functional alkylating agents (including 9 dialkyl N-nitrosoamines) and 10 DNA crosslinkers.

    Science.gov (United States)

    Tsuda, S; Matsusaka, N; Madarame, H; Miyamae, Y; Ishida, K; Satoh, M; Sekihashi, K; Sasaki, Y F

    2000-04-13

    The genotoxicity of 22 mono-functional alkylating agents (including 9 dialkyl N-nitrosoamines) and 10 DNA crosslinkers selected from IARC (International Agency for Research on Cancer) groups 1, 2A, and 2B was evaluated in eight mouse organs with the alkaline single cell gel electrophoresis (SCGE) (comet) assay. Groups of four mice were treated once intraperitoneally at the dose at which micronucleus tests had been conducted, and the stomach, colon, liver, kidney, bladder, lung, brain, and bone marrow were sampled 3, 8, and/or 24 h later. All chemicals were positive in the SCGE assay in at least one organ. Of the 22 mono-functional alkylating agents, over 50% were positive in all organs except the brain and bone marrow. The two subsets of mono-functional alkylating agents differed in their bone marrow genotoxicity: only 1 of the 9 dialkyl N-nitrosoamines was positive in bone marrow as opposed to 8 of the 13 other alkylating agents, reflecting the fact that dialkyl N-nitrosoamines are poor micronucleus inducers in hematopoietic cells. The two groups of mono-functional alkylating agents also differ in hepatic carcinogenicity in spite of the fact that they are similar in hepatic genotoxicity. While dialkyl N-nitrosoamines produce tumors primarily in mouse liver, only one (styrene-7,8-oxide) out of 10 of the other type of mono-functional alkylating agents is a mouse hepatic carcinogen. Taking into consideration our previous results showing high concordance between hepatic genotoxicity and carcinogenicity for aromatic amines and azo compounds, a possible explanation for the discrepancy might be that chemicals that require metabolic activation show high concordance between genotoxicity and carcinogenicity in the liver. A high percent of the 10 DNA crosslinkers were positive in the SCGE assay in the gastrointestinal mucosa, but less than 50% were positive in the liver and lung. In this study, we allowed 10 min alkali-unwinding to obtain low and stable control values

  15. A gel-free approach in vascular smooth muscle cell proteome: perspectives for a better insight into activation

    Directory of Open Access Journals (Sweden)

    Tedeschi Lorena

    2010-03-01

    Full Text Available Abstract Background The use of chromatography coupled with mass spectrometry (MS analysis is a powerful approach to identify proteins, owing to its capacity to fractionate molecules according to different chemical features. The first protein expression map of vascular smooth muscle cells (VSMC was published in 2001 and since then other papers have been produced. The most detailed two-dimensional polyacrylamide gel electrophoresis (2D-PAGE map was presented by Mayr et al who identified 235 proteins, corresponding to the 154 most abundant unique proteins in mouse aortic VSMC. A chromatographic approach aimed at fractionating the VSMC proteome has never been used before. Results This paper describes a strategy for the study of the VSMC proteome. Our approach was based on pre-fractionation with ion exchange chromatography coupled with matrix assisted laser desorption-time of flight mass spectrometry analysis assisted by a liquid chromatography (LC-MALDI-TOF/TOF. Ion exchange chromatography resulted in a good strategy designed to simplify the complexity of the cellular extract and to identify a large number of proteins. Selectivity based on the ion-exchange chemical features was adequate if evaluated on the basis of protein pI. The LC-MALDI approach proved to be highly reproducible and sensitive since we were able to identify up to 815 proteins with a concentration dynamic range of 7 orders of magnitude. Conclusions In our opinion, the large number of identified proteins and the promising quantitative reproducibility made this approach a powerful method to analyze complex protein mixtures in a high throughput way and to obtain statistical data for the discovery of key factors involved in VSMC activation and to analyze a label-free differential protein expression.

  16. Enhanced photocurrent generation in bacteriorhodopsin based bio-sensitized solar cells using gel electrolyte.

    Science.gov (United States)

    Chellamuthu, Jeganathan; Nagaraj, Pavithra; Chidambaram, Sabari Girisun; Sambandam, Anandan; Muthupandian, Ashokkumar

    2016-09-01

    High purity light sensitive photoactive protein Bacteriorhodopsin (BR) was isolated successfully via a simple two phase extraction technique (ATPS) as an alternate method for the tedious sucrose gradient ultracentrifugation procedure (SGU). Bio sensitized solar cells (BSSCs) were fabricated by the integration of BR into TiO2 (photo anode) with acetamide based gel electrolytes and platinum (photo cathode) as a counter electrode. The structural and photoelectrical behaviours of BR and BSSCs were analyzed by Atomic Force Microscopy, Raman spectroscopy, photocurrent and photovoltage (IV) measurement and electrochemical impedance spectroscopy. The short circuit photocurrent (Jsc) and photoelectric conversion efficiency (η) of acetamide based gel electrolyte (AG) (1.08mAcm(-2), 0.49%) are twice higher than that of traditional triiodide based liquid electrolyte (LE) (0.62mAcm(-2), 0.19%). Also, quasi-Fermi level and lifetime of photogenerated electrons in acetamide based gel electrolyte is about four times higher than that observed in traditional triiodide redox electrolyte. A comparison of the observed results with similar BSSCs made of other natural photoactive protein systems shows that BR as sensitizer has better photovoltaic performance. The enhanced photocurrent generation of the BSSC constructed in our study could be due to the interaction of BR with acetamide based modified poly(ethylene)oxide (PEO) gel electrolyte. PMID:27380296

  17. 发酵乳活性双歧杆菌种类快速识别及定量研究%Isolation of Bifidobacteria from Yoghurts and Assessment of the Bifidobacterial Population by PCR-Denaturing Gradient Gel Electrophoresis and Quantitative Real-Time PCR

    Institute of Scientific and Technical Information of China (English)

    王立平; 刘晓莉; 蔡雪凤; 曹悦; 张帆

    2013-01-01

    In this article, a rapid identification and numberation method for bifidobacterium in fermented milk products was established. Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) technique was used to identify Bifidobacterium present in commercial probiotic yoghurts.Real-Time Polymerase Chain Reaction (Real-Time PCR) technique was used to detect Bifidobacteria. The results showed that PCR-DGGE assays enabled identification of the species of bifidobacterium initially present in commercial fermented milk products with a detection threshold of 105 cells per gram. Real-Time PCR assays enabled numbering Bifidobacterium with a detection threshold of 104 cells per gram of product. Established PCR-DGGE analysis method was suitable for identification and detection of Bifidobacterium in commercial probiotic yoghurts.%本文建立了发酵乳制品中双歧杆菌种类和数量快速测定方法.以发酵乳中双歧杆菌为靶标,采用PCR-DGGE技术快速识别双歧杆菌种类;采用Real-Tine PCR手段测定双歧杆菌数量.研究结果表明,PCR-DGGE能准确、快速鉴别双歧杆菌种类,检出限为105 CFU/g; Real-Tine PCR能准确、快速定量双歧杆菌,检出限为104 CFU/g.该方法可用于发酵乳中双歧杆菌的快速识别和定量.

  18. Analysis of pulsed-field gel electrophoresis molecular subtyping and serotyping of Vibrio parahaemolyticus in food%食品中副溶血弧菌血清学分型与分子分型的研究

    Institute of Scientific and Technical Information of China (English)

    贺连华; 吴平芳; 陈妙玲; 王冰; 林爱红; 吕东月

    2011-01-01

    目的 分析深圳市2007~2010年监测食品中副溶血弧菌存在的优势血清型与基因型之间的相似性,初步建立深圳市食源性副溶血弧菌脉冲场凝胶电泳分子分型监测网络.方法 选择2007~2010年监测食品中分离出来的副溶血孤菌主要血清群(O1-O4)55株,基因组DNA经Sfi1酶切,通过脉冲场凝胶电泳PFGE获得图谱,利用BioNumerics 分析软件对图谱进行聚类分析.结果 相似性在90%以上的有15株,其中有9株相似性为100%,分别是2株O2:K28;1株O1:KUT与1株O4:K42;5株O3:K6,其余菌株谱型差异较大.结论 监测食品中分离的副溶血弧菌PFGE型别多,且相互之间关系分散.PFGE分子分型监测网络的建立,有助于食源性疾病发生时的主动监测,爆发调查和传染源追踪.%Objective To analyze the relationship between genotype and serotype of Vibrio parahaemolyticus isolated from food in Shenzhen from 2007 to 2010 and develop primary molecular subtyping surveillance network of Vibrio parahaemolyticus. Methods The 55 strains of Vibrio parahaemolylicus isolated from diarrhea patients containing important serotype O1-O4,chromosomal DNAs were digested with the restriction enzyme Sfil.and then were analyzed by pulsed-field gel electrophoresis. Results The similarity of the 15 strains was over 90% and 9 strains with 100% similarity including 2 strains O2:K28,1 strain 01:KUT and 1 strain O4:K42,5 strains O3:K6. Other strains showed prominent difference. Conclusion Various Vibrio parahaemolyticus patterns exist in food and the relationship is scattered. The development of PFGE molecular subtyping surveillance network would contribute to the surveillance,outbreak investigation and source tracking for Vibrio parahaemolyticus infection.

  19. Analysis of harmful algal bloom species using denaturing gradient gel electrophoresis (DGGE)%常见赤潮藻类的变性梯度凝胶电泳分析

    Institute of Scientific and Technical Information of China (English)

    邵娟; 王朝晖; 林朗聪; 张珂

    2011-01-01

    为了解我国典型有毒有害赤潮藻类的变性梯度凝胶电泳( DGGE)指纹图谱以及DGGE技术在赤潮藻类分析鉴定中的作用,本课题组运用DGGE技术,研究了我国沿海7种重要赤潮藻类的单一种类以及混合种类样品的18S rDNA V3区的DGGE指纹图谱,并且对2009年10月底在广东省珠海海域发生的双胞旋沟藻(Cochlodinium gemtnatum)赤潮样品进行了DGGE分析.结果表明,DGGE技术能够对环节环沟藻、海洋原甲藻、血红哈卡藻、锥状斯氏藻、中肋骨条藻、塔玛亚历山大藻、双胞旋沟藻7种常见的海洋赤潮藻类具有较好的区分效果,同时监测出赤潮样品中双胞旋沟藻、血红哈卡藻、环节环沟藻和海洋原甲藻4种优势种,种类组成与显微镜观察结果具有较好的一致性.结果说明DGGE技术可作为一种辅助方法对赤潮藻类进行分类鉴定.%Denaturing gradient gel electrophoresis (DGGE) fingerprints of 18S rDNA V3 region of single species and multi-species of seven harmful algal bloom ( HAB) taxa were studied in this study. The purpose is to understand DGGE fingerprints of typical HAB species from Chinese sea areas and the use of DGGE in the identification of HAB specie. A nature sample from the Cochlodinium geminatum bloom in Zhuhai coasts in October 2009 was analyzed. Results showed that distinguish lanes appeared in DGGE fingerprints by the seven HAB species including Gyrodinium instriatum, Prorocentrum micans, Akashiwo sanguined, Scrippsiella trochoidea, Skeletonema costatum, Alexandrium tamarense and Cochlodinium geminatum. Meanwhile four dominant species ( Cochlodinium geminatum, Akashiwo sanguined, Gyrodinium instriatum and Prorocentrum micans ) were observed in fingerprint of the bloom sample, which were consistent with the microscopical observation. The results suggested that DGGE technique could be applied as an auxiliary method for HAB species identification and analyzing.

  20. Molecular typing of Laribacter hongkonggensis isolated in Guangxi province by pulsed-field gel electrophoresis%广西香港海鸥菌分离菌株脉冲场凝胶电泳分子分型研究

    Institute of Scientific and Technical Information of China (English)

    孙贵娟; 黄彦; 唐振柱; 卢桂宁; 苏伟东; 甘永新

    2011-01-01

    目的 探讨香港海鸥菌分子分型方法,了解广西水产品监测所分离的香港海鸥菌的相关性.方法 以NotⅠ限制性内切酶对2005年分离的香港海鸥菌酶切后进行脉冲电泳,用BioNumerics 5.1聚类分析获得电泳图谱.结果 7株香港海鸥菌分为6个分子型,其中从南宁分离的与从河池分离的2株香港海鸥菌高度同源,相似度达100%.结论 PFGE可应用于香港海鸥菌分子分型,有助于发现香港海鸥菌流行规律和传播途径,水鸟可能是香港海鸥菌传播环节的一种重要媒介.%Objective To study the molecular typing of Laribacter hongkonggensis by pulsed-field gel electrophoresis (PFCE) , and to find out the relationship of 7 strains of L. Hongkonggensis isolated from fishery products in Guangxi on 2005. Methods Total DNA of each isolate was digested with restriction enzyme Not I, and the DNA fingerprints were obtained by running PFGE. These fingerprints of different stains were compared and their relationship was investigated by BioNumerics 5. 1 clustering. Results Seven strains of L. Hongkonggensis were attributed to six PFGE pattern combinations. One isolate from Nanning and another one from Hechi were homologous with 100% similarity. Conclusion PFGE is an effective way for molecular typing L hongkonggensis and is helpful in discovering the epidemiology and transmission of this bacteria. Waterfowl might be an important medium in the spreading of L. Hongkonggensis.

  1. Molecular Typing of Salmonella Serotype O:4(B) by Using Pulsed-field Gel Electrophoresis%肠道沙门菌O:4(B)菌群脉冲场凝胶电泳分子分型

    Institute of Scientific and Technical Information of China (English)

    王红; 黄彦; 唐振柱; 孙贵娟; 李秀桂; 韦程媛

    2011-01-01

    为了明确2010年食源性疾病监测中分离的肠道沙门菌O:4(B)菌群的PFGE分子型别,探讨其多态性及其与分子流行病学关系,我们将分离获得的29株O:4(B)血清型沙门菌进一步鉴定培养,挑取单个菌落增菌,供试菌株基因组DNA用限制性内切酶Xba Ⅰ消化酶切后进行脉冲场凝胶电泳分型,所得结果用Bionumerics5.1软件进行聚类分析.实验结果表明,根据电泳指纹图谱,可将29株肠道沙门菌O:4(B)菌群分为24个PFGE型别,菌株间的相似值在56.31%~100%之间,同一血清型别的沙门菌有多个PFGE型别.脉冲场凝胶电泳对O:4(B)群沙门菌有较高的分型能力,可有效的应用于食物中沙门菌溯源分析及分子流行病学研究.%The objective of the present study was to document the polymorphism of PFGE molecular type of Salmonella enterica subsp. enterica serotype 0:4(B) which isolated from food-bome diseases and to explore theirs relationship of molecular epidemiological. In this research, 29 Salmonella stains were identified and the single colony was picked and enriched. Then the total genomic DNA of the isolates was digested with restriction enzyme Xba Ⅰ , and run pulsed-field gel electrophoresis (PFGE). The DNA fingerprints of different stains were analyzed by Bionumerics5.1 software to perform clustering. The DNA fingerprints of 29 Salmonella were belonged t0 24 PFGE pattem combinations. Similarity value of these strains was in the range of 56.31%-100%. One serotype Salmonella could be found several PFGE pattem combinations. The PFGE technology is a good method for molecular typing of Salmonella serotype 0:4(B) and could be effectively apply on tracing the suspected source of food contamination and investigate the food-poisoning and also study the molecular epidemiological relationship of different Salmonella stains.

  2. 脉冲场凝胶电泳分子分型方法用于霍乱弧菌相关性分析%Correlation analysis of Vibrio cholerae by pulsed-field gel electrophoresis

    Institute of Scientific and Technical Information of China (English)

    于晓婕; 麻丽丹; 杨帆; 刁保卫

    2012-01-01

    目的 用脉冲场凝胶电泳(PFGE)分子分型方法,分析辽宁丹东和广东珠海两地区从水体和水产品中分离的霍乱弧菌之间的相关性.方法 对39株霍乱弧菌用内切酶Not I酶切DNA后进行PFGE分子分型,并在0.5×TBE电泳缓冲液中加入终浓度为3.8 mg/L的硫脲溶液电泳.结果 所有39株霍乱弧菌的基因组DNA显示出良好的分型结果,从朝鲜排污口、丹东鸭绿江水体中的鲫鱼、河蟹以及丹东排污口分离出的霍乱弧菌之间的相似度达到100%,说明这些产品之间应为同一个污染源;珠海的大头鱼和鳙鱼之间的相似度达到100%,说明这两者之间应为同一个污染源;珠海鲫鱼中检出的霍乱弧菌和鸭绿江水体中检出的霍乱弧菌之间的相似度达到88.4%,说明这两者之间可能为同一个污染源.结论 PFGE技术适用于霍乱弧菌环境样品分离菌株的相关性分析和传染源的追踪.%Objective To study the correlation of Vibrio cholerae by pulsed-field gel elec"rophoresis(PFGE) ,whieh were isolated from Liaoning Dandong and Guangdong Zhuhai in water body and seafood. Methods The chromosome DNA of 40 strains of Vibrio cholerae were digested by Not I enzyme and the PFGE were carried out, and 3.8mg/L finally concentration of Thiourea solution was added into the Thiourea0.5xTBE for Gel electrophoresis buffer. Results The chromosome DNA of 40 strains of Vibrio cholerae were typed well. The similarity of Vibrio cholerae which were isolated from sewage outfall of North Korea, Crucian Carp and river crab in Yalu river of Dandong, and sewage outfall of Dandong was up to 100%, it showed they were polluted by the same pollutant. The similarity of Vibrio cholerae which were isolated from Aspiorhynchus Laticeps and Aristichthys Nobilis in Zhuhai was up to 100%, it showed they were polluted by the same pollutant. The similarity of Vibrio cholerae which were isolated from Crucian Carp in Zhuhai and water body in Yalu river was

  3. Enhancing the performance of dye-sensitized solar cells by incorporating nanomica in gel electrolytes☆

    KAUST Repository

    Lai, Yi-Hsuan

    2010-04-01

    Gel-type dye-sensitized solar cells (DSSCs) were fabricated with 5.0 wt% polyvinyidene fluoride-co-hexafluoro propylene (PVDF-HFP) in methoxy propionitrile (MPN) as gel polymer electrolyte (GPE), 1-butyl-3-methylimidazolium iodide (BMII)/iodine (I2) as redox couple, 4-tertiary butyl pyridine (TBP) and guanidine thiocyanate as additives. The incorporation of alkyl-modified nanomica (AMNM) in the PVDF-HFP gel electrolytes caused the reduction of crystallization of PVDF-HFP, which was confirmed by X-ray diffraction (XRD) analysis. The short-circuit current density (JSC) of the cell increased due to the decrease of diffusion resistance, as judged by the electrochemical impedance spectra (EIS) analysis, while the open-circuit voltage (VOC) remained almost the same. As the loading of AMNM in the PVDF-HFP gel electrolyte was increased to 3.0 wt%, the JSC and power conversion efficiency (η) of the cells increased from 8.3 to 13.6 mA/cm2 and 3.5% to 5.7%, respectively. However, the JSC decreased as the loading of AMNM exceeded 3.0 wt%. At higher AMNM loadings, nanomica acted as a barrier interface between the electrolyte and the dye molecules to hinder electron transfer, and thus reducing the cell\\'s photocurrent density. Furthermore, the DSSCs fabricated by dispersing polymethyl methacrylate (PMMA) microspheres in the TiO2 electrode with the GPE containing 3.0 wt% AMNM improved the η to 6.70%. The TiO2 films would exhibit larger porosity by blending with PMMA, leading the penetration of GPEs into the porous TiO2 easier, thus improving the contact between the dye-adsorbed TiO2 surfaces and the GPEs, as characterized by EIS. Moreover, the η of gel-type DSSCs with a 25 μm thickness of surlyn reached 7.96% as compared with 6.70% for the DSSCs with a 60 μm surlyn. © 2009 Elsevier B.V. All rights reserved.

  4. Detecting irradiation of seeds using microgel electrophoresis (a collaborative trial)

    International Nuclear Information System (INIS)

    Preservation of certain foods by irradiation is permitted in the United Kingdom. However, all irradiated foods must be labelled as such, to ensure consumer choice. To help enforce labelling, a variety of methods have been developed for distinguishing between irradiated and non-irradiated foods. In preliminary trials, microgel electrophoresis -a simple method of assessing DNA damage - has shown considerable promise in this respect. This report describes microgel electrophoresis, and details results obtained in a blind trial carried out in collaboration with the Swedish University of Agricultural Sciences. Microgel electrophoresis facilitates analysis of the leakage of DNA from cells extracted from food material. In irradiated samples, the DNA is fragmented and will leak from cells in an electric current. This leakage can be seen as a 'comet' when the stained gel is viewed with a microscope. The size and shape of the comet can be used to estimate the irradiation dose administered to the sample. In non-irradiated samples the DNA is less fragmented, will tend not to leak from the cells and will not form a comet. (author)

  5. Comparison of Yeast Cell Protein Solubilization Procedures for Two-dimensional Electrophoresis

    DEFF Research Database (Denmark)

    Harder, A; Wildgruber, R; Nawrocki, A;

    1999-01-01

    with sodium dodecyl sulfate (SDS) buffer, consisting of 1% SDS and 100 mM tris(hydroxymethyl)aminomethane (Tris)-HCl, pH 7.0, followed by dilution with "standard" lysis buffer, and (iii) boiling the sample with SDS during cell lysis, followed by dilution with thiourea/urea lysis buffer (2 M thiourea/ 7 M urea...... molecular mass proteins. The procedures employed were sonication, followed by (i) protein solubilization with "standard" lysis buffer (9 M urea, 2% 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS), 1% dithiothreitol (DTT), 2% v/v carrier ampholytes, (ii) presolubilization of proteins...... sonication (method ii). Protein disaggregation and solubilization of high Mr proteins were further improved by pre-boiling with SDS and using thiourea/urea lysis buffer instead of "standard" lysis buffer (procedure iii)....

  6. Whole Cell Imprinting in Sol-Gel Thin Films for Bacterial Recognition in Liquids: Macromolecular Fingerprinting

    Directory of Open Access Journals (Sweden)

    Robert Armon

    2010-03-01

    Full Text Available Thin films of organically modified silica (ORMOSILS produced by a sol-gel method were imprinted with whole cells of a variety of microorganisms in order to develop an easy and specific probe to concentrate and specifically identify these microorganisms in liquids (e.g., water. Microorganisms with various morphology and outer surface components were imprinted into thin sol-gel films. Adsorption of target microorganism onto imprinted films was facilitated by these macromolecular fingerprints as revealed by various microscopical examinations (SEM, AFM, HSEM and CLSM. The imprinted films showed high selectivity toward each of test microorganisms with high adsorption affinity making them excellent candidates for rapid detection of microorganisms from liquids.

  7. Characterization of a gel in the cell wall to elucidate the paradoxical shrinkage of tension wood.

    Science.gov (United States)

    Clair, Bruno; Gril, Joseph; Di Renzo, Francesco; Yamamoto, Hiroyuki; Quignard, Françoise

    2008-02-01

    Wood behavior is characterized by high sensibility to humidity and strongly anisotropic properties. The drying shrinkage along the fibers, usually small due to the reinforcing action of cellulosic microfibrils, is surprisingly high in the so-called tension wood, produced by trees to respond to strong reorientation requirements. In this study, nitrogen adsorption-desorption isotherms of supercritically dried tension wood and normal wood show that the tension wood cell wall has a gel-like structure characterized by a pore surface more than 30 times higher than that in normal wood. Syneresis of the tension wood gel explains its paradoxical drying shrinkage. This result could help to reduce technological problems during drying. Potential applications in biomechanics and biomimetics are worth investigating, considering that, in living trees, tension wood produces tensile growth stresses 10 times higher than that of normal wood.

  8. New Adipose Tissue Formation by Human Adipose-Derived Stem Cells with Hyaluronic Acid Gel in Immunodeficient Mice

    OpenAIRE

    Huang, Shu-Hung; Lin, Yun-Nan; Lee, Su-Shin; Chai, Chee-Yin; Chang, Hsueh-Wei; Lin, Tsai-Ming; Lai, Chung-Sheng; Lin, Sin-Daw

    2015-01-01

    Background: Currently available injectable fillers have demonstrated limited durability. This report proposes the in vitro culture of human adipose-derived stem cells (hASCs) on hyaluronic acid (HA) gel for in vivo growth of de novo adipose tissue. Methods: For in vitro studies, hASCs were isolated from human adipose tissue and were confirmed by multi-lineage differentiation and flow cytometry. hASCs were cultured on HA gel. The effectiveness of cell attachment and proliferation on HA gel was...

  9. Antimicrobial activity and the mechanism of silver nanoparticle thermosensitive gel

    Directory of Open Access Journals (Sweden)

    Chen M

    2011-11-01

    Full Text Available Meiwan Chen1,2,‡, Zhiwen Yang1,‡, Hongmei Wu1, Xin Pan1, Xiaobao Xie3, Chuanbin Wu11Research and Development Center of Pharmaceutical Engineering, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China; 2State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China; 3Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou, China ‡These authors contributed equally to this workPurpose: The purpose of the present study was to elucidate the antimicrobial activity and mechanism of silver nanoparticles incorporated into thermosensitive gel (S-T-Gel on Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa.Patients and methods: This study investigated the growth, permeability, and morphology of Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa cells in order to observe the action of S-T-Gel on the membrane structure of these three bacteria. The cell morphology of normal and treated bacteria cells was assessed by transmission electron microscopy (TEM, and the effects of S-T-Gel on genome DNA of bacterial cells were evaluated by agarose gel electrophoresis.Results: S-T-Gel showed promising activity against Staphylococcus aureus and moderate activity against Escherichia coli and Pseudomonas aeruginosa. The observation with TEM suggested that S-T-Gel may destroy the structure of bacterial cell membranes in order to enter the bacterial cell. S-T-Gel then condensed DNA and combined and coagulated with the cytoplasm of the damaged bacteria, resulting in the leakage of the cytoplasmic component and the eventual death of these three bacteria. In addition, the analysis of agarose gel electrophoresis demonstrated that S-T-Gel could increase the decomposability of genome DNA.Conclusion: These results about promising antimicrobial activity and mechanism of S-T-Gel may be useful for further research

  10. A Single Cell Extraction Chip Using Vibration-Induced Whirling Flow and a Thermo-Responsive Gel Pattern

    Directory of Open Access Journals (Sweden)

    Takeshi Hayakawa

    2014-09-01

    Full Text Available We propose a single cell extraction chip with an open structure, which utilizes vibration-induced whirling flow and a single cell catcher. By applying a circular vibration to a micropillar array spiral pattern, a whirling flow is induced around the micropillars, and target cells are transported towards the single cell catcher placed at the center of the spiral. The single cell catcher is composed of a single-cell-sized hole pattern of thermo-responsive gel. The gel swells at low temperatures (≲32 ◦C and shrinks at high temperatures (≳32 ◦C, therefore, its volume expansion can be controlled by an integrated microheater. When the microheater is turned on, a single cell is trapped by the hole pattern of the single cell catcher. Then, when the microheater is turned off, the single cell catcher is cooled by the ambient temperature. The gel swells at this temperature, and the hole closes to catch the single cell. The caught cell can then be released into culture wells on a microtiter plate by heating the gel again. We conducted single cell extraction with the proposed chip and achieved a 60% success rate, of which 61% cells yielded live cells.

  11. Two-dimensional Electrophoresis Analysis of Differential Protein Expression in Squamous Carcinoma of the Cervix

    Institute of Scientific and Technical Information of China (English)

    ZHU Xue-qiong; WU Jie-li; YU Li-rong; LIN Yi; L(U) Jie-qiang; ZOU Shuang-wei; HU Yue

    2008-01-01

    Objective:To establish and optimize the two-dimensional gel electrophoresis(2-DE)maps of squamous carcinoma of the cervix and to study the protein difference between squamous carcinoma of the cervix(SCC)and normal cervical tissue.Methods:Using Two-dimensional gel electrophoresis followed by computer-assisted image analysis,the differential proteins between squamous carcinoma of the cervical tissue and normal cervical tissue were compared.Then using matrix-assisted laser desorption/ionization-time of flight mass spectrometry,the differential proteins were identified.Results:The well-resolved and reproducible two-dimensional gel electrophoresis patterns of squamous carcinoma of the cervix tissue and normal cervical tissue were obtained.After silver staining.the average matching ratio of squamous carcinoma of the cervix was 86.1%.There was a good reproducibility of spot position in 2-DE map,with average deviation in IEF direction of 0.95±0.13 mm,while in SDS-PAGE direction it was 1.20±0.18 mm.Ten protein spots were identified by mass spectrometry,some of which were involved in cell proliferation,cell apoptosis,intracellular enzymes,structural proteins,cycle regulation,and tumor occurrence.Conclusion:The differentially expressed proteins provide a fundamental basis for further study of human squamous carcinoma of the cervix and screening of its specific markers.

  12. Asymmetric bioreduction of acetophenones by Baker's yeast and its cell-free extract encapsulated in sol–gel silica materials

    International Nuclear Information System (INIS)

    Baker's yeast (BY) encapsulated in silica materials was synthesized using a yeast cell suspension and its cell-free extract during a sol–gel reaction of tetramethoxysilane with nitric acid as a catalyst. The synthesized samples were fully characterized using various methods, such as scanning electron microscopy, nitrogen adsorption–desorption, Fourier transform infrared spectroscopy, thermogravimetry, and differential thermal analysis. The BY cells were easily encapsulated inside silica-gel networks, and the ratio of the cells in the silica gel was approximately 75 wt%, which indicated that a large volume of BY was trapped with a small amount of silica. The enzyme activity (asymmetric reduction of prochiral ketones) of BY and its cell-free extract encapsulated in silica gel was investigated in detail. The activities and enantioselectivities of free and encapsulated BY were similar to those of acetophenone and its fluorine derivatives, which indicated that the conformation structure of BY enzymes inside silica-gel networks did not change. In addition, the encapsulated BY exhibited considerably better solvent (methanol) stability and recyclability compared to free BY solution. We expect that the development of BY encapsulated in sol–gel silica materials will significantly impact the industrial-scale advancement of high-efficiency and low-cost biocatalysts for the synthesis of valuable chiral alcohols.

  13. Asymmetric bioreduction of acetophenones by Baker's yeast and its cell-free extract encapsulated in sol-gel silica materials

    Science.gov (United States)

    Kato, Katsuya; Nakamura, Hitomi; Nakanishi, Kazuma

    2014-02-01

    Baker's yeast (BY) encapsulated in silica materials was synthesized using a yeast cell suspension and its cell-free extract during a sol-gel reaction of tetramethoxysilane with nitric acid as a catalyst. The synthesized samples were fully characterized using various methods, such as scanning electron microscopy, nitrogen adsorption-desorption, Fourier transform infrared spectroscopy, thermogravimetry, and differential thermal analysis. The BY cells were easily encapsulated inside silica-gel networks, and the ratio of the cells in the silica gel was approximately 75 wt%, which indicated that a large volume of BY was trapped with a small amount of silica. The enzyme activity (asymmetric reduction of prochiral ketones) of BY and its cell-free extract encapsulated in silica gel was investigated in detail. The activities and enantioselectivities of free and encapsulated BY were similar to those of acetophenone and its fluorine derivatives, which indicated that the conformation structure of BY enzymes inside silica-gel networks did not change. In addition, the encapsulated BY exhibited considerably better solvent (methanol) stability and recyclability compared to free BY solution. We expect that the development of BY encapsulated in sol-gel silica materials will significantly impact the industrial-scale advancement of high-efficiency and low-cost biocatalysts for the synthesis of valuable chiral alcohols.

  14. 中国肠炎沙门菌脉冲场凝胶电泳分子分型数据库的分析%Characterization of Salmonella enteritidis with pulsed-field gel electrophoresis in China

    Institute of Scientific and Technical Information of China (English)

    娄静; 刁保卫; 李杰; 阚飙; 闫梅英

    2013-01-01

    Objective To understand the pulsed-field gel electrophoresis (PFGE) patterns of the clinical isolates of Salmonella enteritidis and their epidemiological characteristics in China and provide evidence for the laboratory based detection of food borne diseases outbreak and response effort.Methods Molecular typing of 981 Salmonelle enteritidis strains isolated in 13 provinces from 2004 to 2012 were conducted according to PFGE protocol published on PulseNet and epidemiological analysis was conducted.Results The chromosomal DNA of 981 Salmonella enteritidis strains were digested with Xba Ⅰ restriction endonuclease and 126 PFGE patterns were observed.The discriminatory index (D) was 0.8336 for PFGE typing method.The predominate patterns of PFGE included JEGX01.CN0003,JEGX01.CN0001,JEGX01.CN0002,JEGX01.CN0005 and JEGX01.CN0016.Of 126 patterns,JEGX01.CN0003 、JEGX01.CN0001and JEGX01.CN0150 were related with outbreaks caused by Salmonella enteritidis.Common bands (±-0.8%) of 655 kbp,325 kbp,310 kbp,245 kbp,178 kbp and 110 kbp were found in the predominant patterns.Conclusion There were predominant PFGE patterns among the Salmonella enteritidis strains isolated in China,however,double or multiple endonucleotidases analysis of PFGE is necessary for outbreak detection due to the limited discriminatory power of single XbaⅠ digestion.%目的 了解近几年我国肠炎沙门菌临床分离株的流行病学及脉冲场凝胶电泳(PFGE)分子分型特点,为以实验室为基础的食源性疾病暴发的发现及疫情控制提供依据.方法 根据PulseNet公布的沙门菌PFGE分型方案,对2004-2012年分离自我国13个省(直辖市)的981株肠炎沙门菌进行流行病学及PFGE分子分型分析.结果 981株肠炎沙门菌经XbaⅠ酶切,PFGE获得126种带型,其分辨能力(D值)为0.8336.优势带型为JEGX01.CN0003、JEGX01.CN0001、JEGX01.CN0002、JEGX01.CN0005和JEGX01.CN0016.暴发相关带型是JEGX01.CN0003、JEGX01.CN0001和JEGX01.CN0150.肠炎沙

  15. Subspecies typing of Vibrio parahaemolyticus in aquatic products with pulsed-field gel electrophoresis%水产品中副溶血性弧菌脉冲场凝胶电泳分型

    Institute of Scientific and Technical Information of China (English)

    张昕; 汪琦; 张惠媛; 陈广全; 张捷

    2012-01-01

    Objective To assess subspecies typing of Vibrio parahaemolyticus strains from aquatic products with pulsed-field gel electrophoresis(PEGE). Methods A total of 80 selected isolates obtained from aquatic products were characterized with PFGE method. Genomic DNA was digested with restriction endonucleases NotI and Sfil. Results The isolates were grouped into 68 PFGE patterns by NotI and Sfil. Moreover, there were 70 PFGE patterns after compared with the results of the two restriction enzymes. The discrimination power of NotI was 78. 8% and that of Sfil was 76. 3% . Fourteen strains were from Canada four strain groups according to the Dice coefficient of 100% , thereinto, the Dice coefficient of four strains was 91. 8% and the Dice coefficient of ten strains was 93. 3% . Three strains form Norway and two strains from New Zealand belonged to 2 groups, with the Dice coefficient of 100%. There were no other same strains detected. Conclusion The results indicate that PFGE with both NotI and Sfil could be used in discriminant analysis for Vibrio parahaemolyticus, but NotI is more effective. The clustering analysis showes a clear disagreement among the strains and their sources. Furthermore, the strains with virulence genes are included in the same or contiguous clusters.%目的 采用脉冲场凝胶电泳(PFGE)对水产品中副溶血性弧菌进行分子分型.方法 采用PFGE技术,对80株分离自11个国家和中国浙江省和山东省的水产品中的副溶血性弧菌进行分子分型;基因组DNA用Not I和Sfi I2种酶进行消化.结果 Not I和Sfi I 2种内切酶均得到68种带型,综合系统树图中分成70种带型;Not I和Sfi I的分辨率分别为78.8%和76.3%;14株来自加拿大的菌株分聚成相似度100%的4组,其中有4株菌和10株菌分别聚成相似度91.8%和93.3%的2组;挪威和新西兰分别有3株和2株菌相似度为100%;其他国家的菌株无与本国相同的菌株.结论 2种酶均适合于

  16. Standardizing electrophoresis conditions: how to eliminate a major source of error in the comet assay.

    Directory of Open Access Journals (Sweden)

    Gunnar Brunborg

    2015-06-01

    Full Text Available In the alkaline comet assay, cells are embedded in agarose, lysed, and then subjected to further processing including electrophoresis at high pH (>13. We observed very large variations of mean comet tail lengths of cell samples from the same population when spread on a glass or plastic substrate and subjected to electrophoresis. These variations might be cancelled out if comets are scored randomly over a large surface, or if all the comets are scored. The mean tail length may then be representative of the population, although its standard error is large. However, the scoring process often involves selection of 50 – 100 comets in areas selected in an unsystematic way from a large gel on a glass slide. When using our 96-sample minigel format (1, neighbouring sample variations are easily detected. We have used this system to study the cause of the comet assay variations during electrophoresis and we have defined experimental conditions which reduce the variations to a minimum. We studied the importance of various physical parameters during electrophoresis: (i voltage; (ii duration of electrophoresis; (iii electric current; (iv temperature; and (v agarose concentration. We observed that the voltage (V/cm varied substantially during electrophoresis, even within a few millimetres of distance between gel samples. Not unexpectedly, both the potential ( V/cm and the time were linearly related to the mean comet tail, whereas the current was not. By measuring the local voltage with microelectrodes a few millimetres apart, we observed substantial local variations in V/cm, and they increased with time. This explains the large variations in neighbouring sample comet tails of 25% or more. By introducing simple technology (circulation of the solution during electrophoresis, and temperature control, these variations in mean comet tail were largely abolished, as were the V/cm variations. Circulation was shown to be particularly important and optimal conditions

  17. Synthesis of Thermoresponsive Amphiphilic Polyurethane Gel as a New Cell Printing Material near Body Temperature.

    Science.gov (United States)

    Tsai, Yi-Chun; Li, Suming; Hu, Shiaw-Guang; Chang, Wen-Chi; Jeng, U-Ser; Hsu, Shan-hui

    2015-12-23

    Waterborne polyurethane (PU) based on poly(ε-caprolactone) (PCL) diol and a second oligodiol containing amphiphilic blocks was synthesized in this study. The microstructure was characterized by dynamic light scattering (DLS), small-angle X-ray scattering (SAXS), and rheological measurement of the PU dispersion. The surface hydrophilicity measurement, infrared spectroscopy, wide-angle X-ray diffraction, mechanical and thermal analyses were conducted in solid state. It was observed that the presence of a small amount of amphiphilic blocks in the soft segment resulted in significant changes in microstructure. When 90 mol % PCL diol and 10 mol % amphiphilic blocks of poly(l-lactide)-poly(ethylene oxide) (PLLA-PEO) diol were used as the soft segment, the synthesized PU had a water contact angle of ∼24° and degree of crystallinity of ∼14%. The dispersion had a low viscosity below room temperature. As the temperature was raised to body temperature (37 °C), the dispersion rapidly (∼170 s) underwent sol-gel transition with excellent gel modulus (G' ≈ 6.5 kPa) in 20 min. PU dispersions with a solid content of 25-30% could be easily mixed with cells in sol state, extruded by a 3D printer, and deposited layer by layer as a gel. Cells remained alive and proliferating in the printed hydrogel scaffold. We expect that the development of novel thermoresponsive PU system can be used as smart injectable hydrogel and applied as a new type of bio-3D printing ink.

  18. Cell encapsulation in sub-mm sized gel modules using replica molding.

    Directory of Open Access Journals (Sweden)

    Alison P McGuigan

    Full Text Available For many types of cells, behavior in two-dimensional (2D culture differs from that in three-dimensional (3D culture. Among biologists, 2D culture on treated plastic surfaces is currently the most popular method for cell culture. In 3D, no analogous standard method--one that is similarly convenient, flexible, and reproducible--exists. This paper describes a soft-lithographic method to encapsulate cells in 3D gel objects (modules in a variety of simple shapes (cylinders, crosses, rectangular prisms with lateral dimensions between 40 and 1000 microm, cell densities of 10(5-10(8 cells/cm(3, and total volumes between 1x10(-7 and 8x10(-4 cm(3. By varying (i the initial density of cells at seeding, and (ii the dimensions of the modules, the number of cells per module ranged from 1 to 2500 cells. Modules were formed from a range of standard biopolymers, including collagen, Matrigel, and agarose, without the complex equipment often used in encapsulation. The small dimensions of the modules allowed rapid transport of nutrients by diffusion to cells at any location in the module, and therefore allowed generation of modules with cell densities near to those of dense tissues (10(8-10(9 cells/cm(3. This modular method is based on soft lithography and requires little special equipment; the method is therefore accessible, flexible, and well suited to (i understanding the behavior of cells in 3D environments at high densities of cells, as in dense tissues, and (ii developing applications in tissue engineering.

  19. 牙周牙髓联合病变菌群的PCR-DGGE分析%Bacterial analysis of combined periodontal-endodontic lesions using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE)

    Institute of Scientific and Technical Information of China (English)

    夏明慧; 亓庆国

    2012-01-01

    目的 利用变性梯度凝胶电泳(DGGE)技术观察牙周牙髓联合病变患牙牙周组织和根管中原始菌群分布状况及其异同,并通过克隆测序技术来试图探讨两部位可能存在的优势菌.方法 从13例牙周牙髓联合病变患牙分别采集患牙根尖1/3处牙周细菌和根管牙髓细菌,提取细菌总DNA,扩增16S rRNA基因可变区,再进行变性梯度凝胶电泳.应用SPSS17.0软件和Quantity One软件对DGGE图谱菌种条带进行统计学分析和聚类分析.对DGGE凝胶中有代表性的条带进行回收和克隆测序.结果 两取菌部位的菌种条带数间有明显的统计学差异(P<0.01),但二者之间无正相关性.二者间的相似系数为13.1% ~62.5%.牙周牙髓联合病变患牙根尖区1/3处牙周菌属可能有弯曲菌属(Campylobacter)、梭杆菌属(Fusobacterium)、奈瑟菌属(Neisseria)等,该处对应根管中菌属可能有优杆菌属(Mogibacterium)、棒状杆菌属(Corynebacterium)、放线菌属(Actinomyces)等.结论 牙周牙髓联合病变(牙周来源)中牙周组织和邻近根管牙髓组织中菌种在数目和结构上有明显不同.该病变牙周组织和根管中可能存在目前尚未被认知的优势菌种.%Objective To compare the bacterial community profiles present in periodontium and root canals of the same tooth diagnosed as combined periodontal-endodontic lesions by using denaturing gradient gel electrophoresis (DGGE).Methods Samples were collected from 13 extracted teeth with advanced periodontitis,endodontic samples from root tip 1/3 root canal,and periodontal samples from the corresponding neighboring periodontium.Genomic DNA was collected for the following universal bacterial primersPCR.The PCR products were then loaded on the DGGE gels to gain separate bands.The typical DGGE bands were excised,PCR-cloned and sequenced.Results The number of bands,which was indicative of the number of bacterial species,was compared intra-group (periodontal and

  20. Phthaloylchitosan-Based Gel Polymer Electrolytes for Efficient Dye-Sensitized Solar Cells

    Directory of Open Access Journals (Sweden)

    S. N. F. Yusuf

    2014-01-01

    Full Text Available Phthaloylchitosan-based gel polymer electrolytes were prepared with tetrapropylammonium iodide, Pr4NI, as the salt and optimized for conductivity. The electrolyte with the composition of 15.7 wt.% phthaloylchitosan, 31.7 wt.% ethylene carbonate (EC, 3.17 wt.% propylene carbonate (PC, 19.0 wt.% of Pr4NI, and 1.9 wt.% iodine exhibits the highest room temperature ionic conductivity of 5.27 × 10−3 S cm−1. The dye-sensitized solar cell (DSSC fabricated with this electrolyte exhibits an efficiency of 3.5% with JSC of 7.38 mA cm−2, VOC of 0.72 V, and fill factor of 0.66. When various amounts of lithium iodide (LiI were added to the optimized gel electrolyte, the overall conductivity is observed to decrease. However, the efficiency of the DSSC increases to a maximum value of 3.71% when salt ratio of Pr4NI : LiI is 2 : 1. This cell has JSC, VOC and fill factor of 7.25 mA cm−2, 0.77 V and 0.67, respectively.

  1. Mussel-inspired alginate gel promoting the osteogenic differentiation of mesenchymal stem cells and anti-infection.

    Science.gov (United States)

    Zhang, Shiwen; Xu, Kaige; Darabi, Mohammad Ali; Yuan, Quan; Xing, Malcolm

    2016-12-01

    Alginate hydrogels have been used in cell encapsulation for many years but a prevalent issue with pure alginates is that they are unable to provide enough bioactive properties to interact with mammalian cells. This paper discusses the modification of alginate with mussel-inspired dopamine for cell loading and anti-infection. Mouse bone marrow stem cells were immobilized into alginate and alginate-dopamine beads and fibers. Through live-dead and MTT assay, alginates modified by dopamine promoted cell viability and proliferation. In vitro cell differentiation results showed that such an alginate-dopamine gel can promote the osteogenic differentiation of mesenchymal stem cell after PCR and ALP assays. In addition to that, the adhesive prosperities of dopamine allowed for coating the surface of alginate-dopamine gel with silver nanoparticles, which provided the gel with significant antibacterial characteristics. Overall, these results demonstrate that a dopamine-modified alginate gel can be a great tool for cell encapsulation to promote cell proliferation and can be applied to bone regeneration, especially in contaminated bone defects. PMID:27612740

  2. Sol-Gel Process for Making Pt-Ru Fuel-Cell Catalysts

    Science.gov (United States)

    Narayanan, Sekharipuram; Valdez, Thomas; Kumta, Prashant; Kim, Y.

    2005-01-01

    A sol-gel process has been developed as a superior alternative to a prior process for making platinum-ruthenium alloy catalysts for electro-oxidation of methanol in fuel cells. The starting materials in the prior process are chloride salts of platinum and ruthenium. The process involves multiple steps, is time-consuming, and yields a Pt-Ru product that has relatively low specific surface area and contains some chloride residue. Low specific surface area translates to incomplete utilization of the catalytic activity that might otherwise be available, while chloride residue further reduces catalytic activity ("poisons" the catalyst). In contrast, the sol-gel process involves fewer steps and less time, does not leave chloride residue, and yields a product of greater specific area and, hence, greater catalytic activity. In this sol-gel process (see figure), the starting materials are platinum(II) acetylacetonate [Pt(C5H7O2)2, also denoted Pt-acac] and ruthenium(III) acetylacetonate [Ru(C5H7O2)3, also denoted Ru-acac]. First, Pt-acac and Ru-acac are dissolved in acetone at the desired concentrations (typically, 0.00338 moles of each salt per 100 mL of acetone) at a temperature of 50 C. A solution of 25 percent tetramethylammonium hydroxide [(CH3)4NOH, also denoted TMAH] in methanol is added to the Pt-acac/Ruacac/ acetone solution to act as a high-molecular-weight hydrolyzing agent. The addition of the TMAH counteracts the undesired tendency of Pt-acac and Ru-acac to precipitate as separate phases during the subsequent evaporation of the solvent, thereby helping to yield a desired homogeneous amorphous gel. The solution is stirred for 10 minutes, then the solvent is evaporated until the solution becomes viscous, eventually transforming into a gel. The viscous gel is dried in air at a temperature of 170 C for about 10 hours. The dried gel is crushed to make a powder that is the immediate precursor of the final catalytic product. The precursor powder is converted to the

  3. Microfluidics 3D gel-island chip for single cell isolation and lineage-dependent drug responses study.

    Science.gov (United States)

    Zhang, Zhixiong; Chen, Yu-Chih; Cheng, Yu-Heng; Luan, Yi; Yoon, Euisik

    2016-07-01

    3D cell culture in the extracellular matrix (ECM), which not only provides structural support to cellular constituents, but also initiates regulatory biochemical cues for a variety of important cell functions in tissue, has become more and more important in understanding cancer pathology and drug testing. Although the ECM-gel has been used in cell culture both in bulk and on-chip, previous studies focused on collective cell behavior rather than single-cell heterogeneity. To track the behavior of each individual cell, we have developed a gel-island chip, which can form thousands of islands containing single cells encapsulated by the desired ECM. Optimized by Poisson's distribution, the device can attain 34% single cell capture efficiency of the exact number of single cells per island. A good culture media exchange rate and high cell viability can be achieved in the gel-islands. The cells in the islands can be automatically counted for high-throughput analysis. As a proof of concept, we monitored the proliferation and differentiation of single Notch+ (stem-like) T47D breast cancer cells. The 3D collagen gel environment was found to be favorable for the stem-like phenotype through better self-renewal and de-differentiation (Notch- to Notch+ transition). More interestingly, we found that the Notch- de-differentiated cells were more resistant to doxorubicin and cisplatin than the Notch+ cells. Combining the 3D ECM culture and single cell resolution, the presented platform can automatically analyze the individual cell behaviors of hundreds of cells using a small amount of drug and reagents. PMID:27270563

  4. Second-harmonic generation scattering directionality predicts tumor cell motility in collagen gels

    Science.gov (United States)

    Burke, Kathleen A.; Dawes, Ryan P.; Cheema, Mehar K.; Van Hove, Amy; Benoit, Danielle S. W.; Perry, Seth W.; Brown, Edward

    2015-05-01

    Second-harmonic generation (SHG) allows for the analysis of tumor collagen structural changes throughout metastatic progression. SHG directionality, measured through the ratio of the forward-propagating to backward-propagating signal (F/B ratio), is affected by collagen fibril diameter, spacing, and disorder of fibril packing within a fiber. As tumors progress, these parameters evolve, producing concurrent changes in F/B. It has been recently shown that the F/B of highly metastatic invasive ductal carcinoma (IDC) breast tumors is significantly different from less metastatic tumors. This suggests a possible relationship between the microstructure of collagen, as measured by the F/B, and the ability of tumor cells to locomote through that collagen. Utilizing in vitro collagen gels of different F/B ratios, we explored the relationship between collagen microstructure and motility of tumor cells in a "clean" environment, free of the myriad cells, and signals found in in vivo. We found a significant relationship between F/B and the total distance traveled by the tumor cell, as well as both the average and maximum velocities of the cells. Consequently, one possible mechanism underlying the observed relationship between tumor F/B and metastatic output in IDC patient samples is a direct influence of collagen structure on tumor cell motility.

  5. Undergraduate physics laboratory: Electrophoresis in chromatography paper

    Science.gov (United States)

    Hyde, Alexander; Batishchev, Oleg

    2015-12-01

    An experiment studying the physical principles of electrophoresis in liquids was developed for an undergraduate laboratory. We have improved upon the standard agarose gel electrophoresis experimental regime with a straightforward and cost-effective procedure, in which drops of widely available black food coloring were separated by electric field into their dye components on strips of chromatography paper soaked in a baking soda/water solution. Terminal velocities of seven student-safe dyes were measured as a function of the electric potential applied along the strips. The molecular mobility was introduced and calculated by analyzing data for a single dye. Sources of systematic and random errors were investigated.

  6. Platelet-rich plasma gel in combination with Schwann cells for repair of sciatic nerve injury

    Institute of Scientific and Technical Information of China (English)

    Fagang Ye; Haiyan Li; Guangxi Qiao; Feng Chen; Hao Tao; Aiyu Ji; Yanling Hu

    2012-01-01

    Bone marrow mesenchymal stem cells were isolated from New Zealand white rabbits,culture-expanded and differentiated into Schwann cell-like cells.Autologous platelet-rich plasma and Schwann cell-like cells were mixed in suspension at a density of 1 × 106 cells/mL,prior to introduction into a poly (lactic-co-glycolic acid) conduit.Fabricated tissue-engineered nerves were implanted into rabbits to bridge 10 mm sciatic nerve defects (platelet-rich plasma group).Controls were established using fibrin as the seeding matrix for Schwann cell-like cells at identical density to construct tissue-engineered nerves (fibrin group).Twelve weeks after implantation,toluidine blue staining and scanning electron microscopy were used to demonstrate an increase in the number of regenerating nerve fibers and thickness of the myelin sheath in the platelet-rich plasma group compared with the fibrin group.Fluoro-gold retrograde labeling revealed that the number of Fluoro-gold-positive neurons in the dorsal root ganglion and the spinal cord anterior horn was greater in the platelet-rich plasma group than in the fibrin group.Electrophysiological examination confirmed that compound muscle action potential and nerve conduction velocity were superior in the platelet-rich plasma group compared with the fibrin group.These results indicate that autologous platelet-rich plasma gel can effectively serve as a seeding matrix for Schwann cell-like cells to construct tissue-engineered nerves to promote peripheral nerve regeneration.

  7. Direct methods for dynamic monitoring of secretions from single cells by capillary electrophoresis and microscopy with laser-induced native fluorescence detection

    Energy Technology Data Exchange (ETDEWEB)

    Tong, W.

    1997-10-08

    Microscale separation and detection methods for real-time monitoring of dynamic cellular processes (e.g., secretion) by capillary electrophoresis (CE) and microscopic imaging were developed. Ultraviolet laser-induced native fluorescence (LINF) provides simple, sensitive and direct detection of neurotransmitters and proteins without any derivatization. An on-column CE-LINF protocol for quantification of the release from single cell was demonstrated. Quantitative measurements of both the amount of insulin released from and the amount remaining in the cell ({beta}TC3) were achieved simultaneously. Secretion of catecholamines (norepinephrine (NE) and epinephrine (E)) from individual bovine adrenal chromaffin cells was determined using the on-column CE-LINF. Direct visualization of the secretion process of individual bovine adrenal chromaffin cells was achieved by LINF imaging microscopy with high temporal and spatial resolution. The secretion of serotonin from individual leech Retzius neurons was directly characterized by LINF microscopy with high spatial resolution.

  8. Applications of capillary electrophoresis and laser-induced fluorescence detection to the analysis of trace species: From single cells to single molecules

    Energy Technology Data Exchange (ETDEWEB)

    Qifeng, X.

    1995-11-01

    This Ph.D. Thesis describes several separation and detection schemes for the analysis of small volume and amount of samples, such as intracellular components and single enzymes developed during research. Indirect Laser-induced fluorescence detection and capillary electrophoresis were used to quantify lactate and pyruvate in single red blood cells. The assay of specific enzyme activities was achieved by monitoring the highly fluorescent enzymatic reaction product, NADH. LDH activity was found not to be a unique marker for diagnosis of leukemia. Reactions of single LDH-1 molecules were investigated by monitoring the reaction product with LIF detection.

  9. 江西省钩端螺旋体分离株脉冲场凝胶电泳分型和分析%Molecular typing on Leptospira interrogans isolates from Jiangxi province,by pulsed-field gel electrophoresis

    Institute of Scientific and Technical Information of China (English)

    徐建民; 蒋秀高; 李秀文; 张艳; 王健; 熊长辉

    2010-01-01

    Objective To perform a molecular epideminlogical investigation on the types of Leptospira interrogans isolates from leptospirosis patients and animal hosts in Jiangxi province,using a pulsed-field gel electrophoresis (PFGE).Methods The extracted chromosomal DNA from leptospiral isolates were digested with restriction endonuclease Not Ⅰ and the DNA segments were separated by using PFGE.By BiOnurerics V4.0 software and 75% similarity as the standard,the obtained PFGE images from leptospiral isolates were managed to establish a digitization database and then the PFGE maps of leptospiral isolates were compared with those of reference standard strains belonging to 15 serovars in 15 serogroups of L.interrogans,for cluster analysis.Results 139 strains of L.interrogans isolated from different areas of Jiangxi province were classified into 46 PFGE types.Among the PFGE types,LepNot Ⅰ.0071,LepNotⅠ.0072 and LepNot Ⅰ .0043 were the predominant types that accounting for 28.06%,15.11% and 7.19% of all the leptospiral isolates,respectively.The PFGE maps from 84.89% (118/139) of the 139 leptospiral isolates were found to basically match those of 6 reference standard strains belonging to 6 serovar in 6 serogroups of L.interrogans.In the 118 matched ieptospiral isolates,32.37% (45 strains),15.83% (22 strains) and 15.11% (21 strains)belonged to sero-groups Icterohaemorrhagiae serovar Lai,sero-groups Australis serovar Australis and sero-group Javanica serovar Javanica,respectively.Conclusion PFGE seemed a fast,accurate and effective method for typing of L.interrogans isolates.Serogroup Icterohaemorrhagiae serovar Lai and followed by serogroup Australis serovar Australis as well as serogroup Javanica serovar Javanica were the predominant L.interrogans species in humans and animal hosts in Jiangxi province.%目的 采用脉冲场凝胶电泳(PFGE)技术,对江西省钩端螺旋体(钩体)患者及动物宿主中分离的钩体菌株型别进行分子流行病学调查.方法

  10. Micro gel column technique is fit for detecting mixed fields post ABO incompatible hematopoietic stem cell transplantation.

    Science.gov (United States)

    Li, Min-Fang; Liu, Feng; Zhang, Min

    2015-04-01

    How to choose suitable serologic method for assessment of the actual stages of ABO chimera is more important to establish transfusion strategy for patients post-ABO incompatible hematopoietic stem cell transplantation. We reported ABO phenotypes of a patient post-ABO minor incompatible hematopoietic stem cell transplantation from 1+ weak agglutination by tube method was obviously reaffirmed to mixed fields with 4+ positive reaction by micro gel column card. Hence, blood bank technologists must continually work together with hematologist to establish appropriate transfusion strategy, and micro gel column technique can be more appropriate for detecting mixed fields during the whole period of transplantation. PMID:25578650

  11. Fast methods for analysis of neurotransmitters from single cell and monitoring their releases in central nervous system by capillary electrophoresis, fluorescence microscopy and luminescence imaging

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Ziqiang

    1999-12-10

    Fast methods for separation and detection of important neurotransmitters and the releases in central nervous system (CNS) were developed. Enzyme based immunoassay combined with capillary electrophoresis was used to analyze the contents of amino acid neurotransmitters from single neuron cells. The release of amino acid neurotransmitters from neuron cultures was monitored by laser induced fluorescence imaging method. The release and signal transduction of adenosine triphosphate (ATP) in CNS was studied with sensitive luminescence imaging method. A new dual-enzyme on-column reaction method combined with capillary electrophoresis has been developed for determining the glutamate content in single cells. Detection was based on monitoring the laser-induced fluorescence of the reaction product NADH, and the measured fluorescence intensity was related to the concentration of glutamate in each cell. The detection limit of glutamate is down to 10{sup {minus}8} M level, which is 1 order of magnitude lower than the previously reported detection limit based on similar detection methods. The mass detection limit of a few attomoles is far superior to that of any other reports. Selectivity for glutamate is excellent over most of amino acids. The glutamate content in single human erythrocyte and baby rat brain neurons were determined with this method and results agreed well with literature values.

  12. Dye-sensitized solar cell with poly(acrylic acid-co-acrylonitrile)-based gel polymer electrolyte

    International Nuclear Information System (INIS)

    Highlights: ► A nontoxic, easily synthesized poly(acrylic acid-co-acrylonitrile) showed suitable transmittance for dye-sensitized solar cell. ► A cell with relatively large active area fabricated with this polymer material showed acceptable efficiency. ► The gel polymer matrix affected the charge recombination, I3− diffusion, double layer capacitance, and electron lifetime in the cell. - Abstract: A non-conducting, nontoxic poly(acrylic acid-co-acrylonitrile) (PAA) was prepared and used as a supporting matrix for the electrolyte of dye-sensitized solar cells (DSSCs). DSSCs of active area 0.80 cm × 1.10 cm fabricated with PAA, 0.5 M LiI, 0.05 M I2, 0.5 M 3-tert-butylpyridine, and 0.1 M 1-methyl-3-propylimidazolium iodide in 3-methoxypropionitrile solvent showed an average solar energy conversion efficiency of 1.61% under simulated sunlight illumination of 100 mW cm−2, AM 1.5. The effects of the gel polymer matrix on the electrochemical properties of DSSCs were studied using the electrochemical impedance spectroscopy. Relative to the non-gel reference cells, the results showed a decrease in charge recombination, ionic diffusion, and double layer capacitance and an increase in electron lifetime. These results could play an important role in determining the future direction for the development of high-performance gel polymer electrolytes.

  13. Electrokinetic Flow and Dispersion in Capillary Electrophoresis

    Science.gov (United States)

    Ghosal, Sandip

    2006-01-01

    Electrophoretic separation of a mixture of chemical species is a fundamental technique of great usefulness in biology, health care, and forensics. In capillary electrophoresis (which has evolved from its predecessor, slab-gel electrophoresis), the sample migrates through a single microcapillary instead of through the network of pores in a gel. A fundamental design problem is to minimize dispersion in the separation direction. Molecular diffusion is inevitable and sets a theoretical limit on the best separation that can be achieved. But in practice, there are a number of effects arising out of the interplay between fluid flow, chemistry, thermal effects, and electric fields that result in enhanced dispersion. This paper reviews the subject of fluid flow in such capillary microchannels and examines the various causes of enhanced dispersion that limit the efficiency of separation.

  14. Sol–gel derived scattering layers as substrates for thin-film photovoltaic cells

    Energy Technology Data Exchange (ETDEWEB)

    Hegmann, Jan [Lehrstuhl für Chemische Technologie der Materialsynthese, Universität Würzburg, Röntgenring 11, 97070 Würzburg (Germany); Mandl, Magdalena [Fraunhofer-Institut für Silicatforschung, Neunerplatz 2, 97082 Würzburg (Germany); Löbmann, Peer, E-mail: peer.loebmann@isc.fraunhofer.de [Fraunhofer-Institut für Silicatforschung, Neunerplatz 2, 97082 Würzburg (Germany)

    2014-08-01

    Agglomerated silica particles were coated on glass by dip-coating; the resulting films exhibited optical scattering. With constant optical transmittances > 80% their haze could be modified by the withdrawal rate applied for the respective deposition procedure. Film thickness, surface topography and coverage of the substrate were characterized by Scanning Electron Microscopy and Atomic Force Microscopy. For the use in radiation management in thin-film silicon solar cells in a first step the scattering layers were coated with aluminum-doped zinc oxide by sputtering; the optical performance of the resulting bilayer was characterized by haze measurements and angle resolved scattering spectroscopy. Quantum efficiencies of complete solar cells could be determined after the deposition of a hydrogenated amorphous Si/hydrogenated microcrystalline Si tandem absorber and application of metallic back contacts. It turned out that the external quantum efficiency of the resulting cells is not directly related to the light scattering performance of the scattering layer used. - Highlights: • Characterization of sol–gel scattering layers • Combination of different coating-technologies to prepare stacks with optical functionality • Comprehensive material preparation and characterization for complex multilayer.

  15. Gel polymer electrolyte lithium-ion cells with improved low temperature performance

    Energy Technology Data Exchange (ETDEWEB)

    Smart, M.C.; Ratnakumar, B.V.; Behar, A.; Whitcanack, L.D. [Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA 91109 (United States); Yu, J.-S. [LG Chem/Research Park, P.O. Box 61Yu Song, Science Town, Daejon (Korea); Alamgir, M. [Compact Power, Inc., 1857 Technology Drive, Troy, MI 48083 (United States)

    2007-03-20

    For a number of NASA's future planetary and terrestrial applications, high energy density rechargeable lithium batteries that can operate at very low temperature are desired. In the pursuit of developing Li-ion batteries with improved low temperature performance, we have also focused on assessing the viability of using gel polymer systems, due to their desirable form factor and enhanced safety characteristics. In the present study we have evaluated three classes of promising liquid low-temperature electrolytes that have been impregnated into gel polymer electrolyte carbon-LiMn{sub 2}O{sub 4}-based Li-ion cells (manufactured by LG Chem. Inc.), consisting of: (a) binary EC + EMC mixtures with very low EC-content (10%), (b) quaternary carbonate mixtures with low EC-content (16-20%), and (c) ternary electrolytes with very low EC-content (10%) and high proportions of ester co-solvents (i.e., 80%). These electrolytes have been compared with a baseline formulation (i.e., 1.0 M LiPF{sub 6} in EC + DEC + DMC (1:1:1%, v/v/v), where EC, ethylene carbonate, DEC, diethyl carbonate, and DMC, dimethyl carbonate). We have performed a number of characterization tests on these cells, including: determining the rate capacity as a function of temperature (with preceding charge at room temperature and also at low temperature), the cycle life performance (both 100% DOD and 30% DOD low earth orbit cycling), the pulse capability, and the impedance characteristics at different temperatures. We have obtained excellent performance at low temperatures with ester-based electrolytes, including the demonstration of >80% of the room temperature capacity at -60 C using a C/20 discharge rate with cells containing 1.0 M LiPF{sub 6} in EC + EMC + MB (1:1:8%, v/v/v) (MB, methyl butyrate) and 1.0 M LiPF{sub 6} in EC + EMC + EB (1:1:8%, v/v/v) (EB, ethyl butyrate) electrolytes. In addition, cells containing the ester-based electrolytes were observed to support 5C pulses at -40 C, while still

  16. Primary studies on retinal proteome of rds and C3B mice by two-dimensional gel electrophoresis%应用双向电泳对rds和C3B鼠视网膜蛋白质组的初步研究

    Institute of Scientific and Technical Information of China (English)

    李大疆; 张清炯; 肖学珊

    2001-01-01

    Objective To apply two-dimensional (2-D) gel electrophoresis to resolve specially expressed proteins related to retinitis pigmentosa (RP) in the retina of rds mice.Methods Proteins, prepared from the retinas of rds mice and normal C3B mice at different ages, were separated by using two-dimensional electrophoresis and then analyzed by 2-DE imaging analyzer.Results 2-D gel electrophoresis was established for the retinal proteome analysis. Retinal neuronal tissue was lysed by using chemical lysis solution and ultrasonic. Using carrier ampholyte to set up pH gradient as first dimension and casting vertical 12% SDS-acylamide-bis slab as second dimension, the major retinal proteins showed maps of proteome on 2-D gels clearly. Retinal proteome of rds and C3B mice at 37d has different expressive patterns. Some proteins only expressed in the retina of rds mice while another only in the retina of C3B mice and others had different level between the two kinds of mice.Conclusion 2-D gel electrophoresis is effective to separate specially expressed retinal proteins. The expressed proteins in the rds retina are different in quality and quantity from that in the normal C3B mice.%目的应用蛋白质组分析技术,分离rds鼠视网膜中与视网膜色素变性(RP)相关的特异表达蛋白质。方法分别取不同时期的rds鼠和正常C3B鼠视网膜,用双向电泳(2-DE)技术,对比、分析其表达蛋白质点的差异,寻找rds鼠视网膜中与色素变性相关的蛋白质。结果用化学裂解法结合超声波粉碎,可以裂解视网膜神经组织,使其大部分蛋白质得到溶解;采用载体两性电解质pH梯度等电聚焦为第一向,垂直板SDS-PAGE为第二向分离视网膜蛋白质,得到蛋白质组表达谱。37d的rds和C3B鼠视网膜蛋白质组成有较大的差异,有些蛋白质仅在rds小鼠或正常小鼠视网膜中表达,有些蛋白质在rds小鼠视网膜中表达降低或升高,整体上视网

  17. Comparison of a PCR-restriction fragment length polymorphism (PCR-RFLP) assay to pulsed-field gel electrophoresis to determine the effect of repeated subculture and prolonged storage on RFLP patterns of Shiga toxin-producing Escherichia coli O157:H7.

    Science.gov (United States)

    Shima, Kensuke; Wu, Yuluo; Sugimoto, Norihiko; Asakura, Masahiro; Nishimura, Kazuhiko; Yamasaki, Shinji

    2006-11-01

    In this study, we compared a recently developed PCR-restriction fragment length polymorphism (PCR-RFLP) assay with pulsed-field gel electrophoresis (PFGE) using three different Shiga toxin-producing Escherichia coli (STEC) strains to understand whether repeated subculture in vitro and prolonged storage at room temperature affect the RFLP patterns of STEC. The PFGE profiles of the STEC strains changed by 1 to 8 fragments after repeated subculture and prolonged storage; one strain was no longer clonal after repeated subculture compared to the original isolate according to the Tenover criteria. In contrast, RFLP patterns obtained by PCR-RFLP were identical after repeated subculture and prolonged storage. These data clearly indicate that the PCR-RFLP assay which is based on the diversity of region V, a regulatory region of Stx-phage, was not affected by repeated subculture and prolonged storage and is a more practical and reliable method for molecular typing of STEC strains.

  18. Effect of Solvent-Assisted Nanoscaled Organo-Gels on Morphology and Performance of Organic Solar Cells

    DEFF Research Database (Denmark)

    Zuo, Li-Jian; Hu, Xiao-Lian; Ye, Tao;

    2012-01-01

    with that of the organo-gels in solution. Through this knowledge, we eventually achieve controlled morphology and optimized organic solar cells (OSCs) performance. Our results present a significant step forward for understanding the self-assembly behavior of conjugated polymers, control of their morphology...

  19. Encapsulated human hepatocellular carcinoma cells by alginate gel beads as an in vitro metastasis model

    International Nuclear Information System (INIS)

    Hepatocellular carcinoma (HCC) is the most common primary liver cancer and often forms metastases, which are the most important prognostic factors. For further elucidation of the mechanism underlying the progression and metastasis of HCC, a culture system mimicking the in vivo tumor microenvironment is needed. In this study, we investigated the metastatic ability of HCC cells cultured within alginate gel (ALG) beads. In the culture system, HCC cells formed spheroids by proliferation and maintained in nuclear abnormalities. The gene and protein expression of metastasis-related molecules was increased in ALG beads, compared with the traditional adhesion culture. Furthermore, several gene expression levels in ALG bead culture system were even closer to liver cancer tissues. More importantly, in vitro invasion assay showed that the invasion cells derived from ALG beads was 7.8-fold higher than adhesion cells. Our results indicated that the in vitro three-dimensional (3D) model based on ALG beads increased metastatic ability compared with adhesion culture, even partly mimicked the in vivo tumor tissues. Moreover, due to the controllable preparation conditions, steady characteristics and production at large-scale, the 3D ALG bead model would become an important tool used in the high-throughput screening of anti-metastasis drugs and the metastatic mechanism research. -- Highlights: •We established a 3D metastasis model mimicking the metastatic ability in vivo. •The invasion ability of cells derived from our model was increased significantly. •The model is easy to reproduce, convenient to handle, and amenable for large-scale

  20. GEL-STATE NMR OF BALL-MILLED WHOLE CELL WALLS IN DMSO-d6 USING 2D SOLUTION-STATE NMR SPECTROSCOPY

    Science.gov (United States)

    Plant cell walls were used for obtaining 2D solution-state NMR spectra without actual solubilization or structural modification. Ball-milled whole cell walls were swelled directly in the NMR tube with DMSO-d6 where they formed a gel. There are relatively few gel-state NMR studies. Most have involved...

  1. 琼脂糖凝胶电泳法分离金属性和半导体性单壁碳纳米管%Separation of Metallic Single-walled Carbon Nanotubes and Semiconducting Single-walled Carbon Nanotubes by Agarose Gel Electrophoresis

    Institute of Scientific and Technical Information of China (English)

    朱胜男; 张静; 李清文; 李红波; 金赫华; 宋启军

    2012-01-01

    The agarose gel electrophoresis (AGE) is one of the low-cost, large scale technologies for the separation of metallic single-walled carbon nanotubes (m-SWCNTs) and semiconducting single-walled carbon nanotubes(s-SWCNTs). The separated m-SWCNTs are divided into several parts and characterized by the UV-visible-near infrared absorption spectrum and the Raman spectrum respectively. The results show that the moieties with the fastest electrophoresis migration rate contain more m-SWCNTs. Furthermore, the effects of different agarose concentrations on the separating efficiencies of SWCNTs are investigated. It is found that higher concentration of agarose gel is beneficial to the enrichment of the m-SWCNTs and the separating efficiency of the m-SWCNTs could be realized by increasing the charge density on the surface of the SWCNTs.%琼脂糖凝胶电泳(AGE)是实现金属性单壁碳纳米管(m-SWCNTs)和半导体性单壁碳纳米管(s-SWCNTs)低成本、规模化分离的有效技术之一.本研究利用琼脂糖凝胶电泳分离单壁碳纳米管.通过紫外-可见-近红外吸收光谱和拉曼光谱对色谱带进行分段表征,发现电泳中迁移的最快的部分m-SWCNTs含量最高.考察了琼脂糖的浓度对SWCNTs中m-SWCNTs分离的影响.结果表明:高的琼脂糖浓度有利于m-SWCNTs的富集,可以通过扩大电荷密度带来的迁移速率的差异来使SWCNTs中的m-SWCNTs得到更有效的分离.

  2. 应用红外荧光和加尾引物法进行向日葵SSR遗传分析中的多聚PCR和多聚凝胶电泳的优化%Optimization of Multiplex PCR and Multiplex Gel Electrophoresis in Sunflower SSR Analysis Using Infrared Fluorescence and Tailed Primers

    Institute of Scientific and Technical Information of China (English)

    张潞生; Vanessa BECQUET; 李绍华; David ZHANG

    2003-01-01

    In an effort to simplify the procedure and to reduce the cost of fluorescence SSR analysis,the conditions of the multiplex PCR and the multiplex gel electrophoresis were optimized in the genetic analysis of sunflower (Helianthus annuus L.) inbred lines. Results indicated that factors for a successful multiplex PCR assay were related to the cycling touchdown annealing temperature, the balance of primer concentration at the various loci, the concentration of PCR buffer and the Taq DNA polymerase. Based on the optimization, a tailed primer strategy was outlined, and the effective ways were proposed to overcome the troubleshootings commonly encountered in the multiplex PCR and the multiplex gel electrophoresis.%在向日葵(Helianthus annuus L.)自交系SSR遗传分析中,为了提高SSR荧光分析效率、简化分析程序和降低研究费用,我们进行了多聚PCR和多聚凝胶电泳两项技术的优化研究.结果表明,优化多聚PCR和多聚凝胶电泳的影响因子(如逐步降低的退火温度的循环数、各个多聚位点引物浓度的平衡、PCR缓冲液浓度以及Taq DNA多聚酶的浓度等)可以收到更好的实验效果.基于以上的优化研究,系统地提出了一套优化的加尾引物法的策略.同时,提出了在多聚PCR和多聚凝胶电泳中常常遇到的技术难题的有效防止和解决的方法.

  3. 53株龟分支杆菌脓肿亚种临床分离株的同源性研究%Homology evaluation of 53 clinical strains of M. Chel onae abscessus subspecies by using pulsed-field gel electrophoresis

    Institute of Scientific and Technical Information of China (English)

    扈庆华; 李良成

    2001-01-01

    目的 分析引起院内感染爆发的53株龟分支杆菌 脓肿亚种临床分离株的同源性。方法 采用核酸脉冲电泳场分析技术,分 析53株临床分离株酶切电泳图谱,并比较图谱的差异。结果 53株临床分 离株出现两种电泳图谱,49株临床分离株为相同的电泳图谱,4株临床分离株表现为另一种 电泳图谱。结论 分子水平上确认院内术后龟分支杆菌脓肿亚种感染爆发 主要是由同一传染来源引起。核酸脉冲电泳场分析技术适于分析菌株的同源性和传染来源追 踪。%Objective To evaluate homology of 53 clinical str ains of M. chelonae abscessus subspecies which caused the nosocomial infecti on. Methods Large restriction fragment (LRF) pattern analysis of genomic DNA by using pulsed-field gel electrophoresis was performed and differences of patterns were compared. Results 53 clinical strains had two types of LRF pat terns. 49 strains had the same one LRF pattern, the rest 4 had another pattern. Conclusions The nosocomial postoperative M. Chelonae absc essus subspecies outbreak was mainly caused by the same infectious source. So pulsed-field gel electrophoresis was suitable for evaluating strain homolo gy and looking for infectious sourses.

  4. Sliding Fibers: Slidable, Injectable, and Gel-like Electrospun Nanofibers as Versatile Cell Carriers.

    Science.gov (United States)

    Lee, Slgirim; Yun, Seokhwan; Park, Kook In; Jang, Jae-Hyung

    2016-03-22

    Designing biomaterial systems that can mimic fibrous, natural extracellular matrix is crucial for enhancing the efficacy of various therapeutic tools. Herein, a smart technology of three-dimensional electrospun fibers that can be injected in a minimally invasive manner was developed. Open surgery is currently the only route of administration of conventional electrospun fibers into the body. Coordinating electrospun fibers with a lubricating hydrogel produced fibrous constructs referred to as slidable, injectable, and gel-like (SLIDING) fibers. These SLIDING fibers could pass smoothly through a catheter and fill any cavity while maintaining their fibrous morphology. Their injectable features were derived from their distinctive rheological characteristics, which were presumably caused by the combinatorial effects of mobile electrospun fibers and lubricating hydrogels. The resulting injectable fibers fostered a highly favorable environment for human neural stem cell (hNSC) proliferation and neurosphere formation within the fibrous structures without compromising hNSC viability. SLIDING fibers demonstrated superior performance as cell carriers in animal stroke models subjected to the middle cerebral artery occlusion (MCAO) stroke model. In this model, SLIDING fiber application extended the survival rate of administered hNSCs by blocking microglial infiltration at the early, acute inflammatory stage. The development of SLIDING fibers will increase the clinical significance of fiber-based scaffolds in many biomedical fields and will broaden their applicability. PMID:26885937

  5. Effects of the CNTF-collagen gel-controlled delivery system on rat neural stem/progenitor cells behavior

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The injury of central nervous system (CNS) usually causes the cavity formation. Although transplantation of neural stem/precursor cells (NSPCs) into the lesioned area of CNS has been shown to be implicated in the functional restoration, the therapeutic result is limited by the poor survival of NSPCs as well as their insufficient proliferation and differentiation abilities. Type-1 collagen is considered as a candidate scaffold or drug delivery system to overcome the aforementioned obstacle. This study observed the effects of the CNTF (ciliary neurotrophic factor)-collagen gel-controlled delivery system and daily addition of soluble-form CNTF on the NSPC survival, migration, proliferation and differentiation. The results showed that, within 12 h of the initial co-culture, CNTF was released in a burst pattern, then the CNTF-collagen gel-controlled delivery system stably released CNTF for up to 12 d. The cell viability test, together with immunohistochemistry, RT-PCR and Western blotting, showed that the CNTF-collagen gel-controlled delivery system supported the NSPCs seeded on the surface of collagen gel survival and facilitated their migration and proliferation. The daily addition of soluble-form CNTF to the medium had similar effects to the CNTF-collagen gel-controlled delivery system, but large quantities of soluble-form CNTF were consumed during the entire process. Taken together, the CNTF-collagen gel-controlled delivery system not only provides a physical scaffold for the transplanted NSPCs to adhere and migrate, but also facilitates the NSPC survival, growth and proliferation, simultaneously reducing the consumption of the expensive growth factors. This system may be used to enhance the microenvironment in the lesioned area of CNS.

  6. On-line sequential injection-capillary electrophoresis for near-real-time monitoring of extracellular lactate in cell culture flasks.

    Science.gov (United States)

    Alhusban, Ala A; Gaudry, Adam J; Breadmore, Michael C; Gueven, Nuri; Guijt, Rosanne M

    2014-01-01

    Cell culture has replaced many in vivo studies because of ethical and regulatory measures as well as the possibility of increased throughput. Analytical assays to determine (bio)chemical changes are often based on end-point measurements rather than on a series of sequential determinations. The purpose of this work is to develop an analytical system for monitoring cell culture based on sequential injection-capillary electrophoresis (SI-CE) with capacitively coupled contactless conductivity detection (C(4)D). The system was applied for monitoring lactate production, an important metabolic indicator, during mammalian cell culture. Using a background electrolyte consisting of 25mM tris(hydroxymethyl)aminomethane, 35mM cyclohexyl-2-aminoethanesulfonic acid with 0.02% poly(ethyleneimine) (PEI) at pH 8.65 and a multilayer polymer coated capillary, lactate could be resolved from other compounds present in media with relative standard deviations 0.07% for intraday electrophoretic mobility and an analysis time of less than 10min. Using the human embryonic kidney cell line HEK293, lactate concentrations in the cell culture medium were measured every 20min over 3 days, requiring only 8.73μL of sample per run. Combining simplicity, portability, automation, high sample throughput, low limits of detection, low sample consumption and the ability to up- and outscale, this new methodology represents a promising technique for near real-time monitoring of chemical changes in diverse cell culture applications. PMID:24309712

  7. An improved acid polyacrylamid gel electrophoresis method and its application in germ plasm resources analysis%醇溶蛋白酸性电泳及其在种质资源分析中的应用

    Institute of Scientific and Technical Information of China (English)

    刘香利; 郭蔼光; 李玉红

    2001-01-01

    The method of polyacrylamid electrophoresis in acid environment is improved.Using this method,the gliadin of several wheat,rye and triticale is analyzed.The result shows there are significant differences between each varietie s.This method can be used in variety identification and germ plasm analysis not only for wheat but also for rye.%建立了1个新的醇溶蛋白酸性电泳方法,并用此方法对不同倍性小麦品种及黑麦、小黑麦品种的醇溶蛋白组成进行了分析。结果表明,此方法不仅适用于小麦醇溶蛋白分析,而且也适用于黑麦和小黑麦种质资源分析。

  8. Anti-EMP2 diabody blocks Epithelial Membrane Protein 2 (EMP2) and FAK mediated collagen gel contraction in ARPE-19 cells

    OpenAIRE

    Morales, Shawn A.; Telander, David G.; Mareninov, Sergey; Nagy, Agnes; Wadehra, Madhuri; Braun, Jonathan; Gordon, Lynn K.

    2012-01-01

    Epithelial membrane protein 2 (EMP2) regulates collagen gel contraction by the retinal pigment epithelium cell line ARPE-19 by modulating FAK activation. Collagen gel contraction is one in vitro model for an aberrant wound healing response, proliferative vitreoretinopathy (PVR), which occurs as a complication of severe ocular trauma. The purpose of this study is to investigate whether EMP2 specific recombinant diabody decreases activation of FAK and collagen gel contraction in ARPE-19. Anti-E...

  9. Gel electrolytes containing several kinds of particles used in quasi-solid-state dye-sensitized solar cells

    Institute of Scientific and Technical Information of China (English)

    GENG Yi; SUN Xiaodan; CAI Qiang; SHI Yantao; LI Hengde

    2006-01-01

    Composite gel electrolytes containing several kinds of particles used as the quasi-solid-state electrolytes in dye-sensitized solar cells (DSSCs) were reported. Mesoporous particles (MCM-41) with unique structures composed of ordered nanochannels were served as a new kind of gelator for quasi-solid-state electrolytes. MCM-41, hydrophobic fumed silica Aerosil R972 and TiO2 nanopatricles P25 were dispersed into gel electrolytes respectively. The solar energy-to-electricity conversion efficiency of these cells is 4.65%, 6.85% and 5.05% respectively under 30 mW·cm-2 illumination. The preparation methods and the particles sizes exert an influence on the performance of corresponding solar cells. Owing to unique pore structures and high specific BET surface area, mesoporous silica MCM-41 was expected to have the potential to afford conducting nanochannels for redox couple diffusion.

  10. Extracellular matrix gel is necessary for in vitro cultivation of insulin producing cells from human umbilical cord blood derived mesenchymal stem cells

    Institute of Scientific and Technical Information of China (English)

    GAO Feng; WU De-quan; HU Yan-hua; JIN Guang-xin

    2008-01-01

    Background Pancreatic islet cell transplantation is an effective approach to treat type 1 diabetes. However, this therapy is not widely used because of the severe shortage of transplantable donor islets. This study investigated whether mesenchymal stem cells (MSCs) derived from human umbilical cord blood (UCB) could be transdifferentiated into insulin producing cells in vitro and the role of extracellular matrix (ECM) gel in this procedure.Methods Human UCB samples were collected and MSCs were isolated. MSCs specific marker proteins were analyzed by a flow cytometer. The capacities of osteoblast and adipocyte to differentiate were tested. Differentiation into islet like cell was induced by a 15-day protocol with or without ECM gel. Pancreatic characteristics were evaluated with immunofluorescence, reverse transcription polymerase chain reaction (RT-PCR) and flow cytometry. Insulin content and release in response to glucose stimulation were detected with chemiluminescent immunoassay system.Results Sixteen MSCs were isolated from 42 term human UCB units (38%). Human UCB-MSCs expressed MSCs specific markers and could be induced in vitro into osteoblast and adipocyte. Islet like cell clusters appeared about 9 days after pancreatic differentiation in the inducing system with ECM gel. The insulin positive cells accounted for (25.2±3.4)% of the induced cells. The induced cells expressed islet related genes and hormones, but were not very responsive to glucose challenge. When MSCs were induced without ECM gel, clusters formation and secretion of functional islet proteins could not be observed.Conclusions Human UCB-MSCs can differentiate into islet like cells in vitro and ECM gel plays an important role in pancreatic endocrine cell maturation and formation of three dimensional structures.

  11. Therapeutic assessment of mesenchymal stem cells delivered within a PEGylated fibrin gel following an ischemic injury.

    Science.gov (United States)

    Ricles, Laura M; Hsieh, Pei-Ling; Dana, Nicholas; Rybalko, Viktoriya; Kraynak, Chelsea; Farrar, Roger P; Suggs, Laura J

    2016-09-01

    The intent of the current study was to investigate the therapeutic contribution of MSCs to vascular regeneration and functional recovery of ischemic tissue. We used a rodent hind limb ischemia model and intramuscularly delivered MSCs within a PEGylated fibrin gel matrix. Within this model, we demonstrated that MSC therapy, when delivered in PEGylated fibrin, results in significantly higher mature blood vessel formation, which allows for greater functional recovery of skeletal muscle tissue as assessed using force production measurements. We observed initial signs of vascular repair at early time points when MSCs were delivered without PEGylated fibrin, but this did not persist or lead to recovery of the tissue in the long-term. Furthermore, animals which were treated with PEGylated fibrin alone exhibited a greater number of mature blood vessels, but they did not arterialize and did not show improvements in force production. These results demonstrate that revascularization of ischemic tissue may be a necessary but not sufficient step to complete functional repair of the injured tissue. This work has implications on stem cell therapies for ischemic diseases and also potentially on how such therapies are evaluated. PMID:27318932

  12. Sol-gel synthesized mesoporous anatase titanium dioxide nanoparticles for dye sensitized solar cell (DSSC) applications

    Indian Academy of Sciences (India)

    R Govindaraj; M Senthil Pandian; P Ramasamy; Sumita Mukhopadhyay

    2015-04-01

    Hierarchically structured titanium dioxide nanoparticles were successfully synthesized by the sol-gel method. The synthesized nanoparticles were subjected to powder X-ray diffraction, UV-Vis DRS spectroscopy, Brunauer–Emmett–Teller method, Barrett–Joyner–Halenda analysis, field emission scanning electron microscopy, high-resolution transmission electron microscopy and energy-dispersive X-ray analysis. The powder X-ray diffraction pattern shows that the obtained particles are of anatase phase with good crystallite nature. The nitrogen adsorption and desorption isotherms show that the prepared material has surface area of 31.71 m2 g-1 and the pore size distribution analysis shows the average pore diameters of mesoporous TiO2 nanostructures to be 7.1 and 9.3 nm. The UV–Vis DRS spectrum shows that the TiO2 nanoparticles are having absorption in the ultraviolet region. The optical band gap of the nanoparticles is 3.2 eV. The morphological studies show the morphology of the particles as spherical in shape. The elemental compositions of TiO2 nanoparticles were confirmed by energy-dispersive X-ray spectrum analysis. The conversion efficiency of the solar cell was 3.415% with open-circuit voltage (oc), short-circuit current (sc) and fill factor (FF) of 0.607 V, 13.206 mA cm-2 and 42.56%, respectively.

  13. Affinity Capillary Electrophoresis:Study of the Binding of HIV-1 gp41 with a Membrane Protein (P45) on the Human B Cell Line,Raji

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    Affinity capillary electrophoresis has been used to study the interaction between a membrane protein (P45) isolated from the Human B cell line, Raji, and rsgp41. P45, rsgp41 and the complexes were well resolved. The entire separation was achieved in less than 3min. Formations of two kinds of stable P45-rsgp41 complexes were confirmed based on migration time comparison; the binding equilibrium was achieved as soon as two proteins were mixed. The results indicate that the interaction between P45 and rsgp41 is strong with a fast association rate and a slow dissociation rate, and there are at least two kinds of binding sites with different binding constants between P45 and rsgp41.

  14. Determination of NAD+ and NADH level in a Single Cell Under H2O2 Stress by Capillary Electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Xi, Wenjun [Iowa State Univ., Ames, IA (United States)

    2008-01-01

    A capillary electrophoresis (CE) method is developed to determine both NAD+ and NADH levels in a single cell, based on an enzymatic cycling reaction. The detection limit can reach down to 0.2 amol NAD+ and 1 amol NADH on a home-made CE-LIF setup. The method showed good reproducibility and specificity. After an intact cell was injected into the inlet of a capillary and lysed using a Tesla coil, intracellular NAD+ and NADH were separated, incubated with the cycling buffer, and quantified by the amount of fluorescent product generated. NADH and NAD+ levels of single cells of three cell lines and primary astrocyte culture were determined using this method. Comparing cellular NAD+ and NADH levels with and without exposure to oxidative stress induced by H2O2, it was found that H9c2 cells respond to the stress by reducing both cellular NAD+ and NADH levels, while astrocytes respond by increasing cellular NADH/NAD+ ratio.

  15. DNA Sequencing Using capillary Electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Barry Karger

    2011-05-09

    The overall goal of this program was to develop capillary electrophoresis as the tool to be used to sequence for the first time the Human Genome. Our program was part of the Human Genome Project. In this work, we were highly successful and the replaceable polymer we developed, linear polyacrylamide, was used by the DOE sequencing lab in California to sequence a significant portion of the human genome using the MegaBase multiple capillary array electrophoresis instrument. In this final report, we summarize our efforts and success. We began our work by separating by capillary electrophoresis double strand oligonucleotides using cross-linked polyacrylamide gels in fused silica capillaries. This work showed the potential of the methodology. However, preparation of such cross-linked gel capillaries was difficult with poor reproducibility, and even more important, the columns were not very stable. We improved stability by using non-cross linked linear polyacrylamide. Here, the entangled linear chains could move when osmotic pressure (e.g. sample injection) was imposed on the polymer matrix. This relaxation of the polymer dissipated the stress in the column. Our next advance was to use significantly lower concentrations of the linear polyacrylamide that the polymer could be automatically blown out after each run and replaced with fresh linear polymer solution. In this way, a new column was available for each analytical run. Finally, while testing many linear polymers, we selected linear polyacrylamide as the best matrix as it was the most hydrophilic polymer available. Under our DOE program, we demonstrated initially the success of the linear polyacrylamide to separate double strand DNA. We note that the method is used even today to assay purity of double stranded DNA fragments. Our focus, of course, was on the separation of single stranded DNA for sequencing purposes. In one paper, we demonstrated the success of our approach in sequencing up to 500 bases. Other

  16. A method to determine Young's modulus of soft gels for cell adhesion

    Institute of Scientific and Technical Information of China (English)

    Xiaoling Peng; Jianyong Huang; Lei Qin; Chunyang Xiong; Jing Fang

    2009-01-01

    A convenient technique is reported in this note for measuring elastic modulus of extremely soft material for cellular adhesion. Specimens of bending cylinder under gravity are used to avoid contact problem between testing device and sample, and a beam model is presented for evaluating the curvatures of gel beams with large elastic deformation. A self-adaptive algorithm is also proposed to search for the best estimation of gels' elastic moduli by comparing the experimental bending curvatures with those computed from the beam model with preestimated moduli. Application to the measurement of the property of polyacrylamide gels indicates that the material compliance varies with the concentrations of bis-acrylamide, and the gels become softer after being immersed in a culture medium for a period of time, no matter to what extent they are polymerized.

  17. Should routine laboratories stop doing screening serum protein electrophoresis and replace it with screening immune-fixation electrophoresis? No quick fixes: Counterpoint.

    Science.gov (United States)

    Smith, Joel D; Raines, Geoffrey; Schneider, Hans G

    2016-06-01

    Monoclonal gammopathies are characterised by the production of a monoclonal immunoglobulin or free light chains by an abnormal plasma cell or B-cell clone and may indicate malignancy or a precursor (MGUS). There is currently no consensus on the initial test or combination of tests to be performed in suspected monoclonal gammopathies but serum protein electrophoresis and urine protein electrophoresis are commonly requested as initial investigations. If abnormal, immunofixation electrophoresis is then performed to confirm the presence of paraprotein and to determine its heavy and light chain type. Recently, some groups have developed simplified "screening" IFE methods for use in parallel to SPEP for the detection monoclonal gammopathies. We argue here that screening IFE may be of benefit in clinical laboratories using SPEP with poor resolution in the β-region, assisting in the detection of mainly IgA paraprotein, but may be of less benefit in laboratories utilising higher resolution gels. Further it may increase the detection of trace bands of questionable clinical significance, representing transient phenomena in infectious and auto-immune conditions or very low risk MGUS. The increased detection of these bands using screening IFE would require further patient follow up, possibly causing unnecessary patient anxiety and additional follow up healthcare costs. PMID:26677889

  18. Preparation of Collagen-Coated Gels that Maximize In Vitro Myogenesis of Stem Cells by Matching the Lateral Elasticity of In Vivo Muscle

    OpenAIRE

    Chaudhuri, Tathagata; Rehfeldt, Florian; Sweeney, H. Lee; Discher, Dennis E.

    2010-01-01

    The physical nature of a cell’s microenvironment – including the elasticity of the surrounding tissue – appears to exert a significant influence on cell morphology, cytoskeleton, and gene expression. We have previously shown that committed muscle cells will develop sarcomeric striations of skeletal muscle myosin II only when the cells are grown on a compliant gel that closely matches the passive compliance of skeletal muscle. We have more recently shown with the same types of elastic gels tha...

  19. STEM CELLS AND PROTEOMICS

    Institute of Scientific and Technical Information of China (English)

    ZHOU Yong-ming; GUO Tian-nan; HUANG Shi-ang

    2006-01-01

    The distinctive features of proteomics are large-scale and high throughput. The key techniques of proteomics are two-dimensional gel electrophoresis, mass spectrometry and bioinformatics. Stem cell can differentiate into all kinds of cells, tissues and organs. There are many proteins and cytokines involved in the process of differentiation. Applying proteomics techniques to the research of the complex process of stem cell differentiation is of great importance to study the mechanism and applications of stem cell differentiation.

  20. Synthesis and Characterization of a Gel-Type Electrolyte with Ionic Liquid Added for Dye-Sensitized Solar Cells

    Directory of Open Access Journals (Sweden)

    Le-Yan Shi

    2013-01-01

    Full Text Available This study intends to develop the electrolyte needed in dye-sensitized solar cells (DSSCs. Moreover, three different ionic liquids in different molalities are added to the gel-type electrolyte. Experimental results show that the DSSC composed of the gel-type electrolyte with no ionic liquid added can acquire 4.13% photoelectric conversion efficiency. However, the DSSC composed of the gel-type electrolyte with 0.4 M of 1-butyl-3-methylimidazolium chloride added has an open-circuit voltage of 810 mV, a short-circuit current density of 9.56 mA/cm2, and photoelectric conversion efficiency reaching 4.89%. Comparing this DSSC with the DSSC with no ionic liquid added, the photoelectric conversion efficiency can be enhanced by 18.4%. As to durability, the DSSC composed of the gel-type electrolyte with ionic liquid added still has a photoelectric conversion efficiency of 3.28% on the 7th day after it is stored in an enclosed space and maintains 0.72% efficiency on the 14th day. When the proposed DSSC is compared with the DSSC prepared by using a liquid-type electrolyte, the durability of its photoelectric conversion efficiency can be increased by 7 times.