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Sample records for two-dimensional 2-d electrophoresis

  1. Two-Dimensional Gel Electrophoresis and 2D-DIGE.

    Science.gov (United States)

    Meleady, Paula

    2018-01-01

    Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) continues to be one of the most versatile and widely used techniques to study the proteome of a biological system. In particular, a modified version of 2D-PAGE, two-dimensional difference gel electrophoresis (2D-DIGE), which uses differential labeling of protein samples with up to three fluorescent tags, offers greater sensitivity and reproducibility over conventional 2D-PAGE gels for differential quantitative analysis of protein expression between experimental groups. Both these methods have distinct advantages in the separation and identification of thousands of individual proteins species including protein isoforms and post-translational modifications. This review will discuss the principles of 2D-PAGE and 2D-DIGE including limitations to the methods. 2D-PAGE and 2D-DIGE continue to be popular methods in bioprocessing-related research (particularly on recombinant Chinese hamster ovary cells), which will also be discussed in the review chapter.

  2. Removal of interfering substances in samples prepared for two-dimensional (2-D) electrophoresis.

    Science.gov (United States)

    Berkelman, Tom

    2008-01-01

    Biological samples may contain contaminants that interfere with analysis by two-dimensional (2-D) electrophoresis. Lysates or biological fluids are complex mixtures that contain a wide variety of nonprotein substances in addition to the proteins to be analyzed. These substances often interfere with the resolution of the electrophoretic separation or the visualization of the result. Macromolecules (e.g., polysaccharides and DNA) can interfere with electrophoretic separation by clogging gel pores. Small ionic molecules can impair isoelectric focusing (IEF) separation by rendering the sample too conductive. Other substances (e.g., phenolics and lipids) can bind to proteins, influencing their electrophoretic properties or solubility. In many cases, measures to remove interfering substances can result in significantly clearer 2-D patterns with more visible spots and better resolution. It should be borne in mind, however, that analysis of samples by 2-D electrophoresis is usually most successful and informative when performed with minimally processed samples, so it is important that any steps taken to remove interfering substance be appropriate to the sample and only performed when necessary. Procedures for the removal of interfering substances therefore represent a compromise between removing nonprotein contaminants, and minimizing interference with the integrity and relative abundances of the sample proteins. This chapter presents a number of illustrative examples of optimized sample preparation methods in which specific interfering substances are removed by a variety of different strategies.

  3. Comparative Two-Dimensional Fluorescence Gel Electrophoresis.

    Science.gov (United States)

    Ackermann, Doreen; König, Simone

    2018-01-01

    Two-dimensional comparative fluorescence gel electrophoresis (CoFGE) uses an internal standard to increase the reproducibility of coordinate assignment for protein spots visualized on 2D polyacrylamide gels. This is particularly important for samples, which need to be compared without the availability of replicates and thus cannot be studied using differential gel electrophoresis (DIGE). CoFGE corrects for gel-to-gel variability by co-running with the sample proteome a standardized marker grid of 80-100 nodes, which is formed by a set of purified proteins. Differentiation of reference and analyte is possible by the use of two fluorescent dyes. Variations in the y-dimension (molecular weight) are corrected by the marker grid. For the optional control of the x-dimension (pI), azo dyes can be used. Experiments are possible in both vertical and horizontal (h) electrophoresis devices, but hCoFGE is much easier to perform. For data analysis, commercial software capable of warping can be adapted.

  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. 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...

  6. Application of highly sensitive fluorescent dyes (CyDye DIGE Fluor saturation dyes) to laser microdissection and two-dimensional difference gel electrophoresis (2D-DIGE) for cancer proteomics.

    Science.gov (United States)

    Kondo, Tadashi; Hirohashi, Setsuo

    2006-01-01

    Proteome data combined with histopathological information provides important, novel clues for understanding cancer biology and reveals candidates for tumor markers and therapeutic targets. We have established an application of a highly sensitive fluorescent dye (CyDye DIGE Fluor saturation dye), developed for two-dimensional difference gel electrophoresis (2D-DIGE), to the labeling of proteins extracted from laser microdissected tissues. The use of the dye dramatically decreases the protein amount and, in turn, the number of cells required for 2D-DIGE; the cells obtained from a 1 mm2 area of an 8-12 microm thick tissue section generate up to 5,000 protein spots in a large-format 2D gel. This protocol allows the execution of large-scale proteomics in a more efficient, accurate and reproducible way. The protocol can be used to examine a single sample in 5 d or to examine hundreds of samples in large-scale proteomics.

  7. 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...

  8. Two-Dimensional (2D) Polygonal Electromagnetic Cloaks

    Institute of Scientific and Technical Information of China (English)

    LI Chao; YAO Kan; LI Fang

    2009-01-01

    Transformation optics offers remarkable control over electromagnetic fields and opens an exciting gateway to design 'invisible cloak devices' recently.We present an important class of two-dimensional (2D) cloaks with polygon geometries.Explicit expressions of transformed medium parameters are derived with their unique properties investigated.It is found that the elements of diagonalized permittivity tensors are always positive within an irregular polygon cloak besides one element diverges to plus infinity and the other two become zero at the inner boundary.At most positions,the principle axes of permittivity tensors do not align with position vectors.An irregular polygon cloak is designed and its invisibility to external electromagnetic waves is numerically verified.Since polygon cloaks can be tailored to resemble any objects,the transformation is finally generalized to the realization of 2D cloaks with arbitrary geometries.

  9. The separation of whale myoglobins with two-dimensional electrophoresis.

    Science.gov (United States)

    Spicer, G S

    1988-10-01

    Five myoglobins (sperm whale, Sei whale, Hubbs' beaked whale, pilot whale, and Amazon River dolphin) were examined using two-dimensional electrophoresis. Previous reports indicated that none of these proteins could be separated by using denaturing (in the presence of 8-9 M urea) isoelectric focusing. This result is confirmed in the present study. However, all the proteins could be separated by using denaturing nonequilibrium pH-gradient electrophoresis in the first dimension. Additionally, all the myoglobins have characteristic mobilities in the second dimension (sodium dodecyl sulfate), but these mobilities do not correspond to the molecular weights of the proteins. We conclude that two-dimensional electrophoresis can be more sensitive to differences in primary protein structure than previous studies indicate and that the assessment seems to be incorrect that this technique can separate only proteins that have a unit charge difference.

  10. 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...

  11. Extraction of plant proteins for two-dimensional electrophoresis

    OpenAIRE

    Granier, Fabienne

    1988-01-01

    Three different extraction procedures for two-dimensional electrophoresis of plant proteins are compared: (i) extraction of soluble proteins with a nondenaturing Tris-buffer, (ii) denaturing extraction in presence of sodium dodecyl sulfate at elevated temperature allowing the solubilization of membrane proteins in addition to a recovery of soluble proteins, and (iii) a trichloroacetic acid-acetone procedure allowing the direct precipitation of total proteins.

  12. Charge heterogeneity study of a Fc-fusion protein, abatacept, using two-dimensional gel electrophoresis.

    Science.gov (United States)

    Nebija, D; Noe, C R; Lachmann, B

    2015-08-01

    Medicinal products obtained by recombinant DNA technology are complex molecules and demonstrate a high degree of molecular heterogeneity. Charge heterogeneity and isoform pattern of this class of medicines, are parameters important for their quality, safety, and efficacy. In this study we report the application of two-dimensional gel electrophoresis (2-D electrophoresis) for the quality assessment, identification, charge heterogeneity and isoform pattern study of recombinant protein, CTLA4-Ig (abatacept), which has been selected as an example of the drug class, known as Fc-fusion proteins. In order to achieve an efficient separation of this complex analyte,2-D electrophoresis was optimized employing different experimental conditions regarding the selection of an immobilized pH gradient (IPG), sample pretreatment, presentation and detection procedure. Experimental datadocumented that 2-D electrophoresis is a suitable method for the assessment of identity, purity, structural integrity, isoform pattern and to monitor charge heterogeneity and post-translational glycosylation of the Fc-fusion protein, abatacept.

  13. Two-dimensional capillary electrophoresis using tangentially connected capillaries.

    Science.gov (United States)

    Sahlin, Eskil

    2007-06-22

    A novel type of fused silica capillary system is described where channels with circular cross-sections are tangentially in contact with each other and connected through a small opening at the contact area. Since the channels are not crossing each other in the same plane, the capillaries can easily be filled with different solutions, i.e. different solutions will be in contact with each other at the contact point. The system has been used to perform different types of two-dimensional separations and the complete system is fully automated where a high voltage switch is used to control the location of the high voltage in the system. Using two model compounds it is demonstrated that a type of two-dimensional separation can be performed using capillary zone electrophoresis at two different pH values. It is also shown that a compound with acid/base properties can be concentrated using a dynamic pH junction mechanism when transferred from the first separation to the second separation. In addition, the system has been used to perform a comprehensive two-dimensional capillary electrophoresis separation of tryptic digest of bovine serum albumin using capillary zone electrophoresis followed by micellar electrokinetic chromatography.

  14. Procedures for two-dimensional electrophoresis of proteins

    Energy Technology Data Exchange (ETDEWEB)

    Tollaksen, S.L.; Giometti, C.S.

    1996-10-01

    High-resolution two-dimensional gel electrophoresis (2DE) of proteins, using isoelectric focusing in the first dimension and sodium dodecyl sulfate/polyacrylamide gel electrophoresis (SDS-PAGE) in the second, was first described in 1975. In the 20 years since those publications, numerous modifications of the original method have evolved. The ISO-DALT system of 2DE is a high-throughput approach that has stood the test of time. The problem of casting many isoelectric focusing gels and SDS-PAGE slab gels (up to 20) in a reproducible manner has been solved by the use of the techniques and equipment described in this manual. The ISO-DALT system of two-dimensional gel electrophoresis originated in the late 1970s and has been modified many times to improve its high-resolution, high-throughput capabilities. This report provides the detailed procedures used with the current ISO-DALT system to prepare, run, stain, and photograph two-dimensional gels for protein analysis.

  15. Comparative Skeletal Muscle Proteomics Using Two-Dimensional Gel Electrophoresis.

    Science.gov (United States)

    Murphy, Sandra; Dowling, Paul; Ohlendieck, Kay

    2016-09-09

    The pioneering work by Patrick H. O'Farrell established two-dimensional gel electrophoresis as one of the most important high-resolution protein separation techniques of modern biochemistry (Journal of Biological Chemistry1975, 250, 4007-4021). The application of two-dimensional gel electrophoresis has played a key role in the systematic identification and detailed characterization of the protein constituents of skeletal muscles. Protein changes during myogenesis, muscle maturation, fibre type specification, physiological muscle adaptations and natural muscle aging were studied in depth by the original O'Farrell method or slightly modified gel electrophoretic techniques. Over the last 40 years, the combined usage of isoelectric focusing in the first dimension and sodium dodecyl sulfate polyacrylamide slab gel electrophoresis in the second dimension has been successfully employed in several hundred published studies on gel-based skeletal muscle biochemistry. This review focuses on normal and physiologically challenged skeletal muscle tissues and outlines key findings from mass spectrometry-based muscle proteomics, which was instrumental in the identification of several thousand individual protein isoforms following gel electrophoretic separation. These muscle-associated protein species belong to the diverse group of regulatory and contractile proteins of the acto-myosin apparatus that forms the sarcomere, cytoskeletal proteins, metabolic enzymes and transporters, signaling proteins, ion-handling proteins, molecular chaperones and extracellular matrix proteins.

  16. Comparative Skeletal Muscle Proteomics Using Two-Dimensional Gel Electrophoresis

    Directory of Open Access Journals (Sweden)

    Sandra Murphy

    2016-09-01

    Full Text Available The pioneering work by Patrick H. O’Farrell established two-dimensional gel electrophoresis as one of the most important high-resolution protein separation techniques of modern biochemistry (Journal of Biological Chemistry 1975, 250, 4007–4021. The application of two-dimensional gel electrophoresis has played a key role in the systematic identification and detailed characterization of the protein constituents of skeletal muscles. Protein changes during myogenesis, muscle maturation, fibre type specification, physiological muscle adaptations and natural muscle aging were studied in depth by the original O’Farrell method or slightly modified gel electrophoretic techniques. Over the last 40 years, the combined usage of isoelectric focusing in the first dimension and sodium dodecyl sulfate polyacrylamide slab gel electrophoresis in the second dimension has been successfully employed in several hundred published studies on gel-based skeletal muscle biochemistry. This review focuses on normal and physiologically challenged skeletal muscle tissues and outlines key findings from mass spectrometry-based muscle proteomics, which was instrumental in the identification of several thousand individual protein isoforms following gel electrophoretic separation. These muscle-associated protein species belong to the diverse group of regulatory and contractile proteins of the acto-myosin apparatus that forms the sarcomere, cytoskeletal proteins, metabolic enzymes and transporters, signaling proteins, ion-handling proteins, molecular chaperones and extracellular matrix proteins.

  17. 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...

  18. Two-Dimensional Gel Electrophoresis: A Reference Protocol.

    Science.gov (United States)

    Saia-Cereda, Veronica M; Aquino, Adriano; Guest, Paul C; Martins-de-Souza, Daniel

    2017-01-01

    Two-dimensional gel electrophoresis (2DE) has been a mainstay of proteomic techniques for more than four decades. It was even in use for several years before the term proteomics was actually coined in the early 1990s. Over this time, it has been used in the study of many diseases including cancer, diabetes, heart disease, and psychiatric disorders through the proteomic analysis of body fluids and tissues. This chapter presents a general protocol which can be applied in the study of biological samples such as blood serum or plasma and multiple tissues including the brain.

  19. Basics and recent advances of two dimensional- polyacrylamide gel electrophoresis

    Science.gov (United States)

    2014-01-01

    Gel- based proteomics is one of the most versatile methods for fractionating protein complexes. Among these methods, two dimensional- polyacrylamide gel electrophoresis (2-DE) represents a mainstay orthogonal approach, which is popularly used to simultaneously fractionate, identify, and quantify proteins when coupled with mass spectrometric identification or other immunological tests. Although 2-DE was first introduced more than three decades ago, several challenges and limitations to its utility still exist. This review discusses the principles of 2-DE as well as both recent methodological advances and new applications. PMID:24735559

  20. Human muscle proteins: analysis by two-dimensional electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Giometti, C.S.; Danon, M.J.; Anderson, N.G.

    1983-09-01

    Proteins from single frozen sections of human muscle were separated by two-dimensional gel electrophoresis and detected by fluorography or Coomassie Blue staining. The major proteins were identical in different normal muscles obtained from either sex at different ages, and in Duchenne and myotonic dystrophy samples. Congenital myopathy denervation atrophy, polymyositis, and Becker's muscular dystrophy samples, however, showed abnormal myosin light chain compositions, some with a decrease of fast-fiber myosin light chains and others with a decrease of slow-fiber light chains. These protein alterations did not correlate with any specific disease, and may be cause by generalized muscle-fiber damage.

  1. Online comprehensive two-dimensional ion chromatography × capillary electrophoresis.

    Science.gov (United States)

    Ranjbar, Leila; Gaudry, Adam J; Breadmore, Michael C; Shellie, Robert A

    2015-09-01

    A comprehensively coupled online two-dimensional ion chromatography-capillary electrophoresis (IC × CE) system for quantitative analysis of inorganic anions and organic acids in water is introduced. The system employs an in-house built sequential injection-capillary electrophoresis instrument and a nonfocusing modulation interface comprising a tee-piece and a six-port two-position injection valve that allows comprehensive sampling of the IC effluent. High field strength (+2 kV/cm) enables rapid second-dimension separations in which each peak eluted from the first-dimension separation column is analyzed at least three times in the second dimension. The IC × CE approach has been successfully used to resolve a suite of haloacetic acids, dalapon, and common inorganic anions. Two-dimensional peak capacity for IC × CE was 498 with a peak production rate of 9 peaks/min. Linear calibration curves were obtained for all analytes from 5 to 225 ng/mL (except dibromoacetic acid (10-225 ng/mL) and tribromoacetic acid (25-225 ng/mL)). The developed approach was used to analyze a spiked tap water sample, with good measured recoveries (69-119%).

  2. Analysis of Two-Dimensional Electrophoresis Gel Images

    DEFF Research Database (Denmark)

    Pedersen, Lars

    2002-01-01

    This thesis describes and proposes solutions to some of the currently most important problems in pattern recognition and image analysis of two-dimensional gel electrophoresis (2DGE) images. 2DGE is the leading technique to separate individual proteins in biological samples with many biological...... the methods developed in the literature specifically for matching protein spot patterns, the focus is on a method based on neighbourhood relations. These methods are applied to a range of 2DGE protein spot data in a comparative study. The point pattern matching requires segmentation of the gel images...... and since the correct image segmentation can be difficult, a new alternative approach, exploiting prior knowledge from a reference gel about the protein locations to segment an incoming gel image, is proposed....

  3. 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.

  4. 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...

  5. 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; CHENG Yiyu

    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.

  6. [Total protein analysis by two-dimensional electrophoresis in cysticerci of Taenia solium and Taenia asiatica].

    Science.gov (United States)

    Fang, Wen; Xiao, Liang-Liang; Bao, Huai-En; Mu, Rong

    2011-06-01

    Two 20-day-old three-way crossed hybrid pigs were infected with 80000 Taenia solium or T. asiatica eggs, respectively. Immature cysticerci of the two species in liver were collected at 40 days after infection. The total proteins were separated by two-dimensional electrophoresis, and differentially expressed proteins were analyzed by Image-Master 2D Platinum 6.0 software. The results showed that there were (236 +/- 12) and (231 +/- 14) protein spots in 2D electrophoresis gel images of T. solium and T. asiatica, respectively, with 3 proteins up-regulated and 7 proteins down-regulated in T. solium cysticercus by 2-fold or more compared with those in T. asiatica cysticercus.

  7. Two-dimensional fluorescence difference gel electrophoresis analysis of Listeria monocytogenes submitted to a redox shock.

    Science.gov (United States)

    Ignatova, Maria; Guével, Blandine; Com, Emmanuelle; Haddad, Nabila; Rossero, Albert; Bogard, Philippe; Prévost, Hervé; Guillou, Sandrine

    2013-02-21

    The influence of redox alteration on the growth and proteomic pattern of Listeria monocytogenes was investigated. A redox shock was induced in cultures by addition of 3mM ferricyanide (FeCN) and 6mM dithiothreitol (DTT) to increase or to decrease respectively the redox potential naturally occurring at the beginning of growth. In both conditions, the reducing and oxidizing redox shock had a strong influence, decreasing the maximum growth rate by half compared to a control culture. The proteomic analysis of L. monocytogenes performed by two-dimensional difference gel electrophoresis (2D-DIGE) exhibited twenty-three proteins differentially expressed (P<0.05), among these, many were oxidoreductases, and proteins involved in cellular metabolism (glycolysis, protein synthesis), detoxification (kat) or adhesion (Lmo1634).

  8. Superoxide dismutase isozyme detection using two-dimensional gel electrophoresis zymograms.

    Science.gov (United States)

    Niyomploy, Ploypat; Srisomsap, Chantragan; Chokchaichamnankit, Daranee; Vinayavekhin, Nawaporn; Karnchanatat, Aphichart; Sangvanich, Polkit

    2014-03-01

    Superoxide dismutases (SODs) are ubiquitous antioxidant enzymes involved in cell protection from reactive oxygen species. Their antioxidant activities make them of interest to applied biotechnology industries and are usually sourced from plants. SODs are also involved in stress signaling responses in plants, and can be used as indicators of these responses. In this article, a suitable method for the separation of different SOD isoforms using two-dimensional-gel electrophoresis (2D-GE) zymograms is reported. The method was developed with a SOD standard from bovine erythrocytes and later applied to extracts from Stemona tuberosa. The first (non-denaturing isoelectric focusing) and second (denaturing sodium dodecylsulphate-polyacrylamide gel electrophoresis) dimensions of duplicate 2D-GE gels were stained with either Coomassie brilliant blue G-250 for total protein visualization, or SOD activity (zymogram) using riboflavin/nitroblue tetrazolium. For confirmation, putative SOD activity positive spots were subject to trypsin digestion and nano-liquid chromatography tandem mass spectrometry, followed by searching the MASCOT database for potential identification. The method could separate different SOD isoforms from a plant extract and at least partially maintain or allow renaturation to the native forms of the enzyme. Peptide sequencing of the 2D-GE suggested that the SODs were resolved correctly, identifying the control CuZn-SOD from bovine erythrocytes. The two SODs from S. tuberosa tubers were found to be likely homologous of a CuZn-SOD. SOD detection and isoform separation by 2D-GE zymograms was efficient and reliable. The method is likely applicable to SOD detection from plants or other organisms. Moreover, a similar approach could be developed for detection of other important enzymes in the future. Copyright © 2013 Elsevier B.V. All rights reserved.

  9. 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...

  10. Two-dimensional electrophoresis for comparative proteomic analysis of human bile

    Institute of Scientific and Technical Information of China (English)

    Bo Chen; Jing-Qing Dong; Yong-Jun Chen; Jian-Ming Wang; Jun Tian; Chun-Ben Wang; Sheng-Quan Zou

    2007-01-01

    BACKGROUND:Proteomic analysis of bile lfuid holds promise as a method to identify biomarkers of bile tract diseases, especially for tumors. Two-dimensional electrophoresis (2-DE) is a popular and proven separation technique for proteome analysis, but using this strategy for bile lfuid analysis is still not fully developed. This study was undertaken to (a) establish a reliable method for general clean-up to make bile lfuid samples suitable for 2-DE;(b) obtain 2-D biliary maps with high reproducibility and resolution;and (c) identify protein patterns present in 2-D biliary maps for potential tumor biomarker discovery, with the intention of distinguishing malignant from benign causes of bile duct obstruction. METHODS: Bile lfuid samples were obtained from two patients suffering from malignant and benign bile tract obstruction (one patient with cholangiocarcinoma as the experimental case, the other with cholelithiasis as control). A variety of sample preparation options, including delipidation, desalination and nucleic acid removal, were adopted to remove contaminants that affect 2-DE results. After that, each 350 μg puriifed sample was loaded onto nonlinear IPG strips (18 cm, pH 3-10 and pH 4-7) for ifrst-dimension isoelectric focusing, and 12.5% SDS-PAGE electrophoresis for second dimension separation. Then 2-D maps were visualized after silver staining and analyzed with the Image Master 2-D software. RESULTS:A large number of protein spots were separated in 2-D maps from the experimental and control groups, with means of 250 and 216 spots on pH 3-10 IPG strips, and 182 and 176 spots on pH 4-7 strips, respectively. Approximately 16 and 23 spots were differentially expressed in matched pairs from the experimental and control cases using pH 3-10 and pH 4-7 strips. CONCLUSIONS: This study established a reliable sample preparation process suitable for 2-DE of bile lfuid. By this method, 2-D biliary maps with high reproducibility and resolution were obtained. The

  11. Electrophoretic analysis of proteins from Mycoplasma hominis strains detected by SDS-PAGE, two-dimensional gel electrophoresis and immunoblotting

    DEFF Research Database (Denmark)

    Andersen, H; Birkelund, Svend; Christiansen, Gunna

    1987-01-01

    The proteins of 14 strains of Mycoplasma hominis were compared by SDS-PAGE in gradient gels, by two-dimensional (2D) gel electrophoresis of extracts of 35S-labelled cells and by immunoblot analysis of cell proteins. The strains examined included the M. hominis type strain PG21 and 13 others...... isolated variously from genital tract, mouth, blood, upper urinary tract and a wound. These 14 strains shared 76-99% of proteins in SDS-gradient gel analysis and 41-72% in the 2D gels. As expected, the immunoblot analysis likewise revealed the existence of an extensive common protein pattern in M. hominis...

  12. Differential analysis of two-dimensional gel electrophoresis profiles of spermatozoa protein in human normal motility sperm and idiopathic asthenospermia

    Institute of Scientific and Technical Information of China (English)

    SHEN Shu-lin; HE Da-lin; LUO Yong; NING Liang

    2006-01-01

    Objective: To evaluate the application of two-dimensional electrophoresis in the research of differentially expressed proteins in the human asthenospermia. Methods: Two-dimensional gel electrophoresis was performed on 4 normal sperm samples from healthy men and 4 sperm samples from 4 asthenospermia patients. After silver staining, the differential expression proteins were analyzed by PDQuest 2D analysis software. Results: Six differential protein spots were identified. Four spots showed increased expression in the control gels compared with the patient gels. Conclusion: The protein profiles of differential expression between the normal spermatozoa and idiopathic asthenospermia were established and some differential proteins were found. The data of this study would establish the better fundament for further isolation and identification of differentially expressed proteins in human asthenospermia sperm.

  13. 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....... A semiconfluent layer of HeLa cells was grown on tissue culture plates, and changes in protein expression due to 100 U/mL IFN-gamma were investigated at different periods after treatment, using pulse labeling with [35S]methionine/cysteine in combination with 2-D PAGE (IPG). The identity of eight protein spots...

  14. Status for the two-dimensional Navier-Stokes solver EllipSys2D

    DEFF Research Database (Denmark)

    Bertagnolio, F.; Sørensen, Niels N.; Johansen, J.

    2001-01-01

    This report sets up an evaluation of the two-dimensional Navier-Stokes solver EllipSys2D in its present state. This code is used for blade aerodynamics simulations in the Aeroelastic Design group at Risø. Two airfoils are investigated by computing theflow at several angles of attack ranging from...... the linear to the stalled region. The computational data are compared to experimental data and numerical results from other computational codes. Several numerical aspects are studied, as mesh dependency,convective scheme, steady state versus unsteady computations, transition modelling. Some general...... conclusions intended to help in using this code for numerical simulations are given....

  15. Bill2d -- a software package for classical two-dimensional Hamiltonian systems

    CERN Document Server

    Solanpää, Janne; Räsänen, Esa

    2016-01-01

    We present Bill2d, a modern and efficient C++ package for classical simulations of two-dimensional Hamiltonian systems. Bill2d can be used for various billiard and diffusion problems with one or more charged particles with interactions, different external potentials, an external magnetic field, periodic and open boundaries, etc. The software package can also calculate many key quantities in complex systems such as Poincar\\'e sections, survival probabilities, and diffusion coefficients. While aiming at a large class of applicable systems, the code also strives for ease-of-use, efficiency, and modularity for the implementation of additional features. The package comes along with a user guide, a developer's manual, and a documentation of the application program interface (API).

  16. BILL2D - A software package for classical two-dimensional Hamiltonian systems

    Science.gov (United States)

    Solanpää, J.; Luukko, P. J. J.; Räsänen, E.

    2016-02-01

    We present BILL2D, a modern and efficient C++ package for classical simulations of two-dimensional Hamiltonian systems. BILL2D can be used for various billiard and diffusion problems with one or more charged particles with interactions, different external potentials, an external magnetic field, periodic and open boundaries, etc. The software package can also calculate many key quantities in complex systems such as Poincaré sections, survival probabilities, and diffusion coefficients. While aiming at a large class of applicable systems, the code also strives for ease-of-use, efficiency, and modularity for the implementation of additional features. The package comes along with a user guide, a developer's manual, and a documentation of the application program interface (API).

  17. Hysteretic Spin Crossover in Two-Dimensional (2D) Hofmann-Type Coordination Polymers.

    Science.gov (United States)

    Liu, Wei; Wang, Lu; Su, Yu-Jun; Chen, Yan-Cong; Tucek, Jiri; Zboril, Radek; Ni, Zhao-Ping; Tong, Ming-Liang

    2015-09-08

    Three new two-dimensional (2D) Hofmann-type coordination polymers with general formula [Fe(3-NH2py)2M(CN)4] (3-NH2py = 3-aminopyridine, M = Ni (1), Pd (2), Pt (3)) have been synthesized. Magnetic susceptibility measurements show that they exhibited cooperative spin crossover (SCO) with remarkable hysteretic behaviors. Their hysteresis widths are 25, 37, and 30 K for 1-3, respectively. The single-crystal structure of 1 suggest that the pseudo-octahedral Fe sites are equatorially bridged by [M(CN)4](2-) to form 2D grids and axially coordinated by 3-NH2py ligands. The intermolecular interactions between layers (the offset face-to-face π···π interactions, hydrogen bonds, and weak N(amino)···Ni(II) contacts) together with the covalent bonds bridged by [M(CN)4](2-) units are responsible to the significant cooperativity.

  18. IDENTIFICATION OF DIFFERENTIAL PROTEINS IN UTERINE LEIOMYOMA BY TWO-DIMENSIONAL ELECTROPHORESIS

    Institute of Scientific and Technical Information of China (English)

    ZHU Xue-qiong; ZHU Chun-dan; L(U) Jie-qiang; DONG Ke

    2006-01-01

    Objective: To establish and optimize the two-demensional electrophoresis maps of uterine leiomyoma and to study the difference of global protein patterns between uterine leiomyoma and normal myometrium. Methods: Using Two-dimensional electrophoresis followed by computer-assisted image analysis, the differential proteins between uterine leiomyoma and normal myometrium were compared. Results: The well-resolved and reproducible two-dimensional gel electrophoresis patterns of uterine leiomyoma and normal myometrium were established. Totally 1085(108 and 1103(151 protein spots were obtained by using the pH 4-7 IPG strips in uterine leiomyoma and normal myometrium map, respectively, of which 7 spots increased and 15 spots decreased in quantity in uterine leiomyoma compared with normal myometrium. Conclusion: The differentially expressed proteins are useful for studying the mechanism of the cause of uterine leiomyoma.

  19. Simulation of Two Dimensional Electrophoresis and Tandem Mass Spectrometry for Teaching Proteomics

    Science.gov (United States)

    Fisher, Amanda; Sekera, Emily; Payne, Jill; Craig, Paul

    2012-01-01

    In proteomics, complex mixtures of proteins are separated (usually by chromatography or electrophoresis) and identified by mass spectrometry. We have created 2DE Tandem MS, a computer program designed for use in the biochemistry, proteomics, or bioinformatics classroom. It contains two simulations--2D electrophoresis and tandem mass spectrometry.…

  20. Simulation of Two Dimensional Electrophoresis and Tandem Mass Spectrometry for Teaching Proteomics

    Science.gov (United States)

    Fisher, Amanda; Sekera, Emily; Payne, Jill; Craig, Paul

    2012-01-01

    In proteomics, complex mixtures of proteins are separated (usually by chromatography or electrophoresis) and identified by mass spectrometry. We have created 2DE Tandem MS, a computer program designed for use in the biochemistry, proteomics, or bioinformatics classroom. It contains two simulations--2D electrophoresis and tandem mass spectrometry.…

  1. Analysis of total proteins in pollen of Humulus scandens Lour in Wuhan Region of China by two-dimensional electrophoresis

    Institute of Scientific and Technical Information of China (English)

    LI Dongdong; HE Shaoheng

    2007-01-01

    Total proteins in the pollen of Humulus scandens Lour,one of the most popular aeroallergens in China,were analyzed by two-dimensional electrophoresis in the current study.The proteins were extracted by Trichloracetic acid (TCA) method,and then separated by isoelectric focusing as the first dimension and SDS-PAGE as the second dimension.The spots of proteins were visualized by staining with Coomassie Brilliant Blue.After analysis with software (ImageMaster 2D),122 different proteins were detected;isoelectric point (pI),Molecular weight (MW) and relativevolume of each protein in the pollen were also discovered.This is the first high-resolution,two-dimensional protein map of the pollen ofHumulus scandens Lour in China.Our finding has built a solid foundation for identification,characterization,gene cloning and standardization of allergenic proteins in the pollen ofHumulus scandens Lour for further studies.

  2. Separation of basic proteins from Leishmania using a combination of Free flow electrophoresis (FFE) and 2D electrophoresis (2-DE) under basic conditions.

    Science.gov (United States)

    Brotherton, Marie-Christine; Racine, Gina; Ouellette, Marc

    2015-01-01

    Basic proteins, an important class of proteins in intracellular organisms such as Leishmania, are usually underrepresented on 2D gels. This chapter describes a method combining basic proteins fractionation using Free flow electrophoresis in isoelectric focusing mode (IEF-FFE) followed by protein separation using two-dimensional gel electrophoresis (2-DE) in basic conditions. The combination of these two techniques represents a great improvement for the visualization of Leishmania proteins with basic pI using 2D gels.

  3. Comparison of ethanol-soluble proteins from different rye (Secale cereale) varieties by two-dimensional electrophoresis.

    Science.gov (United States)

    Radzikowski, Louise; Nesić, Ljiljana; Hansen, Hanne Boskov; Jacobsen, Susanne; Søndergaard, Ib

    2002-12-01

    The major storage proteins from six rye varieties, grown under the same conditions in 1997 and 1998 in Rønhave, Denmark, were analyzed by two-dimensional (2-D) polyacrylamide gel electrophoresis. The proteins were extracted from ground rye kernels with 70% ethanol and separated by 2-D electrophoresis. The gels were scanned, compared using ImageMaster software and the data sets were analyzed by principal component analysis (PCA) using THE UNSCRAMBLER software. Afterwards MATLAB was used to make a cluster analysis of the varieties based on PCA. The analysis of the gels showed, that the protein patterns (number of different proteins and their isoelectric points and molecular weights) from the six rye varieties were different. Based on the presence of unique cultivar-specific spots it was possible to differentiate between all six varieties if the two harvest years were investigated separately. When the results were combined from the two years five varieties could be differentiated. The results from the PCA confirmed the finding of the unique spots and cluster analysis was made in order to illustrate the results. The combination of the results from 2-D electrophoresis and other grain characteristics showed that one protein spot was located close to the parameters bread volume and bread height.

  4. The multi-concentration and two-dimensional capillary electrophoresis method for the analysis of drugs in urine samples

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    A novel method has been developed by integration of multi-concentration and two-dimensional(2D) capillary electrophoresis(CE) for simultaneous enhancement of detection sensitivity and separation power in complex samples.Capillary zone electrophoresis(CZE) was used as the first dimension separation according to mobilities,from which the effluent fractions were further analyzed by micellar electrokinetic capillary chromatography(MEKC) acting as the second dimension.Cation-selective exhaustive injection(CSEI) preconcentration method was used to introduce more analytes into the capillary.Furthermore,pH junction and sweeping dual concentration strategies were employed to avoid sample zone diffusion at the interface.The resulting electrophoregram was quite different from that of either CZE or MEKC separation.Up to(0.5-1.2) ×104 fold improvements in sensitivity were obtained relative to the conventional electrokinetic injection method.The proposed method was successfully applied to the determination of drugs in human urine.

  5. The latest advancements in proteomic two-dimensional gel electrophoresis analysis applied to biological samples.

    Science.gov (United States)

    Santucci, Laura; Bruschi, Maurizio; Ghiggeri, Gian Marco; Candiano, Giovanni

    2015-01-01

    Two-dimensional gel electrophoresis (2DE) is one of the fundamental approaches in proteomics for the separation and visualization of complex protein mixtures. Proteins can be analyzed by 2DE using isoelectric focusing (IEF) in the first dimension, combined to sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) in the second dimension, gel staining (silver and Coomassie), image analysis, and 2DE gel database. High-resolution 2DE can resolve up to 5,000 different proteins simultaneously (∼2,000 proteins routinely), and detect and quantify <1 ng of protein per spot. Here, we describe the latest developments for a more complete analysis of biological fluids.

  6. Comparison of Yeast Cell Protein Solubilization Procedures for Two-dimensional Electrophoresis

    DEFF Research Database (Denmark)

    Harder, A; Wildgruber, R; Nawrocki, A;

    1999-01-01

    Three different procedures for the solubilization of yeast (S. cerevisiae) cell proteins were compared on the basis of the obtained two-dimensional (2-D) polypeptide patterns. Major emphasis was laid on minimizing handling steps, protein modification or degradation, and quantitative loss of high ...

  7. New Approach for Segmentation and Quantification of Two-Dimensional Gel Electrophoresis Images

    DEFF Research Database (Denmark)

    Anjo, Antonio dos; Laurell Blom Møller, Anders; Ersbøll, Bjarne Kjær;

    2011-01-01

    Motivation: Detection of protein spots in two-dimensional gel electrophoresis images (2-DE) is a very complex task and current approaches addressing this problem still suffer from significant shortcomings. When quantifying a spot, most of the current software applications include a lot of backgro......Motivation: Detection of protein spots in two-dimensional gel electrophoresis images (2-DE) is a very complex task and current approaches addressing this problem still suffer from significant shortcomings. When quantifying a spot, most of the current software applications include a lot....... Results: Five sections from different gels are used to test the performance of the presented method concerning the detection of protein spots, and three gel sections are used to test the quantification of sixty protein spots. Comparisons with a state-of-the-art commercial software and an academic state...

  8. Establishment and Preliminary Application of Two dimensional Electrophoresis and Mass Spectrometry in Ovary Study

    Institute of Scientific and Technical Information of China (English)

    Xiang MA; Ye-fei ZHU; Jia-hao SHA; Zuo-min ZHOU; Jia-yin LIU

    2003-01-01

    Objective To apply two-dimensional electrophoresis and mass spectrometry in the ovary proteome research Methods Protein extractions from mouse ovaries were run in IPGphor isoelectric focus system with 11 cm and 24 cm IPG strips respectively (pH 3~10, 0.3 mm thick), then the protein spots were identified by mass spectrometry.Results The ovary protein exactions separated by two-dimensional electrophoresis have got high resolution, and identifing protein by mass spectrometry was highly efficient and facilitly.These two techniques should facilitate further investigation of female reproduction proteome research.Conclusion These two rapid high resolutions and efficient techniques have a variety of applications foreground in female reproduction proteome pattern research.

  9. Proteomic study of muscle sarcoplasmic proteins using AUT-PAGE/SDS-PAGE as two-dimensional gel electrophoresis.

    Science.gov (United States)

    Picariello, Gianluca; De Martino, Alessandra; Mamone, Gianfranco; Ferranti, Pasquale; Addeo, Francesco; Faccia, Michele; Spagnamusso, Salvatore; Di Luccia, Aldo

    2006-03-20

    In the present study, an alternative procedure for two-dimensional (2D) electrophoretic analysis in proteomic investigation of the most represented basic muscle water-soluble proteins is suggested. Our method consists of Acetic acid-Urea-Triton polyacrylamide gel (AUT-PAGE) analysis in the first dimension and standard sodium dodecyl sulphate polyacrylamide gel (SDS-PAGE) in the second dimension. Although standard two-dimensional Immobilized pH Gradient-Sodium Dodecyl-Sulphate (2D IPG-SDS) gel electrophoresis has been successfully used to study these proteins, most of the water-soluble proteins are spread on the alkaline part of the 2D map and are poorly focused. Furthermore, the similarity in their molecular weights impairs resolution of the classical approach. The addition of Triton X-100, a non-ionic detergent, into the gel induces a differential electrophoretic mobility of proteins as a result of the formation of mixed micelles between the detergent and the hydrophobic moieties of polypeptides, separating basic proteins with a criterion similar to reversed phase chromatography based on their hydrophobicity. The acid pH induces positive net charges, increasing with the isoelectric point of proteins, thus allowing enhanced resolution in the separation. By using 2D AUT-PAGE/SDS electrophoresis approach to separate water-soluble proteins from fresh pork and from dry-cured products, we could spread proteins over a greater area, achieving a greater resolution than that obtained by IPG in the pH range 3-10 and 6-11. Sarcoplasmic proteins undergoing proteolysis during the ripening of products were identified by Matrix Assisted Laser Desorption/Ionization-Time of Flight (MALDI-ToF) mass spectrometry peptide mass fingerprinting in a easier and more effective way. Two-dimensional AUT-PAGE/SDS electrophoresis has allowed to simplify separation of sarcoplasmic protein mixtures making this technique suitable in the defining of quality of dry-cured pork products by immediate

  10. Semiquantitative Proteomic Analysis of the Human Spliceosome via a Novel Two-Dimensional Gel Electrophoresis Method ▿ §

    Science.gov (United States)

    Agafonov, Dmitry E.; Deckert, Jochen; Wolf, Elmar; Odenwälder, Peter; Bessonov, Sergey; Will, Cindy L.; Urlaub, Henning; Lührmann, Reinhard

    2011-01-01

    More than 200 proteins associate with human spliceosomes, but little is known about their relative abundances in a given spliceosomal complex. Here we describe a novel two-dimensional (2D) electrophoresis method that allows separation of high-molecular-mass proteins without in-gel precipitation and thus without loss of protein. Using this system coupled with mass spectrometry, we identified 171 proteins altogether on 2D maps of stage-specific spliceosomal complexes. By staining with a fluorescent dye with a wide linear intensity range, we could quantitate and categorize proteins as present in high, moderate, or low abundance. Affinity-purified human B, Bact, and C complexes contained 69, 63, and 72 highly/moderately abundant proteins, respectively. The recruitment and release of spliceosomal proteins were followed based on their abundances in A, B, Bact, and C spliceosomal complexes. Staining with a phospho-specific dye revealed that approximately one-third of the proteins detected in human spliceosomal complexes by 2D gel analyses are phosphorylated. The 2D gel electrophoresis system described here allows for the first time an objective view of the relative abundances of proteins present in a particular spliceosomal complex and also sheds additional light on the spliceosome's compositional dynamics and the phosphorylation status of spliceosomal proteins at specific stages of splicing. PMID:21536652

  11. Identifying differentially expressed proteins in two-dimensional electrophoresis experiments: inputs from transcriptomics statistical tools.

    Science.gov (United States)

    Artigaud, Sébastien; Gauthier, Olivier; Pichereau, Vianney

    2013-11-01

    Two-dimensional electrophoresis is a crucial method in proteomics that allows the characterization of proteins' function and expression. This usually implies the identification of proteins that are differentially expressed between two contrasting conditions, for example, healthy versus diseased in human proteomics biomarker discovery and stressful conditions versus control in animal experimentation. The statistical procedures that lead to such identifications are critical steps in the 2-DE analysis workflow. They include a normalization step and a test and probability correction for multiple testing. Statistical issues caused by the high dimensionality of the data and large-scale multiple testing have been a more active topic in transcriptomics than proteomics, especially in microarray analysis. We thus propose to adapt innovative statistical tools developed for microarray analysis and incorporate them in the 2-DE analysis pipeline. In this article, we evaluate the performance of different normalization procedures, different statistical tests and false discovery rate calculation methods with both real and simulated datasets. We demonstrate that the use of statistical procedures adapted from microarrays lead to notable increase in power as well as a minimization of false-positive discovery rate. More specifically, we obtained the best results in terms of reliability and sensibility when using the 'moderate t-test' from Smyth in association with classic false discovery rate from Benjamini and Hochberg. The methods discussed are freely available in the 'prot2D' open source R-package from Bioconductor (http://www.bioconductor.org//) under the terms of the GNU General Public License (version 2 or later). sebastien.artigaud@univ-brest.fr or sebastien.artigaud@gmx.com.

  12. Enhanced detergent extraction for analysis of membrane proteomes by two-dimensional gel electrophoresis

    OpenAIRE

    Hsu Kimberly K; Lang John C; Butt R Hussain; Churchward Matthew A; Coorssen Jens R

    2005-01-01

    Abstract Background The analysis of hydrophobic membrane proteins by two-dimensional gel electrophoresis has long been hampered by the concept of inherent difficulty due to solubility issues. We have optimized extraction protocols by varying the detergent composition of the solubilization buffer with a variety of commercially available non-ionic and zwitterionic detergents and detergent-like phospholipids. Results After initial analyses by one-dimensional SDS-PAGE, quantitative two-dimensiona...

  13. 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.

  14. 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.

  15. Separation and sequencing of familiar and novel murine proteins using preparative two-dimensional gel electrophoresis.

    Science.gov (United States)

    Merrick, B A; Patterson, R M; Witcher, L L; He, C; Selkirk, J K

    1994-05-01

    Strategies are needed for rapid protein isolation in order to identify disease-related proteins and facilitate the design of oligonucleotides for further molecular inquiry. In our laboratory, C3H10T1/2 murine fibroblasts have been found to express a variety of proteins in various subcellular fractions which are relevant to experimental transformation and carcinogenesis. Preparative two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) procedures were developed to identify major cytoplasmic proteins by electroblotting and microsequencing. Isoelectric focusing tube gels were enlarged to 6 mm ID to accommodate larger protein loads at 0.5 to 2 mg protein. Separated proteins were electrotransferred from 6 mm thick slab gels onto 0.22 mu polyvinylidene difluoride membranes. Nearly 100 prominent blotted proteins were stained with Coomassie Brilliant Blue between pI 4.5-7.0 and 18-106 kDa and, of these, 27 prominent and well-resolved proteins were selected for sequencing. Sequences of 14 to 24 amino acid residues in length were obtained from 11 proteins which were identified from computerized databases. Some of these identified proteins had structural or enzymatic functions while others had only recently been discovered, including a newly reported Hsp 70 class member and a novel calcium-binding protein, reticulocalbin. The new heat shock protein has a molecular mass of 75 kDa and has been designated as Grp75, PBP74, CSA or p66mot-1 in mice and humans with purported roles in transformation and antigen processing. Reticulocalbin is an endoplasmic reticular protein which contains six domains of the EF-hand motif associated with high-affinity calcium-binding proteins. It may be involved in protein transport and luminal protein processing. In addition, sequences of 5 to 11 residues in length were also obtained from six other unidentified proteins. Thus, we have found that preparative 2-D PAGE serves as a powerful one-step purification method for protein isolation and

  16. Rheological and mechanical behavior of polyacrylamide hydrogels chemically crosslinked with allyl agarose for two-dimensional gel electrophoresis.

    Science.gov (United States)

    Suriano, R; Griffini, G; Chiari, M; Levi, M; Turri, S

    2014-02-01

    Two-dimensional (2-D) gel electrophoresis currently represents one of the most standard techniques for protein separation. In addition to the most commonly employed polyacrylamide crosslinked hydrogels, acrylamide-agarose copolymers have been proposed as promising systems for separation matrices in 2-D electrophoresis, because of the good resolution of both high and low molecular mass proteins made possible by careful control and optimization of the hydrogel pore structure. As a matter of fact, a thorough understanding of the nature of the hydrogel pore structure as well as of the parameters by which it is influenced is crucial for the design of hydrogel systems with optimal sieving properties. In this work, a series of acrylamide-based hydrogels covalently crosslinked with different concentrations of allyl agarose (0.2-1%) is prepared and characterized by creep-recovery measurements, dynamic rheology and tensile tests, in the attempt to gain a clearer understanding of structure-property relationships in crosslinked polyacrylamide-based hydrogels. The rheological and mechanical properties of crosslinked acrylamide-agarose hydrogels are found to be greatly affected by crosslinker concentration. Dynamic rheological tests show that hydrogels with a percentage of allyl agarose between 0.2% and 0.6% have a low density of elastically effective crosslinks, explaining the good separation of high molecular mass proteins in 2-D gel electrophoresis. Over the same range of crosslinker concentration, creep-recovery measurements reveal the presence of non-permanent crosslinks in the hydrogel network that justifies the good resolution of low molecular mass proteins as well. In tensile tests, the hydrogel crosslinked with 0.4% of allyl agarose exhibits the best results in terms of mechanical strength and toughness. Our results show how the control of the viscoelastic and the mechanical properties of these materials allow the design of mechanically stable hydrogels with improved

  17. Optimized preparation of urine samples for two-dimensional electrophoresis and initial application to patient samples

    DEFF Research Database (Denmark)

    Lafitte, Daniel; Dussol, Bertrand; Andersen, Søren;

    2002-01-01

    protein excretion patterns of 49 healthy men and 4 patients with renal disease were obtained by 2D electrophoresis. Silver nitrate stained protein spots were identified by mass spectrometry. RESULTS: Reproductive 2D gels identified 5 classes of proteins systematically found in healthy subjects...... was constant over time and reveal for the first time the relative abundance of albumin fragments in healthy subjects' urine. The profiles of the 4 patients, were specific of their renal disease....

  18. Enhanced detergent extraction for analysis of membrane proteomes by two-dimensional gel electrophoresis

    Directory of Open Access Journals (Sweden)

    Hsu Kimberly K

    2005-06-01

    Full Text Available Abstract Background The analysis of hydrophobic membrane proteins by two-dimensional gel electrophoresis has long been hampered by the concept of inherent difficulty due to solubility issues. We have optimized extraction protocols by varying the detergent composition of the solubilization buffer with a variety of commercially available non-ionic and zwitterionic detergents and detergent-like phospholipids. Results After initial analyses by one-dimensional SDS-PAGE, quantitative two-dimensional analyses of human erythrocyte membranes, mouse liver membranes, and mouse brain membranes, extracted with buffers that included the zwitterionic detergent MEGA 10 (decanoyl-N-methylglucamide and the zwitterionic lipid LPC (1-lauroyl lysophosphatidylcholine, showed selective improvement over extraction with the common 2-DE detergent CHAPS (3 [(3-cholamidopropyldimethylammonio]-1-propanesulfonate. Mixtures of the three detergents showed additive improvements in spot number, density, and resolution. Substantial improvements in the analysis of a brain membrane proteome were observed. Conclusion This study demonstrates that an optimized detergent mix, coupled with rigorous sample handling and electrophoretic protocols, enables simple and effective analysis of membrane proteomes using two-dimensional electrophoresis.

  19. PRONTO 2D: A two-dimensional transient solid dynamics program

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, L.M.; Flanagan, D.P.

    1987-03-01

    PRONTO 2D is a two-dimensional transient solid dynamics code for analyzing large deformations of highly nonlinear materials subjected to extremely high strain rates. This Lagrangian finite element program uses an explicit time integration operator to integrate the equations of motion. Four node uniform strain quadrilateral elements are used in the finite element formulation. A number of new numerical algorithms which have been developed for the code are described in this report. An adaptive time step control algorithm is described which greatly improves stability as well as performance in plasticity problems. A robust hourglass control scheme which eliminates hourglass distortions without disturbing the finite element solution is included. All constitutive models in PRONTO are cast in an unrotated configuration defined using the rotation determined from the polar decomposition of the deformation gradient. An accurate incremental algorithm was developed to determine this rotation and is described in detail. A robust contact algorithm was developed which allows for the impact and interaction of deforming contact surfaces of quite general geometry. A number of numerical examples are presented to demonstrate the utility of these algorithms. 41 refs., 51 figs., 5 tabs.

  20. Micropreparative one- and two-dimensional electrophoresis: improvement with new photopolymerization systems.

    Science.gov (United States)

    Rabilloud, T; Vincon, M; Garin, J

    1995-08-01

    To improve the efficiency of one- and two-dimensional electrophoresis for micropreparative purposes, the use of gels polymerized with other initiators than the standard N,N,N',N'-tetramethylethylenediamine (TEMED)/persulfate systems for sodium dodecyl sulfate electrophoresis has been investigated. We show here that the recently described photoinitiator system, composed of methylene blue, toluene sulfinate and diphenyliodonium chloride, leads to a decreased resolution. Resolution can be restored if methylene blue is replaced by riboflavin. Two-dimensional electrophoresis with mg loadings of proteins has also been evaluated with these systems. Independently of the polymerization system, resolution for the first dimension is low with rod gels, increases with gel strips and is further improved when immobilized pH gradients are used. Here too, only the riboflavin/sulfinate/iodonium system results in a resolution that matches the one obtained with the standard TEMED/persulfate system. Gels polymerized with the riboflavin/sulfinate/iodonium system yield better results upon N-terminal microsequencing after blotting than gels polymerized with the standard TEMED/persulfate system.

  1. Comparison of human hair and nail low-sulfur protein compositions on two-dimensional electrophoresis.

    Science.gov (United States)

    Dekio, S; Jidoi, J

    1989-08-01

    Compositions of human normal hair and nail low-sulfur proteins were compared using two-dimensional electrophoresis of their S-carboxymethylated (SCM) derivatives. Six SCM low-sulfur protein components with molecular weights (MWs) of 76,000, 73,000, 72,000, 64,000, 61,000 and 55,000 were common to the hair and nail. One component with a MW of 61,000 was specific to hair, and two components, both with a MW of 50,000, were specific to nail.

  2. 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

    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......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...

  3. Protein differences between normal and oligospermic human sperm demonstrated by two-dimensional gel electrophoresis.

    Science.gov (United States)

    Morgentaler, A; Schopperle, W M; Crocker, R H; DeWolf, W C

    1990-11-01

    Protein expression by sperm obtained from men with normal semen analysis and men with oligospermia were evaluated by two-dimensional gel electrophoresis. Proteins were solubilized in a 9.5 M urea/2% Nonidet-P40 (LKB, Bromma, Sweden) lysis buffer and underwent second dimension separation on 10 to 16% polyacrylamide gradient gels. A set of 36 invariant proteins was identified in all normospermic samples, whereas 8 of 10 evaluable oligospermic samples lacked 1 or more of the invariant proteins. Proteins absent in oligospermic samples may be critical to normal sperm function and may serve as markers for infertility.

  4. Quantification of proteome changes in bovine muscle from two-dimensional electrophoresis data

    Directory of Open Access Journals (Sweden)

    Daniel Franco

    2015-09-01

    Full Text Available Proteome changes in the longissimus thoracis bovine muscle in response to pre-slaughter stress were assessed on the basis of two-dimensional electrophoresis (2-DE data. In this study, the bootstrap resampling statistical technique and a new measure of relative change of the volume of 2-DE protein spots are shown to be more efficient than commonly used statistics to reliably quantify changes in protein abundance in stress response. The data are supplied in this article and are related to “Tackling proteome changes in the longissimus thoracis bovine muscle in response to pre-slaughter stress” by Franco et al. [1].

  5. 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......-, middle- or low-metastatic potential have been characterized in vivo. In this study, the comprehensive protein expression profiles of the CMT cell lines were analyzed at passages 5, 15 and 35 in order to assess the cell line stability. During the passages 5 to 15, the expression profiles of CMT cells...... 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....

  6. Primary establishment of human uterine muscle proteomic profiling by two-dimensional electrophoresis and mass spectrometry

    Institute of Scientific and Technical Information of China (English)

    Lin Hai-yuan; Lang Jing-he; Liu Zhu-feng; Zhu Lan; Leng Jin-hua; Sun Da-wei; Wang Xiao-rong

    2008-01-01

    Objective:To establish the protein profiling of human uterine muscle by two-dimensional electrophoresis.Methods:Five patients who underwent trans-abdominal hysterectomy due to cervical carcinoma in situ were in-cluded in this study.Postoperative uterine muscles were normal histologically.The total protein extracts from uter-ine muscle were separated using two-dimensional electrophoresis(2DE).Protein spots were stained by silver and de-tected by image analysis software.Matrix-assisted laser desorption/ionization time of flight mass spectrometry(MALDI-TOF-MS)and peptide mass fingerprint(PMF)were used to identify the selected protein spots.Results:Well-resolved,reproducible 2DE maps of human uterine muscle were obtained.Average protein spots were 468±52 and matching rate was 82.76%.Five protein spots were successfully identified by mass spectrome-try.Conclusions:2DE coupled with MALDI-TOF-MS and PMF is a useful approach for establishing human uterine muscle proteomic profiling.This data will be useful for establishing human uterine muscle proteome database.

  7. Two-dimensional Electrophoresis Analysis of Proteins Extracted from Alexandrium sp. LC3

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Two-dimensional electrophoresis(2-DE) of protein extracted and purified from Alexandrium sp. LC3 was conducted. In the SDS-PAGE study, the relative molecular weights of the proteins were mainly in the range of 14 kDa-31 kDa and 43 kDa-66 kDa, and more proteins were detected between 14 kDa and 31 kDa. With the improved protein preparation, the two-dimensional electrophoresis patterns indicated that the relative molecular weights of the proteins were between 14 kDa and 100 kDa, and most of them ranged from 14 kDa to 31 kDa. This was consistent with the result of the SDS-PAGE analysis. The isoelectric points were found to lie between 3.0 and 8.0, and most of them were in the range of 3.0-6.0. Better separation effect was acquired with pre-prepared immobilized gradient (IPG) strip (pH 3-5.6), and about 320 protein spots could be visualized on the 2-DE map by staining. Within pH 3-10 and pH 3-5.6 strips, the protein samples of Alexandriun sp. LC3 could be separated well.

  8. Application of Two-Dimensional Electrophoresis in the Research of Retinal Proteins of Diabetic Rat

    Institute of Scientific and Technical Information of China (English)

    Shangqing Liu; Yanyan Zhang; Xianyong Xie; Weiming Hu; Rong Cai; Jian Kang; Huijun Yang

    2007-01-01

    Diabetes mellitus (DM) is a chronic disease which is associated with numerous serious health complications such as diabetic retinopathy, and is the leading cause of new cases of blindness in adults at the age of 20-74 years old. The aim of the study was to establish and optimize a two-dimensional polyacrylamide gel electrophoresis (2-DE) technique for retina proteomics to improve the resolution and reproducibility, and to observe the proteomic changes of retinal tissues in diabetic and normal rats. Proteins were extracted from retinal tissues of normal and 8 weeks diabetic SD rats and used in two-dimensional electrophoresis. Various conditions of retina proteomic 2-DE were adjusted, optimized and protein spots of differential expression were obtained through analysis of 2-DE images with PDQuest software. By choosing appropriate sample amount, using pre-cast IPG dry strips (pH 5-8)and casting 12% equal gel, satisfactory 2-DE images of retina were obtained and a steady 2-DE technique was established. In this way, we found 36 spots in 2-DE gel of diabetic retinas that exhibited statistically significant variations, including up-regulation of 5 proteins in diabetic rat retinas, down-regulation of 23, and disappearance of 8, in comparison with normal tissues. The differences of protein expression were observed in retinas between diabetic and normal rats. Our established 2-DE technique of retina proteins could be effectively applied in proteomics of retina diseases.

  9. 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.

  10. Two-dimensional Fourier transform ESR in the slow-motional and rigid limits: 2D-ELDOR

    Science.gov (United States)

    Patyal, Baldev R.; Crepeau, Richard H.; Gamliel, Dan; Freed, Jack H.

    1990-12-01

    The two-dimensional Fourier transform ESP techniques of stimulated SECSY and 2D-ELDOR are shown to be powerful methods for the study of slow motions for nitroxides. Stimulated SECSY provides magnetization transfer rates, whereas 2D-ELDOR displays how the rotational motions spread the spins out from their initial spectral positions to new spectral positions, as a function of mixing time. The role of nuclear modulation in studies of structure and dynamics is also considered.

  11. Proteins isolated with TRIzol are compatible with two-dimensional electrophoresis and mass spectrometry analyses.

    Science.gov (United States)

    Young, Clifford; Truman, Penelope

    2012-02-01

    TRIzol is used for RNA isolation but also permits protein recovery. We investigated whether proteins prepared with TRIzol were suitable for two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization mass spectrometry. Proteins from TRIzol-treated SH-SY5Y cells produced 2-DE spot patterns similar to those from an equivalent untreated sample. Subsequent identification of TRIzol-treated proteins using peptide mass fingerprinting was successful. TRIzol exposure altered neither the mass of myoglobin extracted from sodium dodecyl sulfate (SDS) gels nor the masses of myoglobin peptides produced by in-gel trypsin digestion. These findings suggest that proteins isolated with TRIzol remain amenable to proteomic analyses.

  12. Protein expression of sensory and motor nerves: Two-dimensional gel electrophoresis and mass spectrometry.

    Science.gov (United States)

    Ren, Zhiwu; Wang, Yu; Peng, Jiang; Zhang, Li; Xu, Wenjing; Liang, Xiangdang; Zhao, Qing; Lu, Shibi

    2012-02-15

    The present study utilized samples from bilateral motor branches of the femoral nerve, as well as saphenous nerves, ventral roots, and dorsal roots of the spinal cord, to detect differential protein expression using two-dimensional gel electrophoresis and nano ultra-high performance liquid chromatography electrospray ionization mass spectrometry tandem mass spectrometry techniques. A mass spectrum was identified using the Mascot search. Results revealed differential expression of 11 proteins, including transgelin, Ig kappa chain precursor, plasma glutathione peroxidase precursor, an unnamed protein product (gi|55628), glyceraldehyde-3-phosphate dehydrogenase-like protein, lactoylglutathione lyase, adenylate kinase isozyme 1, two unnamed proteins products (gi|55628 and gi|1334163), and poly(rC)-binding protein 1 in motor and sensory nerves. Results suggested that these proteins played roles in specific nerve regeneration following peripheral nerve injury and served as specific markers for motor and sensory nerves.

  13. Protein expression of sensory and motor nerves Two-dimensional gel electrophoresis and mass spectrometry

    Institute of Scientific and Technical Information of China (English)

    Zhiwu Ren; Yu Wang; Jiang Peng; Li Zhang; Wenjing Xu; Xiangdang Liang; Qing Zhao; Shibi Lu

    2012-01-01

    The present study utilized samples from bilateral motor branches of the femoral nerve, as well as saphenous nerves, ventral roots, and dorsal roots of the spinal cord, to detect differential protein expression using two-dimensional gel electrophoresis and nano ultra-high performance liquid chromatography electrospray ionization mass spectrometry tandem mass spectrometry techniques. A mass spectrum was identified using the Mascot search. Results revealed differential expression of 11 proteins, including transgelin, Ig kappa chain precursor, plasma glutathione peroxidase precursor, an unnamed protein product (gi|55628), glyceraldehyde-3-phosphate dehydrogenase-like protein, lactoylglutathione lyase, adenylate kinase isozyme 1, two unnamed proteins products (gi|55628 and gi|1334163), and poly(rC)-binding protein 1 in motor and sensory nerves. Results suggested that these proteins played roles in specific nerve regeneration following peripheral nerve injury and served as specific markers for motor and sensory nerves.

  14. Statistical analysis of image data provided by two-dimensional gel electrophoresis for discovery proteomics.

    Science.gov (United States)

    Crossett, Ben; Edwards, Alistair V G; White, Melanie Y; Cordwell, Stuart J

    2008-01-01

    Standardized methods for the solubilization of proteins prior to proteomics analyses incorporating two-dimensional gel electrophoresis (2-DE) are essential for providing reproducible data that can be subjected to rigorous statistical interrogation for comparative studies investigating disease-genesis. In this chapter, we discuss the imaging and image analysis of proteins separated by 2-DE, in the context of determining protein abundance alterations related to a change in biochemical or biophysical conditions. We then describe the principles behind 2-DE gel statistical analysis, including subtraction of background noise, spot detection, gel matching, spot quantitation for data comparison, and statistical requirements to create meaningful gel data sets. We also emphasize the need to develop reproducible and robust protocols for protein sample preparation and 2-DE itself.

  15. Alpha1-acid glycoprotein post-translational modifications: a comparative two dimensional electrophoresis based analysis

    Directory of Open Access Journals (Sweden)

    P. Roncada

    2010-04-01

    Full Text Available Alpha1-acid glycoprotein (AGP is an immunomodulatory protein expressed by hepatocytes in response to the systemic reaction that follows tissue damage caused by inflammation, infection or trauma. A proteomic approach based on two dimensional electrophoresis, immunoblotting and staining of 2DE gels with dyes specific for post-translational modifications (PTMs such as glycosylation and phosphorylation has been used to evaluate the differential interspecific protein expression of AGP purified from human, bovine and ovine sera. By means of these techniques, several isoforms have been identified in the investigated species: they have been found to change both with regard to the number of isoforms expressed under physiological condition and with regard to the quality of PTMs (i.e. different oligosaccharidic chains, presence/absence of phosphorilations. In particular, it is suggested that bovine serum AGP may have one of the most complex pattern of PTMs among serum proteins of mammals studied so far.

  16. MULTI2D - a computer code for two-dimensional radiation hydrodynamics

    Science.gov (United States)

    Ramis, R.; Meyer-ter-Vehn, J.; Ramírez, J.

    2009-06-01

    Simulation of radiation hydrodynamics in two spatial dimensions is developed, having in mind, in particular, target design for indirectly driven inertial confinement energy (IFE) and the interpretation of related experiments. Intense radiation pulses by laser or particle beams heat high-Z target configurations of different geometries and lead to a regime which is optically thick in some regions and optically thin in others. A diffusion description is inadequate in this situation. A new numerical code has been developed which describes hydrodynamics in two spatial dimensions (cylindrical R-Z geometry) and radiation transport along rays in three dimensions with the 4 π solid angle discretized in direction. Matter moves on a non-structured mesh composed of trilateral and quadrilateral elements. Radiation flux of a given direction enters on two (one) sides of a triangle and leaves on the opposite side(s) in proportion to the viewing angles depending on the geometry. This scheme allows to propagate sharply edged beams without ray tracing, though at the price of some lateral diffusion. The algorithm treats correctly both the optically thin and optically thick regimes. A symmetric semi-implicit (SSI) method is used to guarantee numerical stability. Program summaryProgram title: MULTI2D Catalogue identifier: AECV_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECV_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 151 098 No. of bytes in distributed program, including test data, etc.: 889 622 Distribution format: tar.gz Programming language: C Computer: PC (32 bits architecture) Operating system: Linux/Unix RAM: 2 Mbytes Word size: 32 bits Classification: 19.7 External routines: X-window standard library (libX11.so) and corresponding heading files (X11/*.h) are

  17. A new model for two-dimensional numerical simulation of pseudo-2D gas-solids fluidized beds

    Energy Technology Data Exchange (ETDEWEB)

    Li, Tingwen; Zhang, Yongmin

    2013-10-11

    Pseudo-two dimensional (pseudo-2D) fluidized beds, for which the thickness of the system is much smaller than the other two dimensions, is widely used to perform fundamental studies on bubble behavior, solids mixing, or clustering phenomenon in different gas-solids fluidization systems. The abundant data from such experimental systems are very useful for numerical model development and validation. However, it has been reported that two-dimensional (2D) computational fluid dynamic (CFD) simulations of pseudo-2D gas-solids fluidized beds usually predict poor quantitative agreement with the experimental data, especially for the solids velocity field. In this paper, a new model is proposed to improve the 2D numerical simulations of pseudo-2D gas-solids fluidized beds by properly accounting for the frictional effect of the front and back walls. Two previously reported pseudo-2D experimental systems were simulated with this model. Compared to the traditional 2D simulations, significant improvements in the numerical predictions have been observed and the predicted results are in better agreement with the available experimental data.

  18. Immunoreactivity and two-dimensional gel-electrophoresis characterization of Egyptian cobra venom proteome.

    Science.gov (United States)

    Almehdar, Hussein Abduelrahman; Adel-Sadek, Mahmoud Abass; Redwan, Elrashdy Moustafa

    2015-01-01

    The first and second (two) dimensional gel electrophoresis has a broad protein resolution power. It was used to separate and identify cobra venom proteome. The importance of characterizing venom proteins contents from the Egyptian elapidae, specifically neurotoxins, is based on the need to produce effective anti-venom. About 30-55distinct protein spots were identified on silver stained two-dimensional gels. Around two-thirds of the venom proteins displayed low a molecular weight and a migration into hydrophobic side. The venoms from Naja haja and Naja nigricollus showed 45-55 spots, while Walternnesia aegyptia had less (31-37) spots. The commercial prepared polyclonal antivenom had a strong signal for anionic and cationic venom protein spots with molecular weight 20-115 kDa. However, it showed weak or non immunoreactivity toward anionic low molecular weight spots (2.5-15 kDa). These results suggest the need to change the immunization schedule to include low molecular weight toxin-proteomes as separate dose or sequester injection.

  19. Topological patterns in two-dimensional gel electrophoresis of DNA knots.

    Science.gov (United States)

    Michieletto, Davide; Marenduzzo, Davide; Orlandini, Enzo

    2015-10-06

    Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. Although there is a large body of experimental work that allows us to accurately separate different topoisomers of a molecule, a full theoretical understanding of these experiments has not yet been achieved. Here we show that the mobility of DNA knots depends crucially and subtly on the physical properties of the gel and, in particular, on the presence of dangling ends. The topological interactions between these and DNA molecules can be described in terms of an "entanglement number" and yield a nonmonotonic mobility at moderate fields. Consequently, in 2D electrophoresis, gel bands display a characteristic arc pattern; this turns into a straight line when the density of dangling ends vanishes. We also provide a novel framework to accurately predict the shape of such arcs as a function of molecule length and topological complexity, which may be used to inform future experiments.

  20. A tunable isoelectric focusing via moving reaction boundary for two-dimensional gel electrophoresis and proteomics.

    Science.gov (United States)

    Guo, Chen-Gang; Shang, Zhi; Yan, Jian; Li, Si; Li, Guo-Qing; Liu, Rong-Zhong; Qing, Ying; Fan, Liu-Yin; Xiao, Hua; Cao, Cheng-Xi

    2015-05-01

    Routine native immobilized pH gradient isoelectric focusing (IPG-IEF) and two-dimensional gel electrophoresis (2DE) are still suffering from unfortunate reproducibility, poor resolution (caused by protein precipitation) and instability in characterization of intact protein isoforms and posttranslational modifications. Based on the concept of moving reaction boundary (MRB), we firstly proposed a tunable non-IPG-IEF system to address these issues. By choosing proper pairs of catholyte and anolyte, we could achieve desired cathodic and anodic migrating pH gradients in non-IPG-IEF system, effectively eliminating protein precipitation and uncertainty of quantitation existing in routine IEF and 2DE, and enhancing the resolution and sensitivity of IEF. Then, an adjustable 2DE system was developed by combining non-IPG-IEF with polyacrylamide gel electrophoresis (PAGE). The improved 2DE was evaluated by testing model proteins and colon cancer cell lysates. The experiments revealed that (i) a tunable pH gradient could be designed via MRB; (ii) up to 1.65 fold improvement of resolution was achieved via non-IPG-IEF; (iii) the sensitivity of developed techniques was increased up to 2.7 folds; and (iv) up to about 16.4% more protein spots could be observed via the adjustable 2DE as compared with routine one. The developed techniques might contribute to complex proteome research, especially for screening of biological marker and analysis of extreme acidic/alkaline proteins. Copyright © 2015 Elsevier B.V. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    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].

  2. 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...

  3. Antioxidant effects of carnitine supplementation on 14-3-3 protein isoforms in the aged rat hippocampus detected using fully automated two-dimensional chip gel electrophoresis.

    Science.gov (United States)

    Iwamoto, M; Miura, Y; Tsumoto, H; Tanaka, Y; Morisawa, H; Endo, T; Toda, T

    2014-12-01

    We here described the antioxidant effects of carnitine supplementation on 14-3-3 protein isoforms in the aged rat hippocampus detected using the fully automated two-dimensional chip gel electrophoresis system (Auto2D). This system was easy and convenient to use, and the resolution obtained was more sensitive and higher than that of conventional two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). We separated and identified five isoforms of the 14-3-3 protein (beta/alpha, gamma, epsilon, zeta/delta, and eta) using the Auto2D system. We then examined the antioxidant effects of carnitine supplementation on the protein profiles of the cytosolic fraction in the aged rat hippocampus, demonstrating that carnitine supplementation suppressed the oxidation of methionine residues in these isoforms. Since methionine residues are easily oxidized to methionine sulfoxide, the convenient and high-resolution 2-D PAGE system can be available to analyze methionine oxidation avoiding artifactual oxidation. We showed here that the Auto2D system was a very useful tool for studying antioxidant effects through proteomic analysis of protein oxidation.

  4. Sample Preparation and Staining Methods for Two-Dimensional Polyacrylamide Gel Electrophoresis of Proteins from Animal Tissues

    Directory of Open Access Journals (Sweden)

    Levente Czegledi

    2010-05-01

    Full Text Available Proteomics in animal science as well as in other biological sciences is a significant tool in the post-genomic era. In proteomic studies the presence and relative abundance of expressed proteins of a cell, tissue or biological fluid is studied. Recently, the whole genome of more and more domestic animal species is known, but genes and the transcribed mRNA have no direct effect on biological systems as they are regulated by proteins, which explain the importance of proteomics. The most common tool in proteomic approach is the two-dimensional polyacrylamide gel electrophoresis (2D PAGE, when proteins are separated by their isoelectric point followed by their mass separation as a second dimension. In this study authors used different sample preparation and protein staining methods on meat,  liver and blood plasma and carried out 2D PAGE experiments. The most appropriate sample preparation methods are described in this paper. We concluded that depletion of major proteins in plasma is required but not necessary for meat and liver samples.

  5. Optical properties of two-dimensional (2D) CdSe nanostructures

    Science.gov (United States)

    Cherevkov, S. A.; Baranov, A. V.; Fedorov, A. V.; Litvin, A. P.; Artemyev, M. V.; Prudnikau, A. V.

    2013-09-01

    The resonant and off-resonant Raman spectra of optical phonons in two-dimensional CdSe nanocrystals of 5, 6, and 7 monolayers are analysed. The spectra are dominated by SO and LO phonon bands of CdSe, whose frequencies are thickness-independent in the off-resonant Raman scattering but demonstrate an evident thickness dependence in the case of the resonant Raman scattering.

  6. MARG2D code. 1. Eigenvalue problem for two dimensional Newcomb equation

    Energy Technology Data Exchange (ETDEWEB)

    Tokuda, Shinji [Japan Atomic Energy Research Inst., Naka, Ibaraki (Japan). Naka Fusion Research Establishment; Watanabe, Tomoko

    1997-10-01

    A new method and a code MARG2D have been developed to solve the 2-dimensional Newcomb equation which plays an important role in the magnetohydrodynamic (MHD) stability analysis in an axisymmetric toroidal plasma such as a tokamak. In the present formulation, an eigenvalue problem is posed for the 2-D Newcomb equation, where the weight function (the kinetic energy integral) and the boundary conditions at rational surfaces are chosen so that an eigenfunction correctly behaves as the linear combination of the small solution and the analytical solutions around each of the rational surfaces. Thus, the difficulty on solving the 2-D Newcomb equation has been resolved. By using the MARG2D code, the ideal MHD marginally stable state can be identified for a 2-D toroidal plasma. The code is indispensable on computing the outer-region matching data necessary for the resistive MHD stability analysis. Benchmark with ERATOJ, an ideal MHD stability code, has been carried out and the MARG2D code demonstrates that it indeed identifies both stable and marginally stable states against ideal MHD motion. (author)

  7. Adult-onset nemaline rods in a patient treated for suspected dermatomyositis: study with two-dimensional electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Danon, M.J.; Giometti, C.S.; Manaligod, J.R.; Perurena, O.H.; Skosey, J.L.

    1981-12-01

    A 65-year-old woman with progressive muscle weakness and a diffuse rash of three years' duration was examined. Muscle tissue was studied with histochemical techniques, phase-contrast microscopy, electron microscopy, and two-dimensional electrophoresis. Histochemical studies showed numerous nemaline rods, with a normal ratio of types I and II fibers. Two-dimensional electrophoresis revealed abnormalities in the myosin light chain and tropomyosin protein patterns when compared with normal and diseased muscle biopsy samples, including those from two patients with adult-onset dermatomyositis.

  8. Total protein extraction and 2-D gel electrophoresis methods for Burkholderia species.

    Science.gov (United States)

    Velapatiño, Billie; Zlosnik, James E A; Hird, Trevor J; Speert, David P

    2013-10-15

    The investigation of the intracellular protein levels of bacterial species is of importance to understanding the pathogenic mechanisms of diseases caused by these organisms. Here we describe a procedure for protein extraction from Burkholderia species based on mechanical lysis using glass beads in the presence of ethylenediamine tetraacetic acid and phenylmethylsulfonyl fluoride in phosphate buffered saline. This method can be used for different Burkholderia species, for different growth conditions, and it is likely suitable for the use in proteomic studies of other bacteria. Following protein extraction, a two-dimensional (2-D) gel electrophoresis proteomic technique is described to study global changes in the proteomes of these organisms. This method consists of the separation of proteins according to their isoelectric point by isoelectric focusing in the first dimension, followed by separation on the basis of molecular weight by acrylamide gel electrophoresis in the second dimension. Visualization of separated proteins is carried out by silver staining.

  9. 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

    improvements of two-dimensional gel electrophoresis with immobilized pH gradients (IPG) compared to isoelectric focusing with carrier ampholytes, a highly reproducible method for examining global changes in HeLa cell protein expression due to different stimuli is now available. Therefore, we have initiated...

  10. 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

    improvements of two-dimensional gel electrophoresis with immobilized pH gradients (IPG) compared to isoelectric focusing with carrier ampholytes, a highly reproducible method for examining global changes in HeLa cell protein expression due to different stimuli is now available. Therefore, we have initiated...

  11. Identification of tumor markers using two-dimensional electrophoresis in gastric carcinoma

    Institute of Scientific and Technical Information of China (English)

    Kai-Juan Wang; Run-Tian Wang; Jian-Zhong Zhang

    2004-01-01

    AIM: To study the differential expression of proteins in normal and cancerous gastric tissues, and further identify new molecular markers for diagnosis and prognosis of gastric carcinoma, as well as develop new therapeutic targets of the disease.METHODS: Matched pairs of tissues from 6 gastric cancer patients were analyzed for their two-dimensional electrophoresis (2DE) profiles. Soluble fraction proteins from human normal and cancerous gastric tissue were separated in the first dimension by isoelectric focusing on immobilized pH gradient (IPG, pH3-10) strips, and by 125 g/L sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) in the second dimension with silver nitrate staining. Protein differential expression was analyzed by use of image analysis software to find out candidates for gastric cancer-associated proteins.RESULTS: Nine protein spots overexpressed in tumor tissues as compared with noncancerous regions. In the next step, 9 tumor-specific spots were cut off from Coomassie Brilliant Blue staining gels, digested in gel with L-1-tosylamide-2-phenylethyl chloromethyl ketone (TPCK)-trypsin. Protein identification was done by peptide mass fingerprinting with matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS).In total, 5 tumor-specific protein spots corresponding to 5 different polypeptide chains were identified, including annexin V, carbonic anhydrase, prohibitin, fibrin beta and fibrinogen fragment D. Among these 5 spots, the potential significance of the differential expressions is discussed.CONCLUSION Differential expression analysis of proteomes may be useful for the development of new molecular markers for diagnosis and prognosis of gastric carcinoma.

  12. Optimization of Protein Extraction and Two-Dimensional Electrophoresis Protocols for Oil Palm Leaf.

    Science.gov (United States)

    Daim, Leona Daniela Jeffery; Ooi, Tony Eng Keong; Yusof, Hirzun Mohd; Majid, Nazia Abdul; Karsani, Saiful Anuar Bin

    2015-08-01

    Oil palm (Elaeis guineensis) is an important economic crop cultivated for its nutritional palm oil. A significant amount of effort has been undertaken to understand oil palm growth and physiology at the molecular level, particularly in genomics and transcriptomics. Recently, proteomics studies have begun to garner interest. However, this effort is impeded by technical challenges. Plant sample preparation for proteomics analysis is plagued with technical challenges due to the presence of polysaccharides, secondary metabolites and other interfering compounds. Although protein extraction methods for plant tissues exist, none work universally on all sample types. Therefore, this study aims to compare and optimize different protein extraction protocols for use with two-dimensional gel electrophoresis of young and mature leaves from the oil palm. Four protein extraction methods were evaluated: phenol-guanidine isothiocyanate, trichloroacetic acid-acetone precipitation, sucrose and trichloroacetic acid-acetone-phenol. Of these four protocols, the trichloroacetic acid-acetone-phenol method was found to give the highest resolution and most reproducible gel. The results from this study can be used in sample preparations of oil palm tissue for proteomics work.

  13. Comparison of Three Methods of Protein Extraction from Dermatophagoides Pteronyssinus for Two-dimensional Electrophoresis

    Institute of Scientific and Technical Information of China (English)

    Jin-lu Sun; Hong-yu Zhang; Zhi-yi Guo; Wan-tao Ying; Xiao-hong Qian; Jing-lan Wang

    2009-01-01

    Objective To explore an effective method of Dermatophagoides pteronyssinus protein extraction suitable for two-dimensional electrophoresis (2-DE) analysis. Methods The extracts of Dermatophagoides pteronyssinus were prepared with Coca's solution, lysis buffer of 2-DE, and Trizol reagent, respectively. Bicinchoninic acid (BCA) assay was used to determine the total protein concentration of the samples. The efficiency of different protein extraction methods were evaluated with 2-DE analysis. Results The concentrations of extracted protein by methods of Coca's solution, lysis buffer, and Trizol reagent were 0.63 g/L, 0.90 g/L, and 0.80 g/L, respectively. The 2-DE analysis results showed that some protein spots in low molecular weight (LMW) range could be detected with the Coca's solution method. With the lysis buffer of 2-DE method, more protein spots in LMW range could be detected, while the medium molecular weight (MMW) protein spots were absent. Several MMW protein spots (174-178 kD and 133 kD) and more LMW protein spots were detected with Trizol reagent method. Conclusions Among Coca's solution, lysis buffer of 2-DE, and Trizol reagent, the concentration of extracted protein of Dermatophagoides pteronyssinus by lysis buffer of 2-DE is the highest. However, most protein components of Dermatophagoides pteronyssinus purified mite bodies can be extracted by Trizol reagent, which may generally reflect the whole profile of Dermatophagoides pteronyssinus allergens.

  14. Identification of cholesterol gallstone with two-dimensional gel electrophoresis and mass spectrometry.

    Science.gov (United States)

    Qian, Changlin; Shen, Zhiyong; Zhang, Jie; Ji, Fu; Liu, Hua

    2015-01-01

    We aimed to provide novel information to better understand the molecular mechanisms underlying gallstones formation and explore the potential protein markers for gallstones progression. The gallbladder tissues were collected from 20 patients with cholesterol gallstone and 10 liver transplant donors from November 2010 to April 2011. The proteomics were compared between gallstone patients and controls by two-dimensional gel electrophoresis (2-DE). The differentially expressed proteins were identified and validated by western blotting and real-time PCR. Total 19 protein spots were found to be different between two groups and 11 proteins were identified, among which 4 ones (such as Peroxiredoxin 3/Prdx3) were down-regulated and 7 (such as Tropomyosin 4/TPM4, Transgelin/SM22, Transthyretin/ TTR) were up-regulated in gallstone group. Results of western blotting and RT-PCR were consistent with the 2-DE results. The differentially expressed proteins of TTR, TPM4, SM22 and Prdx3 may play key roles in gallstone formation and may be markers for gallstone progression.

  15. Synchronous two-dimensional MIR correlation spectroscopy (2D-COS) as a novel method for screening smoke tainted wine.

    Science.gov (United States)

    Fudge, Anthea L; Wilkinson, Kerry L; Ristic, Renata; Cozzolino, Daniel

    2013-08-15

    In this study, two-dimensional correlation spectroscopy (2D-COS) combined with mid-infrared (MIR) spectroscopy was evaluated as a novel technique for the identification of spectral regions associated with smoke-affected wine, for the purpose of screening taint arising from grapevine exposure to smoke. Smoke-affected wines obtained from experimental and industry sources were analysed using MIR spectroscopy and chemometrics, and calibration models developed. 2D-COS analysis was used to generate synchronous data maps for red and white cask wines spiked with guaiacol, a marker of smoke taint. Correlations were observed at wavelengths that could be attributable to aromatic C-C stretching, i.e., between 1400 and 1500 cm(-1), indicative of volatile phenols. These results demonstrate the potential of 2D-COS as a rapid, high-throughput technique for the preliminary screening of smoke tainted wine.

  16. Horizontal comparative fluorescence two-dimensional gel electrophoresis for improved spot coordinate detection.

    Science.gov (United States)

    Hanneken, Marina; König, Simone

    2014-04-01

    Vertical comparative 2D fluorescence gel electrophoresis (CoFGE) has recently been shown to increase the reproducibility of coordinate assignment for protein spots, in particular in singular experiments, which cannot be investigated using DIGE. The method applies a standardized marker grid formed by a set of purified proteins to the sample proteome in a conglomerate of 1DE, 2DE, and DIGE. Here, improvements are demonstrated by transferring CoFGE to horizontal 2DE. These include the elimination of the protein modification by residual acrylamide monomer unavoidable in vertical CoFGE, reduced buffer volumes, and highly efficient laboratory procedures. Spot patterns are well defined and can be easily analyzed using commercially available warping algorithms. With horizontal CoFGE also a correction for changes in pI was introduced using a third fluorescent dye. Horizontal CoFGE holds high promises in comparative proteomics. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Proteomic comparisons of opaque and transparent variants of Streptococcus pneumoniae by two dimensional-differential gel electrophoresis.

    Science.gov (United States)

    Chai, Melissa H; Weiland, Florian; Harvey, Richard M; Hoffmann, Peter; Ogunniyi, Abiodun D; Paton, James C

    2017-05-26

    Streptococcus pneumoniae (the pneumococcus) is a human pathogen, accounting for massive global morbidity and mortality. Although asymptomatic colonization of the nasopharynx almost invariably precedes disease, the critical determinants enabling pneumococcal progression from this niche to cause invasive disease are poorly understood. One mechanism proposed to be central to this transition involves opacity phase variation, whereby pneumococci harvested from the nasopharynx are typically transparent, while those simultaneously harvested from the blood are opaque. Here, we used two dimensional-differential gel electrophoresis (2D-DIGE) to compare protein expression profiles of transparent and opaque variants of 3 pneumococcal strains, D39 (serotype 2), WCH43 (serotype 4) and WCH16 (serotype 6A) in vitro. One spot comprising a mixture of capsular polysaccharide biosynthesis protein and other proteins was significantly up-regulated in the opaque phenotype in all 3 strains; other proteins were differentially regulated in a strain-specific manner. We conclude that pneumococcal phase variation is a complex and multifactorial process leading to strain-specific pathogenicity.

  18. Buffer optimization for high resolution of human lung cancer tissue proteins by two-dimensional gel electrophoresis.

    Science.gov (United States)

    Lee, Kibeom; Pi, Kyungbae; Lee, Keeman

    2009-01-01

    A problem in proteomic analysis of lung cancer tissue is the presence of complex components of different histological backgrounds (squamous cell carcinoma, small cell lung carcinoma, and adenocarcinoma). The efficient solubilization of protein components before two-dimensional electrophoresis (2-DE) is a very critical. Poor solubilization has been associated with a failure to detect proteins and diffuse, streaked and/or trailing protein spots. Here, we have optimized the solubilization of human lung cancer tissue to increase protein resolution. Isoelectric focusing (IEF) rehydration buffer containing a thiourea-urea mixture provided superior resolution, whereas a buffer without thiourea yielded consistently poor results. In addition, IEF rehydration buffers containing CHAPS and DTT gave superior resolution, whereas buffers containing Nonidet P-40 (NP-40) and/or Triton X-100 did not. A tributylphosphine-containing buffer gave consistently poor results. Using optimized conditions, we used 2-D gel analysis of human lung cancer tissue to identify 11 differentially-expressed protein spots by MALDI-mass spectrometry. This study provides a methodological tool to study the complex mammalian proteomes.

  19. 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.

  20. 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...

  1. 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...

  2. Comparison of protein patterns after two-dimensional gel electrophoresis from leaves of in vitro cultures and seedlings of Rubus chamaemorus L.

    Directory of Open Access Journals (Sweden)

    Barbara Thiem

    2014-01-01

    Full Text Available Proteins from leaves of Rubus chamaemorus propagated in vitro were subjected to miniaturized 2-D electrophoresis. The 2-DE patterns of proteins showed qualitative differences between plants propagated in vitro and control seedlings. More proteins of a high molecular weight were observed in leaves of plants from in vitro culture. A two-dimensional map of proteins from leaves provides detailed data concerning both polymorphism and protein patterns of this species. This makes it possible to start constructing a protein map of R. chamaemorus. The reasons for qualitative differences are discussed.

  3. Optical theorem for two-dimensional (2D) scalar monochromatic acoustical beams in cylindrical coordinates.

    Science.gov (United States)

    Mitri, F G

    2015-09-01

    The optical theorem for plane waves is recognized as one of the fundamental theorems in optical, acoustical and quantum wave scattering theory as it relates the extinction cross-section to the forward scattering complex amplitude function. Here, the optical theorem is extended and generalized in a cylindrical coordinates system for the case of 2D beams of arbitrary character as opposed to plane waves of infinite extent. The case of scalar monochromatic acoustical wavefronts is considered, and generalized analytical expressions for the extinction, absorption and scattering cross-sections are derived and extended in the framework of the scalar resonance scattering theory. The analysis reveals the presence of an interference scattering cross-section term describing the interaction between the diffracted Franz waves with the resonance elastic waves. The extended optical theorem in cylindrical coordinates is applicable to any object of arbitrary geometry in 2D located arbitrarily in the beam's path. Related investigations in optics, acoustics and quantum mechanics will benefit from this analysis in the context of wave scattering theory and other phenomena closely connected to it, such as the multiple scattering by a cloud of particles, as well as the resulting radiation force and torque.

  4. Proteomic Analysis of Colorectal Cancer: Prefractionation Strategies Using two-Dimensional Free-Flow Electrophoresis

    Directory of Open Access Journals (Sweden)

    Richard J. Simpson

    2006-04-01

    Full Text Available This review deals with the application of a new prefractionation tool, free-flow electrophoresis (FFE, for proteomic analysis of colorectal cancer (CRC. CRC is a leading cause of cancer death in the Western world. Early detection is the single most important factor influencing outcome of CRC patients. If identified while the disease is still localized, CRC is treatable. To improve outcomes for CRC patients there is a pressing need to identify biomarkers for early detection (diagnostic markers, prognosis (prognostic indicators, tumour responses (predictive markers and disease recurrence (monitoring markers. Despite recent advances in the use of genomic analysis for risk assessment, in the area of biomarker identification genomic methods alone have yet to produce reliable candidate markers for CRC. For this reason, attention is being directed towards proteomics as a complementary analytical tool for biomarker identification. Here we describe a proteomics separation tool, which uses a combination of continuous FFE, a liquid-based isoelectric focusing technique, in the first dimension, followed by rapid reversed-phase HPLC (1–6 min/analysis in the second dimension. We have optimized imaging software to present the FFE/RP-HPLC data in a virtual 2D gel-like format. The advantage of this liquid based fractionation system over traditional gel-based fractionation systems is the ability to fractionate large quantity protein samples. Unlike 2D gels, the method is applicable to both high-Mr proteins and small peptides, which are difficult to separate, and in the case of peptides, are not retained in standard 2D gels.

  5. Characterization of Purified Glutathione S-Transferase (GSTs from Fasciola hepatica and Liver Tissue by Two-Dimensional Electrophoresis (2-DE

    Directory of Open Access Journals (Sweden)

    A Farahnak 1

    2005-07-01

    Full Text Available Two-dimensional electrophoresis (2-D electrophoresis is a powerful and extensively used method for analysis of complex protein mixtures extracted from cells, tissue, or other biological samples such as helminth parasites including, F. hepatica. Each spot on the resulting two-dimensional collection corresponds to a single protein species in the sample. This study was carried out to detect of GSTs isoenzyme spots map for collection of highly specific proteins. For this purpose, GSTs were purified from adult parasite of F.hepatica and sheep liver tissue as an enzyme pool by a glutathione affinity matrix using a wash-bath method and investigated for sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE pattern. For 2-DE, purified GSTs from F.hepatica and sheep liver tissue were resuspended in sample buffer and then run on a IPG strip in the first dimension and then on an Excel Gel SDS in the second dimension before protein spots staining with Coomassie blue. The obtaining spots in the gels were compared and GSTs protein spots were detected with similar molecular weight, 26 kDa. The protein spots which are recorded in this paper could be GSTs isoenzymes and are highly specific peptids. These findings may be considered for vaccination or chemotherapeutic targets in sheep and human fascioliasis.

  6. Two-Dimensional Differential Gel Electrophoresis to Identify Protein Biomarkers in Amniotic Fluid of Edwards Syndrome (Trisomy 18 Pregnancies.

    Directory of Open Access Journals (Sweden)

    Te-Yao Hsu

    Full Text Available Edwards syndrome (ES is a severe chromosomal abnormality with a prevalence of about 0.8 in 10,000 infants born alive. The aims of this study were to identify candidate proteins associated with ES pregnancies from amniotic fluid supernatant (AFS using proteomics, and to explore the role of biological networks in the pathophysiology of ES.AFS from six second trimester pregnancies with ES fetuses and six normal cases were included in this study. Fluorescence-based two-dimensional difference gel electrophoresis (2D-DIGE and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS were used for comparative proteomic analysis. The identified proteins were further validated by Western blotting and the role of biological networks was analyzed.Twelve protein spots were differentially expressed by more than 1.5-fold in the AFS of the ES pregnancies. MALDI-TOF/MS identified one up-regulated protein: apolipoprotein A1 (ApoA1, and four under-regulated proteins: vitamin D binding protein (VDBP, alpha-1-antitrypsin (A1AT, insulin-like growth factor-binding protein 1 (IGFBP-1, and transthyretin (TTR. Western blot and densitometric analysis of ApoA1, A1AT, IGFBP-1, and TTR confirmed the alteration of these proteins in the amniotic fluid samples. Biological network analysis revealed that the proteins of the ES AFS were involved mainly in lipid and hormone metabolism, immune response, and cardiovascular disease.These five proteins may be involved in the pathogenesis of ES. Further studies are needed to explore.

  7. Two-dimensional crystal melting and D4-D2-D0 on toric Calabi-Yau singularities

    CERN Document Server

    Nishinaka, Takahiro; Yoshida, Yutaka

    2013-01-01

    We construct a two-dimensional crystal melting model which reproduces the BPS index of D2-D0 states bound to a non-compact D4-brane on an arbitrary toric Calabi-Yau singularity. The crystalline structure depends on the toric divisor wrapped by the D4-brane. The molten crystals are in one-to-one correspondence with the torus fixed points of the moduli space of the quiver gauge theory on D-branes. The F- and D-term constraints of the gauge theory are regarded as a generalization of the ADHM constraints on instantons. We also show in several examples that our model is consistent with the wall-crossing formula for the BPS index.

  8. Proteomic Analysis of Bovine Pregnancy-specific Serum Proteins by 2D Fluorescence Difference Gel Electrophoresis

    Directory of Open Access Journals (Sweden)

    Jae Eun Lee

    2015-06-01

    Full Text Available Two dimensional-fluorescence difference gel electrophoresis (2D DIGE is an emerging technique for comparative proteomics, which improves the reproducibility and reliability of differential protein expression analysis between samples. The purpose of this study was to investigate bovine pregnancy-specific proteins in the proteome between bovine pregnant and non-pregnant serum using DIGE technique. Serums of 2 pregnant Holstein dairy cattle at day 21 after artificial insemination and those of 2 non-pregnant were used in this study. The pre-electrophoretic labeling of pregnant and non-pregnant serum proteins were mixed with Cy3 and Cy5 fluorescent dyes, respectively, and an internal standard was labeled with Cy2. Labeled proteins with Cy2, Cy3, and Cy5 were separated together in a single gel, and then were detected by fluorescence image analyzer. The 2D DIGE method using fluorescence CyDye DIGE flour had higher sensitivity than conventional 2D gel electrophoresis, and showed reproducible results. Approximately 1,500 protein spots were detected by 2D DIGE. Several proteins showed a more than 1.5-fold up and down regulation between non-pregnant and pregnant serum proteins. The differentially expressed proteins were identified by MALDI-TOF mass spectrometer. A total 16 protein spots were detected to regulate differentially in the pregnant serum, among which 7 spots were up-regulated proteins such as conglutinin precursor, modified bovine fibrinogen and IgG1, and 6 spots were down-regulated proteins such as hemoglobin, complement component 3, bovine fibrinogen and IgG2a three spots were not identified. The identified proteins demonstrate that early pregnant bovine serum may have several pregnancy-specific proteins, and these could be a valuable information for the development of pregnancy-diagnostic markers in early pregnancy bovine serum.

  9. An effective placental cotyledons proteins extraction method for 2D gel electrophoresis.

    Science.gov (United States)

    Tan, Niu J; Daim, Leona D J; Jamil, Amilia A M; Mohtarrudin, Norhafizah; Thilakavathy, Karuppiah

    2017-03-01

    Effective protein extraction is essential especially in producing a well-resolved proteome on 2D gels. A well-resolved placental cotyledon proteome, with good reproducibility, have allowed researchers to study the proteins underlying the physiology and pathophysiology of pregnancy. The aim of this study is to determine the best protein extraction protocol for the extraction of protein from placental cotyledons tissues for a two-dimensional gel electrophoresis (2D-GE). Based on widely used protein extraction strategies, 12 different extraction methodologies were carefully selected, which included one chemical extraction, two mechanical extraction coupled protein precipitations, and nine chemical extraction coupled protein precipitations. Extracted proteins were resolved in a one-dimensional gel electrophoresis and 2D-GE; then, it was compared with set criteria: extraction efficacy, protein resolution, reproducibility, and recovery efficiency. Our results revealed that a better profile was obtained by chemical extraction in comparison to mechanical extraction. We further compared chemical extraction coupled protein precipitation methodologies, where the DNase/lithium chloride-dense sucrose homogenization coupled dichloromethane-methanol precipitation (DNase/LiCl-DSH-D/MPE) method showed good protein extraction efficiency. This, however, was carried out with the best protein resolution and proteome reproducibility on 2D-gels. DNase/LiCl-DSH-D/MPE was efficient in the extraction of proteins from placental cotyledons tissues. In addition, this methodology could hypothetically allow the protein extraction of any tissue that contains highly abundant lipid and glycogen. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Proteomic Analysis of Bovine Pregnancy-specific Serum Proteins by 2D Fluorescence Difference Gel Electrophoresis

    Science.gov (United States)

    Lee, Jae Eun; Lee, Jae Young; Kim, Hong Rye; Shin, Hyun Young; Lin, Tao; Jin, Dong Il

    2015-01-01

    Two dimensional-fluorescence difference gel electrophoresis (2D DIGE) is an emerging technique for comparative proteomics, which improves the reproducibility and reliability of differential protein expression analysis between samples. The purpose of this study was to investigate bovine pregnancy-specific proteins in the proteome between bovine pregnant and non-pregnant serum using DIGE technique. Serums of 2 pregnant Holstein dairy cattle at day 21 after artificial insemination and those of 2 non-pregnant were used in this study. The pre-electrophoretic labeling of pregnant and non-pregnant serum proteins were mixed with Cy3 and Cy5 fluorescent dyes, respectively, and an internal standard was labeled with Cy2. Labeled proteins with Cy2, Cy3, and Cy5 were separated together in a single gel, and then were detected by fluorescence image analyzer. The 2D DIGE method using fluorescence CyDye DIGE flour had higher sensitivity than conventional 2D gel electrophoresis, and showed reproducible results. Approximately 1,500 protein spots were detected by 2D DIGE. Several proteins showed a more than 1.5-fold up and down regulation between non-pregnant and pregnant serum proteins. The differentially expressed proteins were identified by MALDI-TOF mass spectrometer. A total 16 protein spots were detected to regulate differentially in the pregnant serum, among which 7 spots were up-regulated proteins such as conglutinin precursor, modified bovine fibrinogen and IgG1, and 6 spots were down-regulated proteins such as hemoglobin, complement component 3, bovine fibrinogen and IgG2a three spots were not identified. The identified proteins demonstrate that early pregnant bovine serum may have several pregnancy-specific proteins, and these could be a valuable information for the development of pregnancy-diagnostic markers in early pregnancy bovine serum. PMID:25925056

  11. Analysis of Soluble Proteins in Natural Cordyceps sinensis from Different Producing Areas by Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis and Two-dimensional Electrophoresis.

    Science.gov (United States)

    Li, Chun-Hong; Zuo, Hua-Li; Zhang, Qian; Wang, Feng-Qin; Hu, Yuan-Jia; Qian, Zheng-Ming; Li, Wen-Jia; Xia, Zhi-Ning; Yang, Feng-Qing

    2017-01-01

    As one of the bioactive components in Cordyceps sinensis (CS), proteins were rarely used as index components to study the correlation between the protein components and producing areas of natural CS. Protein components of 26 natural CS samples produced in Qinghai, Tibet, and Sichuan provinces were analyzed and compared to investigate the relationship among 26 different producing areas. Proteins from 26 different producing areas were extracted by Tris-HCl buffer with Triton X-100, and separated using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and two-dimensional electrophoresis (2-DE). The SDS-PAGE results indicated that the number of protein bands and optical density curves of proteins in 26 CS samples was a bit different. However, the 2-DE results showed that the numbers and abundance of protein spots in protein profiles of 26 samples were obviously different and showed certain association with producing areas. Based on the expression values of matched protein spots, 26 batches of CS samples can be divided into two main categories (Tibet and Qinghai) by hierarchical cluster analysis. The number of protein bands and optical density curves of proteins in 26 Cordyceps sinensis samples were a bit different on the sodium dodecyl sulfate-polyacrylamide gel electrophoresis protein profilesNumbers and abundance of protein spots in protein profiles of 26 samples were obvious different on two-dimensional electrophoresis mapsTwenty-six different producing areas of natural Cordyceps sinensis samples were divided into two main categories (Tibet and Qinghai) by Hierarchical cluster analysis based on the values of matched protein spots. Abbreviations Used: SDS-PAGE: Sodium dodecyl sulfate polyacrylamide gel electrophoresis, 2-DE: Two-dimensional electrophoresis, Cordyceps sinensis: CS, TCMs: Traditional Chinese medicines.

  12. FireStem2D--a two-dimensional heat transfer model for simulating tree stem injury in fires.

    Directory of Open Access Journals (Sweden)

    Efthalia K Chatziefstratiou

    Full Text Available FireStem2D, a software tool for predicting tree stem heating and injury in forest fires, is a physically-based, two-dimensional model of stem thermodynamics that results from heating at the bark surface. It builds on an earlier one-dimensional model (FireStem and provides improved capabilities for predicting fire-induced mortality and injury before a fire occurs by resolving stem moisture loss, temperatures through the stem, degree of bark charring, and necrotic depth around the stem. We present the results of numerical parameterization and model evaluation experiments for FireStem2D that simulate laboratory stem-heating experiments of 52 tree sections from 25 trees. We also conducted a set of virtual sensitivity analysis experiments to test the effects of unevenness of heating around the stem and with aboveground height using data from two studies: a low-intensity surface fire and a more intense crown fire. The model allows for improved understanding and prediction of the effects of wildland fire on injury and mortality of trees of different species and sizes.

  13. Changes in muscle protein composition induced by disuse atrophy - Analysis by two-dimensional electrophoresis

    Science.gov (United States)

    Ellis, S.; Giometti, C. S.; Riley, D. A.

    1985-01-01

    Using 320 g rats, a two-dimensional electrophoretic analysis of muscle proteins in the soleus and EDL muscles from hindlimbs maintained load-free for 10 days is performed. Statistical analysis of the two-dimensional patterns of control and suspended groups reveals more protein alteration in the soleus muscle, with 25 protein differences, than the EDL muscle, with 9 protein differences, as a result of atrophy. Most of the soleus differences reside in minor components. It is suggested that the EDL may also show alteration in its two-dimensional protein map, even though no significant atrophy occurred in muscle wet weight. It is cautioned that strict interpretation of data must take into account possible endocrine perturbations.

  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. Cytokine- or chemically derived nitric oxide alters the expression of proteins detected by two-dimensional gel electrophoresis in neonatal rat islets of Langerhans.

    Science.gov (United States)

    John, N E; Andersen, H U; Fey, S J; Larsen, P M; Roepstorff, P; Larsen, M R; Pociot, F; Karlsen, A E; Nerup, J; Green, I C; Mandrup-Poulsen, T

    2000-11-01

    Interleukin-1beta (IL-1beta) treatment of neonatal rat islets for 24 h induces changes in the expression of 105 of 2,200 proteins, as determined previously by two-dimensional (2D) gel electrophoresis. Nitric oxide (NO) has been implicated as one of the mediators of IL-1beta effects in insulin-containing cell lines and rat islets. The aims of this study were 1) to determine the involvement of NO in IL-1beta-induced alterations in protein expression and 2) to investigate the effects of chemically generated NO on protein expression by 2D gel electrophoresis of neonatal rat islet samples. IL-1beta-induced NO production was prevented by incubation of islets in arginine-free medium supplemented with the arginine analog NG-nitro-L-arginine. [35S]methionine-labeled islet proteins were separated using 2D gel electrophoresis and analyzed using the BioImage computer program. Analysis revealed that the expression levels of 23 protein spots of the 105 protein spots, altered by prior treatment with IL-1beta (60 U/ml) alone, were significantly affected (P < 0.01 [n = 4] and P < 0.05 [n = 19]) when NO production was prevented. The effects of chemically generated NO were investigated by exposing islets to the NO donor GSNO (100 micromol/l) for 24 h before labeling with [35S]methionine and 2D gel electrophoresis. Computer-based analysis identified alterations in the expression of 19 of a total of 1,600 detectable proteins in GSNO-treated islets (P < 0.01). We conclude 1) that the expression of up to 42 proteins is altered by cytokine-induced or chemically generated NO in the precise experimental conditions chosen and 2) that the majority of proteins altered by prior treatment with IL-1beta may be the result of NO-independent IL-1beta-mediated regulation of gene expression. This study demonstrates that the combination of 2D gel electrophoresis and mass spectrometry is a powerful tool in the identification of beta-cell proteins involved in the response to toxic mediators.

  16. 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.

  17. 2D electrophoresis-based expression proteomics: a microbiologist's perspective.

    Science.gov (United States)

    Sá-Correia, Isabel; Teixeira, Miguel C

    2010-12-01

    Quantitative proteomics based on 2D electrophoresis (2-DE) coupled with peptide mass fingerprinting is still one of the most widely used quantitative proteomics approaches in microbiology research. Our view on the exploitation of this global expression analysis technique and its contribution and potential to push forward the field of molecular microbial physiology towards a molecular systems microbiology perspective is discussed in this article. The advances registered in 2-DE-based quantitative proteomic analysis leading to increased protein resolution, sensitivity and accuracy, and the promising use of 2-DE to gain insights into post-translational modifications at a proteome-wide level (considering all the proteins/protein forms expressed by the genome) are focused on. Given the progress made in this field, it is foreseen that the 2-DE-based approach to quantitative proteomics will continue to be a fundamental tool for microbiologists working at a genome-wide scale. Guidelines are also provided for the exploitation of expression proteomics data, based on useful computational tools, and for the integration of these data with other genome-wide expression information. The advantages and limitations of a complete 2-DE-based expression proteomics analysis, envisaging the quantification of the global changes occurring in the proteome of a given cell depending on environmental or genetic manipulations, are discussed from the microbiologist's perspective. Particular focus is given to the emerging field of toxicoproteomics, a new systems toxicity approach that offers a powerful tool to directly monitor the earliest stages of the toxicological response by identifying critical proteins and pathways that are affected by, and respond to, a chemical stress. The experimental design and the bioinformatics analysis of data used in our laboratory to gain mechanistic insights through expression proteomics into the responses of the eukaryotic model Saccharomyces cerevisiae or of

  18. 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.

  19. 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.

  20. Proteins of human urine. II. Identification by two-dimensional electrophoresis of a new candidate marker for prostatic cancer

    Energy Technology Data Exchange (ETDEWEB)

    Edwards, J.J. (Argonne National Lab., IL); Anderson, N.G.; Tollaksen, S.L.; von Eschenbach, A.C.; Guevara, J. Jr.

    1982-01-01

    A protein series common to the urine and prostatic tissue of 16 of 17 patients with prostatic adenocarcinoma has been identified by high-resolution two-dimensional gel electrophoresis. These proteins, designated PCA-1, have a relative molecular mass in sodium dodecyl sulfate of about 40,000. Analyses of urines from eight age-matched controls, seven patients with other types of urogenital malignancies, two patients with benign prostatic hyperplasia, and five patients with malignancies not associated with the urogenital system failed to show PCA-1 in the patterns. These preliminary findings suggest that this protein should be systematically investigated as a candidate marker for prostatic adenocarcinoma in man.

  1. WSJointInv2D-MT-DCR: An efficient joint two-dimensional magnetotelluric and direct current resistivity inversion

    Science.gov (United States)

    Amatyakul, Puwis; Vachiratienchai, Chatchai; Siripunvaraporn, Weerachai

    2017-05-01

    An efficient joint two-dimensional direct current resistivity (DCR) and magnetotelluric (MT) inversion, referred to as WSJointInv2D-MT-DCR, was developed with FORTRAN 95 based on the data space Occam's inversion algorithm. Our joint inversion software can be used to invert just the MT data or the DCR data, or invert both data sets simultaneously to get the electrical resistivity structures. Since both MT and DCR surveys yield the same resistivity structures, the two data types enhance each other leading to a better interpretation. Two synthetic and a real field survey are used here to demonstrate that the joint DCR and MT surveys can help constrain each other to reduce the ambiguities occurring when inverting the DCR or MT alone. The DCR data increases the lateral resolution of the near surface structures while the MT data reveals the deeper structures. When the MT apparent resistivity suffers from the static shift, the DCR apparent resistivity can serve as a replacement for the estimation of the static shift factor using the joint inversion. In addition, we also used these examples to show the efficiency of our joint inversion code. With the availability of our new joint inversion software, we expect the number of joint DCR and MT surveys to increase in the future.

  2. Two Dimensional Electrophoresis of Proteins from Cultures of Erysiphe graminis f.sp. hordei

    DEFF Research Database (Denmark)

    Torp, J.; Andersen, Brian

    1982-01-01

    Conidial proteins from barley powdery mildew, Erysiphe graminis f. sp. hordei, were separated by 2-dimensional electrophoresis in polyacrylamide slab gels. Isoelectric focusing was used in the first dimension and separation according to molecular weight in a gel containing sodium dodecyl sulphate...

  3. [THE USE OF THE COMMERCIAL APPARATUS DUAL GEL MODULE FOR THE TWO-DIMENSIONAL POLYACRYLAMIDE GEL ELECTROPHORESIS].

    Science.gov (United States)

    Evteeva, I N; Starkova, T Yu; Artemov, A V; Barlev, N A

    2015-01-01

    Two-dimensional gel electrophoresis, continues to be one of the fundamental methods to study the biological protein diversity. This method described by O'Farrell in 1975 includes two following steps: isoelectric focusing in the first dimension and polyacrylamide gel electrophoretic fractionation of proteins according to their molecular weight in the second dimension. In this manuscript we described several technical parameters of the commercial apparatus Dual Gel Module for the gel electrophoresis by means of which it is possible to accomplish the electrophoretic protein fractionation in both dimensions. The distribution of the highly purified commercial proteins used as molecular standards in the detection system of the apparatus Dual Gel Module was identical to the commercial strips of the device GE Healthcare, USA.

  4. Simultaneous immobilization of dehydrogenases on polyvinylidene difluoride resin after separation by non-denaturing two-dimensional electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Shimazaki, Youji [Graduate School of Science and Engineering (Science Section) and Venture Business Laboratory, Ehime University, Bunkyo-cho 2-5, Matsuyama City 790-8577 (Japan)], E-mail: yoji@dpc.ehime-u.ac.jp; Kadota, Mariko [Faculty of Science, Ehime University, Matsuyama (Japan)

    2008-06-16

    We detected mouse liver malate, sorbitol and aldehyde dehydrogenases by negative staining, analysis of malate and sorbitol dehydrogenase activities using each substrate, and electron transfers including nicotinamide adenine dinucleotide (NAD) and nitroblue tetrazolium in non-denaturing two-dimensional electrophoresis (2-DE) gel. Dehydrogenases were also identified by electrospray ionization tandem mass spectrometry (ESI-MS/MS) after 2-DE separation and protein detection by negative staining. Spots of dehydrogenases separated by 2-DE were excised, and simultaneously transferred and immobilized on polyvinylidene difuoride (PVDF) resin by electrophoresis. The dehydrogenase activities remained intact after immobilization. In conclusion, resin-immobilized dehydrogenases can be simultaneously obtained after separation by non-denaturing 2-DE, detection by negative staining and transferring to resins.

  5. 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.

  6. 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.

  7. 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.

  8. User's Guide for ECAP2D: an Euler Unsteady Aerodynamic and Aeroelastic Analysis Program for Two Dimensional Oscillating Cascades, Version 1.0

    Science.gov (United States)

    Reddy, T. S. R.

    1995-01-01

    This guide describes the input data required for using ECAP2D (Euler Cascade Aeroelastic Program-Two Dimensional). ECAP2D can be used for steady or unsteady aerodynamic and aeroelastic analysis of two dimensional cascades. Euler equations are used to obtain aerodynamic forces. The structural dynamic equations are written for a rigid typical section undergoing pitching (torsion) and plunging (bending) motion. The solution methods include harmonic oscillation method, influence coefficient method, pulse response method, and time integration method. For harmonic oscillation method, example inputs and outputs are provided for pitching motion and plunging motion. For the rest of the methods, input and output for pitching motion only are given.

  9. Validation of a prefractionation method followed by two-dimensional electrophoresis – Applied to cerebrospinal fluid proteins from frontotemporal dementia patients

    Directory of Open Access Journals (Sweden)

    Sjögren Magnus

    2004-11-01

    Full Text Available Abstract Background The aim of this study was firstly, to improve and validate a cerebrospinal fluid (CSF prefractionation method followed by two-dimensional electrophoresis (2-DE and secondly, using this strategy to investigate differences between the CSF proteome of frontotemporal dementia (FTD patients and controls. From each subject three ml of CSF was prefractionated using liquid phase isoelectric focusing prior to 2-DE. Results With respect to protein recovery and purification potential, ethanol precipitation of the prefractionated CSF sample was found superior, after testing several sample preparation methods. The reproducibility of prefractionated CSF analyzed on 2-D gels was comparable to direct 2-DE analysis of CSF. The protein spots on the prefractionated 2-D gels had an increased intensity, indicating a higher protein concentration, compared to direct 2-D gels. Prefractionated 2-DE analysis of FTD and control CSF showed that 26 protein spots were changed at least two fold. Using mass spectrometry, 13 of these protein spots were identified, including retinol-binding protein, Zn-α-2-glycoprotein, proapolipoproteinA1, β-2-microglobulin, transthyretin, albumin and alloalbumin. Conclusion The results suggest that the prefractionated 2-DE method can be useful for enrichment of CSF proteins and may provide a new tool to investigate the pathology of neurodegenerative diseases. This study confirmed reduced levels of retinol-binding protein and revealed some new biomarker candidates for FTD.

  10. Analysis of Sperm Membrane Protein Relevant to Antisperm Antibody by Two-Dimensional Gel Electrophoresis and Western Blotting

    Institute of Scientific and Technical Information of China (English)

    Hao-fei WANG; Zhu-qiong XIANG; Yi-xing WANG

    2003-01-01

    Objective To identify the sperm membrane proteins that are associated with antisperm antibodyMethods Using antisperm antibody positive serum through unidimensional polyacrylamide gel electrophoresis and 2-dimensional gel electrophoresis followed by Western blot analysis to determine the molecular weights (MW) and isoelectric points (pI) of sperm membrane proteins that are associated with antisperm antibody.Results Eight kinds of MW with more than ten sperm membrane proteins can be recognized by antisperm antibody positive serum, of which the MWs and pI were 23 kD, 31 kD, 32 kD, 34 kD, 41 kD, 51 kD, 60 kD, 78 kD and 5.3, 5.5,5.7, 5.0, 5.3, 5.8, 6.0, 5.5~6.2, 4.6,5.1,5.5~5.8 respectively. The identification ratios of the sperm membrane proteins on 78 kD (60.7%), 60 kD (71.4%), 51 kD (14.9%) and 23 kD (14.29%) were higher.Conclusion The sperm membrane proteins with MW of 78 kD, 60 kD, 51 kD and 23 kD were associated with antisperm antibody and immunological infertility. Two-dimensional gel electrophoresis and Western blotting can precisely identify the sperm membrane proteins that are associated with antisperm antibody.

  11. Detection of low-molecular weight allergens resolved on two-dimensional electrophoresis with acid-urea polyacrylamide gel.

    Science.gov (United States)

    Kitta, Kazumi; Ohnishi-Kameyama, Mayumi; Moriyama, Tatsuya; Ogawa, Tadashi; Kawamoto, Shinichi

    2006-04-15

    Two-dimensional electrophoresis with immobilized pH gradient (IPG) followed by acetic acid/urea-polyacrylamide gel electrophoresis (AU-PAGE) was developed for the detection of low-molecular weight food allergens. Wheat proteins were used to test the applicability of AU-PAGE for the analysis of food allergens. Isoelectric focusing (IEF) for first dimension was performed with IPG pH 3-10. AU-PAGE was performed as a second-dimensional electrophoresis and high resolution was obtained, especially for proteins below 15 kDa. For immunodetection, the proteins resolved on AU gel were transferred to a polyvinylidene difluoride membrane. The assembly of semidry electroblotting for AU gel was set reversed as for sodium dodecyl sulfate (SDS)-PAGE gel. The electroblotted membrane was immunolabeled with serum from a radio-allergosorbent test-positive individual for wheat to identify allergenic proteins. Protein spots strongly recognized by the patient's serum were chosen for further analysis. Mass spectrometry analysis revealed that these proteins were alpha-amylase/trypsin inhibitors and lipid transfer protein. The system developed in this study was shown to be useful as a standard protocol for the separation of low-molecular weight proteins. Moreover, the IPG strips on which IEF was performed could be used either for SDS-PAGE or AU-PAGE by only changing equilibrating conditions, allowing for a wide range of allergen analysis.

  12. An innovative method for quality control of conjugated Haemophilus influenzae vaccines: A short review of two-dimensional nanoparticle electrophoresis.

    Science.gov (United States)

    Tietz, Dietmar

    2009-12-25

    This article provides an overview of a 2D agarose electrophoretic procedure for the characterization of semi-synthetic Haemophilus influenzae type b meningitis vaccines that were prepared for the immunization of small children. The analysis of such vaccines has been particularly challenging because the vaccine particles (i) are highly negatively charged, (ii) are as large as or even larger than intact viruses, and (iii) have a continuous (polydisperse) size distribution because of randomizing steps in the vaccine production (sonification and crosslinking). As a result of these characteristics, 1D electrophoresis of the vaccines produced smears without discernable peaks, but with a second dimension of separation a characteristic vaccine fingerprint was obtained. Whereas O'Farrell gels can accomplish a 2D separation according to size and charge for samples with protein-sized particles, nondenaturing 2D agarose electrophoresis achieves a similar result for much larger virus-sized particles. The separation principle, however, is different. Even though the 2D electrophoretic method was developed from 1983 to 1995, it remains a promising tool for vaccine quality control and for predicting vaccine effectiveness. Modern technology makes the analysis significantly more practical and affordable than it was more than 10 years ago, and the method is applicable to a variety of conjugated vaccines and complex mixtures of virus-sized particles.

  13. Development in electrophoresis: instrumentation for two-dimensional gel electrophoresis of protein separation and application of capillary electrophoresis in micro-bioanalysis

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Aoshuang [Iowa State Univ., Ames, IA (United States)

    2008-01-01

    This dissertation begins with a general introduction of topics related to this work. The following chapters contain three scientific manuscripts, each presented in a separate chapter with accompanying tables, figures, and literature citations. The final chapter summarizes the work and provides some prospective on this work. This introduction starts with a brief treatment of the basic principles of electrophoresis separation, followed by a discussion of gel electrophoresis and particularly polyacrylamide gel electrophoresis for protein separation, a summary of common capillary electrophoresis separation modes, and a brief treatment of micro-bioanalysis application of capillary electrophoresis, and ends with an overview of protein conformation and dynamics.

  14. The Response of Rice Root to Time Course Water Deficit Stress-Two Dimensional Electrophoresis Approach

    Directory of Open Access Journals (Sweden)

    Mahmood Toorchi

    2015-11-01

    Full Text Available Rice (Oryza sativa L. is the staple food of more than half of the population worldwide. Water deficit stress is one of the harsh limiting factors for successful production of crops. Rice during its growing period comes a cross different environmental hazards like drought stress. Recent advance in molecular physiology are promising for more progress in increasing rice yield by identification of novel candidate proteins for drought tolerance. To investigate the effect of water deficit on rice root protein expression pattern, an experiment was conducted in completely randomize design with four replications. With holding water for 24, 36 and 48 hours along with control constituted the experimental treatments. The experiment was conducted in growth chamber under controlled condition and root samples, after stress imposition, were harvested for two-dimensional electrophorese (2-DE. Proteome analysis of root tissue by 2-DE indicated that out of 135 protein spots diagnosed by Coomassie blue staining, 14 spots showed significant expression change under water deficit condition, seven of them at 1% and the other seven at 5% probability levels. Differentially changed proteins were taken into account for search in data bank using isoelectric point and molecular weight to identify the most probable responsive proteins. Up- regulation of ferredoxin oxidoreductase at first 24 hour after applying stress indicates the main role of this protein in reducing water deficit stress effects. On the other hand ribosomal proteins, GAP-3 and ATP synthase were down regulated under water deficit stress. Fructose 1,6-bisphosphate aldolase, glucose- 6-phosphate dehydrogenase and chitinase down regulated up to 36 h of stress imposition but, were later up- regulated by prolonging stress up to 48 h. It could be inferred the plant tries to decrease the effect of oxidative stress.

  15. Proteomic analysis of Chelidonium majus milky sap using two-dimensional gel electrophoresis and tandem mass spectrometry.

    Science.gov (United States)

    Nawrot, Robert; Kalinowski, Andrzej; Gozdzicka-Jozefiak, Anna

    2007-06-01

    Milky sap, a milky-like orange fluid, isolated from the Greater Celandine (Chelidonium majus L.), family Papaveraceae, serves as a rich source of various biologically active substances such as alkaloids, several flavonoids, phenolic acids and proteins. The objective of this study was to separate Ch. majus milky sap extract proteins using two-dimensional gel electrophoresis (2-DE) to demonstrate for the first time the protein composition in the sap and to identify them using liquid chromatography-tandem mass spectrometry analysis (LC-ESI-MS/MS). It was possible to identify 21 proteins, which comprise disease/defence-related, signalling, Krebs cycle, nucleic acid binding and other proteins. The majority of the identified proteins can be linked to direct and indirect stress and defence reactions, e.g. against different pathogens. The specific protein composition of the milky sap suggests an important role of these proteins for the whole plant physiology and development.

  16. [Development of a droplet-interfaced high performance liquid chromatography-capillary electrophoresis two dimensional separation platform].

    Science.gov (United States)

    Ye, Linquan; Wu, Qingshi; Dai, Simin; Xiao, Zhiliang; Zhang, Bo

    2011-09-01

    Proteomics demands high resolution multidimensional separation techniques due to its extremely high complexity. Droplet microfluidics provides a series of unique advantages in manipulating micro and nanolitre samples, such as micro-volume operation, limited diffusion and none cross-contaminating, therefore has the potential to be an ideal interface strategy for multidimensional separation. Using the microchips of different structures, functions such as "droplet generation" and "oil depletion" can be realized. Based on these functions, samples can be transferred from continuous flow to segmented flow and then back to continuous flow. In this way, different separation modes can be combined. In this study, droplet technology was utilized as a novel interface strategy in combining high performance liquid chromatography (HPLC) and capillary electrophoresis (CE). Using tryptic peptides mixture as a sample, this two dimensional HPLC-CE system provided high resolution separation with a peak capacity over 3000. This proof-of-principle study has demonstrated the usefulness of droplet interface technology in multidimensional separation.

  17. Evaluation of Protein Extraction Methods for Vitis vinifera Leaf and Root Proteome Analysis by Two-Dimensional Electrophoresis

    Institute of Scientific and Technical Information of China (English)

    Neila Jellouli; Asma Ben Salem; Abdelwahed Ghorbel; Hatem Ben Jouira

    2010-01-01

    An efficient protein extraction method is crucial to ensure successful separation by two-dimensional electrophoresis(2-DE)for recalcitrant plant species, in particular for grapevine(Vitis vinifera L.). Trichloroacetic acid-acetone(TCA-acetone)and phenol extraction methods were evaluated for proteome analysis of leaves and roots from the Tunisian cultivar 'Razegui'. The phenol-based protocol proved to give a higher protein yield,a greater spot resolution, and a minimal streaking on 2-DE gels for both leaf and root tissues compared with the TCA-based protocol. Furthermore, the highest numbers of detected proteins on 2-DE gels were observed using the phenol extraction from leaves and roots as compared with TCA-acetone extraction.

  18. 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.

  19. Proteomic study of malignant pleural mesothelioma by laser microdissection and two-dimensional difference gel electrophoresis identified cathepsin D as a novel candidate for a differential diagnosis biomarker.

    Science.gov (United States)

    Hosako, Mutsumi; Muto, Taika; Nakamura, Yukiko; Tsuta, Koji; Tochigi, Naobumi; Tsuda, Hitoshi; Asamura, Hisao; Tomonaga, Takeshi; Kawai, Akira; Kondo, Tadashi

    2012-01-04

    To investigate the proteomic background of malignancies of the pleura, we examined and compared the proteomic profile of malignant pleural mesothelioma (MPM)(10 cases), lung adenocarcinoma (11 cases), squamous cell carcinoma of the lung (13 cases), pleomorphic carcinoma of the lung (3 cases) and synovial sarcoma (6 cases). Cellular proteins were extracted from specific populations of tumor cells recovered by laser microdissection. The extracted proteins were labeled with CyDye DIGE Fluor saturation dyes and subjected to two-dimensional difference gel electrophoresis (2D-DIGE) using a large format electrophoresis device. Among 3875 protein spots observed, the intensity of 332 was significantly different (Wilcoxon p value less than 0.05) and with more than two-fold inter-sample-group average difference between the different histology groups. Among these 332, 282 were annotated by LC-MS/MS and included known biomarker proteins for MPM, such as calretinin, as well as proteins previously uncharacterized in MPM. Tissue microarray immunohistochemistry revealed that the expression of cathepsin D was lower in MPM than in lung adenocarcinoma (15% vs. 44% of cases respectively in immunohistochemistry). In conclusion, we examined the protein expression profile of MPM and other lung malignancies, and identified cathepsin D to distinguish MPM from most popular lung cancer such as lung adenocarcinoma. Copyright © 2011 Elsevier B.V. All rights reserved.

  20. Noise reduction methods applied to two-dimensional correlation spectroscopy (2D-COS) reveal complementary benefits of pre- and post-treatment.

    Science.gov (United States)

    Foist, Rod B; Schulze, H Georg; Ivanov, Andre; Turner, Robin F B

    2011-05-01

    Two-dimensional correlation spectroscopy (2D-COS) is a powerful spectral analysis technique widely used in many fields of spectroscopy because it can reveal spectral information in complex systems that is not readily evident in the original spectral data alone. However, noise may severely distort the information and thus limit the technique's usefulness. Consequently, noise reduction is often performed before implementing 2D-COS. In general, this is implemented using one-dimensional (1D) methods applied to the individual input spectra, but, because 2D-COS is based on sets of successive spectra and produces 2D outputs, there is also scope for the utilization of 2D noise-reduction methods. Furthermore, 2D noise reduction can be applied either to the original set of spectra before performing 2D-COS ("pretreatment") or on the 2D-COS output ("post-treatment"). Very little work has been done on post-treatment; hence, the relative advantages of these two approaches are unclear. In this work we compare the noise-reduction performance on 2D-COS of pretreatment and post-treatment using 1D (wavelets) and 2D algorithms (wavelets, matrix maximum entropy). The 2D methods generally outperformed the 1D method in pretreatment noise reduction. 2D post-treatment in some cases was superior to pretreatment and, unexpectedly, also provided correlation coefficient maps that were similar to 2D correlation spectroscopy maps but with apparent better contrast.

  1. 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.

  2. A comparison of imputation procedures and statistical tests for the analysis of two-dimensional electrophoresis data.

    Science.gov (United States)

    Miecznikowski, Jeffrey C; Damodaran, Senthilkumar; Sellers, Kimberly F; Rabin, Richard A

    2010-12-15

    Numerous gel-based softwares exist to detect protein changes potentially associated with disease. The data, however, are abundant with technical and structural complexities, making statistical analysis a difficult task. A particularly important topic is how the various softwares handle missing data. To date, no one has extensively studied the impact that interpolating missing data has on subsequent analysis of protein spots. This work highlights the existing algorithms for handling missing data in two-dimensional gel analysis and performs a thorough comparison of the various algorithms and statistical tests on simulated and real datasets. For imputation methods, the best results in terms of root mean squared error are obtained using the least squares method of imputation along with the expectation maximization (EM) algorithm approach to estimate missing values with an array covariance structure. The bootstrapped versions of the statistical tests offer the most liberal option for determining protein spot significance while the generalized family wise error rate (gFWER) should be considered for controlling the multiple testing error. In summary, we advocate for a three-step statistical analysis of two-dimensional gel electrophoresis (2-DE) data with a data imputation step, choice of statistical test, and lastly an error control method in light of multiple testing. When determining the choice of statistical test, it is worth considering whether the protein spots will be subjected to mass spectrometry. If this is the case a more liberal test such as the percentile-based bootstrap t can be employed. For error control in electrophoresis experiments, we advocate that gFWER be controlled for multiple testing rather than the false discovery rate.

  3. A comparison of imputation procedures and statistical tests for the analysis of two-dimensional electrophoresis data

    Directory of Open Access Journals (Sweden)

    Sellers Kimberly F

    2010-12-01

    Full Text Available Abstract Background Numerous gel-based softwares exist to detect protein changes potentially associated with disease. The data, however, are abundant with technical and structural complexities, making statistical analysis a difficult task. A particularly important topic is how the various softwares handle missing data. To date, no one has extensively studied the impact that interpolating missing data has on subsequent analysis of protein spots. Results This work highlights the existing algorithms for handling missing data in two-dimensional gel analysis and performs a thorough comparison of the various algorithms and statistical tests on simulated and real datasets. For imputation methods, the best results in terms of root mean squared error are obtained using the least squares method of imputation along with the expectation maximization (EM algorithm approach to estimate missing values with an array covariance structure. The bootstrapped versions of the statistical tests offer the most liberal option for determining protein spot significance while the generalized family wise error rate (gFWER should be considered for controlling the multiple testing error. Conclusions In summary, we advocate for a three-step statistical analysis of two-dimensional gel electrophoresis (2-DE data with a data imputation step, choice of statistical test, and lastly an error control method in light of multiple testing. When determining the choice of statistical test, it is worth considering whether the protein spots will be subjected to mass spectrometry. If this is the case a more liberal test such as the percentile-based bootstrap t can be employed. For error control in electrophoresis experiments, we advocate that gFWER be controlled for multiple testing rather than the false discovery rate.

  4. 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…

  5. 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…

  6. Two-dimensional capillary electrophoresis: capillary isoelectric focusing and capillary zone electrophoresis with laser-induced fluorescence detection.

    Science.gov (United States)

    Dickerson, Jane A; Ramsay, Lauren M; Dada, Oluwatosin O; Cermak, Nathan; Dovichi, Norman J

    2010-08-01

    CIEF and CZE are coupled with LIF detection to create an ultrasensitive 2-D separation method for proteins. In this method, two capillaries are joined through a buffer-filled interface. Separate power supplies control the potential at the injection end of the first capillary and at the interface; the detector is held at ground potential. Proteins are labeled with the fluorogenic reagent Chromeo P503, which preserves the isoelectric point of the labeled protein. The labeled proteins were mixed with ampholytes and injected into the first-dimension capillary. A focusing step was performed with the injection end of the capillary at high pH and the interface at low pH. To mobilize components, the interface was filled with a high pH buffer, which was compatible with the second-dimension separation. A fraction was transferred to the second-dimension capillary for separation. The process of fraction transfer and second dimension separation was repeated two dozen times. The separation produced a spot capacity of 125.

  7. Tear film proteins deposited on high water content contact lenses identified with two-dimensional gel electrophoresis and mass spectrometry.

    Science.gov (United States)

    Nielsen, Kim; Vorum, Henrik; Ehlers, Niels; Aagaard, Nicolaj; Hjortdal, Jesper; Honoré, Bent

    2015-11-01

    Tear film proteins adhere to the surface of contact lenses (CLs). While the proteins in the tears have been extensively studied with various proteomic techniques, adhered proteins to CLs are less studied. In this pilot study, we have separated proteins with 2D gel electrophoresis prior to the conventional mass spectrometry (MS) in order to analyse the deposited proteins on hydrogel CLs from myopic patients. pHEMA and PVA hydrogel CLs worn by 3 patients for different time lengths were analysed. After wear, the CLs were frozen at -20°C. Proteins were extracted in lysis buffer, separated on 12% polyacrylamide gels and silver-stained. Protein spots were excised and identified with liquid chromatography - tandem MS. Deposited proteins were extracted with a yield of 26-66 μg and separated by 2D gel electrophoresis. The silver-stained gels showed similar protein patterns independent of the patient, hydrogel type and wear time. Seventy-two spots were analysed with MS, representing at least 12 different tear film proteins or protein fragments. Deposited tear film proteins from a single set of CLs worn for 1 day can successfully be analysed first with 2D gel electrophoresis and subsequently with MS, thus making examination of individual patients possible. The protein composition appeared homogeneous between the test persons which is a necessity for additional comparison analysis. The molecular masses of the identified proteins indicate that protein degradation occurs only as a minor event. Myopic patients were investigated in this pilot study, but the combined techniques can easily be applied to other eye diseases. © 2015 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

  8. Comparative Proteomic Analysis of B. henselae Houston and B. henselae Marseille by Two-dimensional Gel Electrophoresis

    Institute of Scientific and Technical Information of China (English)

    SU-QING ZHAO; YAN-FEI CAI; ZHEN-YU ZHU

    2005-01-01

    Objective To compare the protein difference between B. henselae Houston and B. henselae Marseille by two-dimensional gel electrophoresis. Method Protein samples were prepared by vorterx, ultrasonic treatment, and centrifugation. Protein concentrations were determined by Bradford method. Protein difference was compared by the first IEF and the second SDS-polyacrylamide gel electrophoresis. Results Protein concentrations in samples of Bartonella henselae Houston and Bartonella henselae Marseille were 2.117 μg/μL and 2.200 μg/μL respectively. Sample protein of 40 μg for IPG strips loading was perfect. The results of 2-DE in pH 4 to 7 IPG strips showed that the total protein spots of Bartonella henselae Houston and Bartonella henselae Marseille were 375 and 379 respectively, 95% of the spots were the same between the two strains of Bartonella henselae. Conclusion The procedure of 2-DE may prove successful for the proteomic analysis of Bartonella henselae. Bartonella henselae Houston and Bartonella henselae Marseille are different genotypes.

  9. Cu2+-assisted two dimensional charge-mass double focusing gel electrophoresis and mass spectrometric analysis of histone variants.

    Science.gov (United States)

    Zhang, Wenyang; Tang, Xuemei; Ding, Mengjie; Zhong, Hongying

    2014-12-10

    Abundant isoforms and dynamic posttranslational modifications cause the separation and identification of histone variants to be experimentally challenging. To meet this need, we employ two-dimensional electrophoretic gel separation followed by mass spectrometric detection which takes advantage of the chelation of Cu(2+) with amino acid residues exposed on the surfaces of the histone proteins. Acid-extracted rat liver histones were first mixed with CuSO4 solution and then separated in one dimension with triton-acid-urea (TAU) gel electrophoresis and in a second dimension using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The separations result from both the changes in charge and mass upon Cu(2+) chelation. Identities of each separated gel bands were obtained by using matrix-assisted laser desorption-ionization mass spectrometry (MALDI-MS). It was found that the migration of H3 histone isoforms of rat liver is markedly affected by the use of Cu(2+) ions. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. Chromatofocusing fractionation and two-dimensional difference gel electrophoresis for low abundance serum proteins.

    Science.gov (United States)

    Qin, Shuzhen; Ferdinand, Angeline S; Richie, Jerome P; O'Leary, Michael P; Mok, Samuel C; Liu, Brian C-S

    2005-08-01

    The technical challenge to analysis of the serum proteome is that the serum proteins are present at unequal concentrations. A few are so dominant, such as serum albumin and immunoglobulins, that they mask detection of other proteins. Because of these high abundance proteins, current technologies, while theoretically capable of analyzing protein amounts spanning four orders of magnitude, are only able to analyze proteins ranging over two orders of magnitude and cannot analyze the lower abundance proteins that may be the next biomarkers and drug targets. To facilitate the identification of low abundance proteins, we fractionated serum samples from patients with prostate cancer and patients with benign prostate hyperplasia using anion displacement liquid chromatofocusing chromatography, which separates proteins by a pH gradient and a positively charged column. Differential expression of proteins from fractions was then determined and identified by IEF gels and 2-D DIGE. Results demonstrate improved resolution of proteins within the chosen pH gradient when compared to the unfractionated samples. Several proteins that were differentially expressed in serum from patients with prostate cancer were identified in the fractionated serum. Three of these proteins, squamous cell carcinoma antigen 1 (SCCA1), calgranulin B, and haptoglobin-related protein, are present in the serum at levels below the classical protein level of mg/mL. SCCA1 is normally expressed in serum at ng/mL levels, and calgranulin B is an intracellular protein. Our results demonstrate that the use of anion displacement liquid chromatofocusing chromatography may reduce the complexity of the serum proteome by separating proteins into distinct pH ranges, and facilitate the identification of low abundance proteins.

  11. 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.

  12. 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.

  13. Major proteins in normal human lymphocyte subpopulations separated by fluorescence-activated cell sorting and analyzed by two-dimensional gel electrophoresis

    DEFF Research Database (Denmark)

    Madsen, P S; Hokland, M; Ellegaard, J

    1988-01-01

    We have compared the overall patterns of protein synthesis of normal human lymphocyte subpopulations taken from five volunteers using high resolution two-dimensional gel electrophoresis. The lymphocytes were isolated using density gradient centrifugation, labeled with subtype-specific Mo......Abs, and separated to a high degree of homogeneity by FACS into CD4+ helper T cells, CD8+ suppressor T cells, CD20+ B cells, and N901 (NHK-1)+ NK cells. The four lymphocyte subpopulations were labeled with [35S]methionine for 14 hr, solubilized in lysis buffer, and analyzed by two-dimensional gel electrophoresis...

  14. Introducing 2D Materials—a new multidisciplinary journal devoted to all aspects of graphene and related two-dimensional materials

    Science.gov (United States)

    Fal'ko, Vladimir I.

    2014-06-01

    On behalf of the Editorial Board and IOP Publishing, I am pleased to announce the opening of 2D Materials. Research on two-dimensional materials, such as graphene, now involves thousands of researchers worldwide cutting across physics, chemistry, engineering and biology, and extending from fundamental science to novel applications. It is this situation which defines the scope and mission of 2D Materials, a new journal that will serve all sides of this multidisciplinary field by publishing urgent research of the highest quality and impact.

  15. Evaluation of different protein extraction methods for banana (Musa spp.) root proteome analysis by two-dimensional electrophoresis.

    Science.gov (United States)

    Vaganan, M Mayil; Sarumathi, S; Nandakumar, A; Ravi, I; Mustaffa, M M

    2015-02-01

    Four protocols viz., the trichloroacetic acid-acetone (TCA), phenol-ammonium acetate (PAA), phenol/SDS-ammonium acetate (PSA) and trisbase-acetone (TBA) were evaluated with modifications for protein extraction from banana (Grand Naine) roots, considered as recalcitrant tissues for proteomic analysis. The two-dimensional electrophoresis (2-DE) separated proteins were compared based on protein yield, number of resolved proteins, sum of spot quantity, average spot intensity and proteins resolved in 4-7 pI range. The PAA protocol yielded more proteins (0.89 mg/g of tissues) and protein spots (584) in 2-DE gel than TCA and other protocols. Also, the PAA protocol was superior in terms of sum of total spot quantity and average spot intensity than TCA and other protocols, suggesting phenol as extractant and ammonium acetate as precipitant of proteins were the most suitable for banana rooteomics analysis by 2-DE. In addition, 1:3 ratios of root tissue to extraction buffer and overnight protein precipitation were most efficient to obtain maximum protein yield.

  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. Secretomic analysis of large cell lung cancer cell lines using two-dimensional gel electrophoresis coupled to mass spectrometry

    Directory of Open Access Journals (Sweden)

    Zahra Yousefi

    2012-10-01

    Full Text Available

    The secretome of cancer cells is a valuable source of biomarkers that can ultimately reach the serum or other body fluids. Cancer biomarkers can facilitate early diagnosis and monitoring of the disease, contribute to our understanding of tumor biology, and support the development of more efficient therapies. Recently, high-throughput proteomic analysis of the conditioned media of cancer cell lines has shown potential to identify novel biomarkers in cancer. We used two-dimensional gel electrophoresis coupled to liquid chromatography tandem mass spectrometry to identify the secretome of the large cell lung cancer cell lines QU-DB and Mehr-80, which they were established from a Canadian and a Persian patient, respectively. A total of 130 distinct protein species were identified. Of these, 124 were previously found in serum or other body fluids, the membrane compartment or conditioned media of other cancer cell lines. Some of the proteins that we identified, e.g. IL-6, triosephosphate isomerase, PGP9.5, α-enolase, Dickkopf-1, and peroxiredoxin-1 are known putative serum markers for lung cancer, whereas others might be candidate markers for further validation in lung cancer body fluids such as IL-25, stathmin, vimentin, peptidyl-prolyl cis-trans isomerase A, transgelin-2, and chloride intracellular channel protein 4.

  18. The star chart to Ta bladder cancer: an unsophisticated analysis of two-dimensional gel electrophoresis proteome maps.

    Science.gov (United States)

    Røtterud, Ranveig; Malmström, Per-Uno; Wahlqvist, Rolf; Taskén, Kristin A

    2010-03-01

    To explore the use of two-dimensional gel electrophoresis (2DE) for analysing the proteome of clinically relevant tissue samples such as biopsies from transurethral resections of the bladder (TURB), by generating a Ta proteome map, possibly identifying technical or biological artefacts, and searching for biological subgroups associated with clinical data. Biopsies from 23 patients were homogenized and the protein content was separated by 2DE. The gels were silver stained and scanned, and the resulting pictures were analysed for similarities in the spot pattern. A majority of 18 patients displayed a consistent protein expression profile and a Ta proteome map was constructed by averaging the grey value of each pixel in all 18 pictures. Spot detection was performed on a project proteome map (based on all 23 samples) and resulted in 1583 detected spots. 416 of these which were positively detected in all 18 "Ta-map" samples. Three patients displayed a pattern with some marked alterations to the majority profile, possibly artefacts of yet unknown heredity. One patient revealed a protein pattern deemed to constitute a separate group, later revealed as a blinded control from a T4 tumour. Only one sample was sparse in protein spots, probably containing mostly blood owing to inadequate sampling. No biological subgroups associated with clinical data were identified. A Ta proteome map was successfully created from TURB samples. Deviating protein expression profiles were identified, indicating a future potential to reveal biologically relevant subgroups in this or other stages of urothelial cell carcinomas.

  19. Analysis of Male Sterility-Related Proteins of Young Panicle in Rice (Oryza sativa L.) by Two-Dimensional Electrophoresis

    Institute of Scientific and Technical Information of China (English)

    HU Yao-jun; WEI Lei; LIU Shu-nan; YU Jin-hong; DING Yi

    2005-01-01

    For searching out male sterility-related proteins (polypeptides) in rice (Oryza sativa L.), we examined the difference of panicle protein (polypeptides) between hybrid rice (Wujin2A/R168, Wujin5A/R988) and their parents (male-sterile line Wujin2A, Wujin5A, and restorer line R168, R988) at the formation stage of pollen mother cell by two-dimensional electrophoresis (2-DE). The results revealed that the 2-DE polypeptide maps were similar among these experimental materials. A small group of polypeptides were disappeared in 2-DE polypeptide maps of male-sterile line (Wujin2A, Wujin5A) by comparing to restorer line (R168, R988) and the first filial (F1) generation (Wujin2A/R168, Wujin5A/R988). The isoelectric points of these polypeptides were pI 5.8-6.5, molecular weight 42.7×103-66.2×103.

  20. Differentially expressed phosphoproteins in diazoxide-pretreated ventricular myocytes by two-dimensional electrophoresis and mass spectrometry in vitro

    Institute of Scientific and Technical Information of China (English)

    LI Hong; XIAO Ying-bin; GAO Yu-qi; YANG Tian-de

    2006-01-01

    Objective:To analyze and identify differentially expressed phosphoproteins associated with mitochondrial KATP channel opening. Methods: Adult rat ventricular myocytes were isolated, cultured,and identified, and pretreated without or with 100μmol/L diazoxide for 10 min. Phosphoproteins prepared and enriched from the control and diazoxide-pretreated cells were separated by two-dimensional gel electrophoresis (2-DE) followed by sliver staining. The obtained interesting phosphoproteins were further identified by mass spectrometry. Results: Associated with diazoxide preconditioning, the proteins of chaperonin containing TCP-1 and hypothetical protein XP_ 346548 were phosphorylated significantly (P<0. 01), while the 94-kDa glucose-regulated protein, calpactin I heavy chain and ferritin were dephosphorylated markedly (P<0. 01). Conclusion: These findings suggest that cardiomyocytes undergo significant posttranslational modification via phosphorylation in a multitude of proteins in order to respond diazoxide preconditioning, and these phosphorylated protein may mediate the downstream signaling of cardioprotection by mitochondrial KATP channel opening induced by ischemic preconditioning.

  1. 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.

  2. 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.

  3. 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.

  4. Two-dimensional electrophoresis of urinary mucopolysaccharides on cellulose acetate after f-cetylpyridiniumchloride (CPC) precipitation: A method suitable for the routine laboratory

    NARCIS (Netherlands)

    Abeling, N.G.G.M.; Wadman, S.K.; Gennip, A.H. van

    1974-01-01

    A technique for two-dimensional electrophoresis of urinary mucopolysaccharides (MPS) is described. The method allows differentiation of a number of mucopolysaccharidoses and is suitable for application in the routine laboratory. This technique should be used to evaluate urines from patients who

  5. 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...

  6. Effects of interferon gamma on Chlamydia trachomatis serovar A and L2 protein expression investigated by two-dimensional gel electrophoresis

    DEFF Research Database (Denmark)

    Shaw, A; Christiansen, Gunna; Birkelund, Svend

    1999-01-01

    ]methionine and two-dimensional gel electrophoresis with immobilized pH gradients in order to investigate changes in the protein expression of C. trachomatis serovar A and L2 caused by treatment with IFN-gamma. In contrast to what was observed in C. trachomatis L2, our results showed that, in C. trachomatis A, down...

  7. Major proteins in normal human lymphocyte subpopulations separated by fluorescence-activated cell sorting and analyzed by two-dimensional gel electrophoresis

    DEFF Research Database (Denmark)

    Madsen, P S; Hokland, M; Ellegaard, J;

    1988-01-01

    We have compared the overall patterns of protein synthesis of normal human lymphocyte subpopulations taken from five volunteers using high resolution two-dimensional gel electrophoresis. The lymphocytes were isolated using density gradient centrifugation, labeled with subtype-specific MoAbs, and ...

  8. Mapping of Chlamydia trachomatis proteins by immobiline-polyacrylamide two-dimensional electrophoresis: spot identification by N-terminal sequencing and immunoblotting

    DEFF Research Database (Denmark)

    Bini, L; Sanchez-Campillo, M; Santucci, A;

    1996-01-01

    Proteins from purified elementary bodies of Chlamydia trachomatis were separated by two-dimensional gel electrophoresis on nonlinear wide-range immobilized pH gradients in the first dimension and polyacrylamide gradient gels in the second dimension. The maps obtained with this system are highly...

  9. Quality control and stability studies with the monoclonal antibody, trastuzumab: application of 1D- vs. 2D-gel electrophoresis.

    Science.gov (United States)

    Nebija, Dashnor; Noe, Christian R; Urban, Ernst; Lachmann, Bodo

    2014-04-15

    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.

  10. 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

  11. 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.

  12. Efficient method of protein extraction from Theobroma cacao L. roots for two-dimensional gel electrophoresis and mass spectrometry analyses.

    Science.gov (United States)

    Bertolde, F Z; Almeida, A-A F; Silva, F A C; Oliveira, T M; Pirovani, C P

    2014-07-04

    Theobroma cacao is a woody and recalcitrant plant with a very high level of interfering compounds. Standard protocols for protein extraction were proposed for various types of samples, but the presence of interfering compounds in many samples prevented the isolation of proteins suitable for two-dimensional gel electrophoresis (2-DE). An efficient method to extract root proteins for 2-DE was established to overcome these problems. The main features of this protocol are: i) precipitation with trichloroacetic acid/acetone overnight to prepare the acetone dry powder (ADP), ii) several additional steps of sonication in the ADP preparation and extractions with dense sodium dodecyl sulfate and phenol, and iii) adding two stages of phenol extractions. Proteins were extracted from roots using this new protocol (Method B) and a protocol described in the literature for T. cacao leaves and meristems (Method A). Using these methods, we obtained a protein yield of about 0.7 and 2.5 mg per 1.0 g lyophilized root, and a total of 60 and 400 spots could be separated, respectively. Through Method B, it was possible to isolate high-quality protein and a high yield of roots from T. cacao for high-quality 2-DE gels. To demonstrate the quality of the extracted proteins from roots of T. cacao using Method B, several protein spots were cut from the 2-DE gels, analyzed by tandem mass spectrometry, and identified. Method B was further tested on Citrus roots, with a protein yield of about 2.7 mg per 1.0 g lyophilized root and 800 detected spots.

  13. Differential metalloprotease content and activity of three Loxosceles spider venoms revealed using two-dimensional electrophoresis approaches.

    Science.gov (United States)

    Trevisan-Silva, Dilza; Bednaski, Aline Viana; Gremski, Luiza Helena; Chaim, Olga Meiri; Veiga, Silvio Sanches; Senff-Ribeiro, Andrea

    2013-12-15

    Loxosceles bites have been associated with characteristic dermonecrotic lesions with gravitational spreading and systemic manifestations. Venom primarily comprises peptides and protein molecules (5-40 kDa) with multiple biological activities. Although poorly studied, metalloproteases have been identified in venoms of several Loxosceles species, presenting proteolytic effects on extracellular matrix components. The characterization of an Astacin-like protease (LALP) in Loxosceles intermedia venom was the first report of an Astacin family member as a component of animal venom. Recently, these proteases were described as a gene family in L. intermedia, Loxosceles laeta and Loxosceles gaucho. Herein, the whole venom complexity of these three Loxosceles species was analyzed using two-dimensional electrophoresis (2DE). Subproteomes of LALPs were explored through 2DE immunostaining using anti-LALP1 antibodies and 2DE gelatin zymogram. Proteins presented molecular masses ranging from 24 to 29 kDa and the majority of these molecules had basic or neutral isoelectric points (6.89-9.93). Likewise, the measurement of gelatinolytic effects of Loxosceles venom using fluorescein-gelatin showed that the three venoms have distinct proteolytic activities. The metalloprotease fibrinogenolytic activities were also evaluated. All venoms showed fibrinogenolytic activity with different proteolytic effects on Aα and Bβ chains of fibrinogen. The results reported herein suggest that the LALP family is larger than indicated in previously published data and that the complex profile of the gelatinolytic activity reflects their relevance in loxoscelism. Furthermore, our investigation implicates the brown spider venom as a source of Astacin-like proteases for use in loxoscelism studies, cell biology research and biotechnological applications.

  14. Surface plasmon hurdles leading to a strongly localized giant field enhancement on two-dimensional (2D) metallic diffraction gratings.

    Science.gov (United States)

    Brûlé, Yoann; Demésy, Guillaume; Gralak, Boris; Popov, Evgeny

    2015-04-01

    An extensive numerical study of diffraction of a plane monochromatic wave by a single gold cone on a plane gold substrate and by a periodical array of such cones shows formation of curls in the map of the Poynting vector. They result from the interference between the incident wave, the wave reflected by the substrate, and the field scattered by the cone(s). In case of a single cone, when going away from its base along the surface, the main contribution in the scattered field is given by the plasmon surface wave (PSW) excited on the surface. As expected, it has a predominant direction of propagation, determined by the incident wave polarization. Two particular cones with height approximately 1/6 and 1/3 of the wavelength are studied in detail, as they present the strongest absorption and field enhancement when arranged in a periodic array. While the PSW excited by the smaller single cone shows an energy flux globally directed along the substrate surface, we show that curls of the Poynting vector generated with the larger cone touch the diopter surface. At this point, their direction is opposite to the energy flow of the PSW, which is then forced to jump over the vortex regions. Arranging the cones in a two-dimensional subwavelength periodic array (diffraction grating), supporting a specular reflected order only, resonantly strengthens the field intensity at the tip of cones and leads to a field intensity enhancement of the order of 10 000 with respect to the incident wave intensity. The enhanced field is strongly localized on the rounded top of the cones. It is accompanied by a total absorption of the incident light exhibiting large angular tolerances. This strongly localized giant field enhancement can be of much interest in many applications, including fluorescence spectroscopy, label-free biosensing, surface-enhanced Raman scattering (SERS), nonlinear optical effects and photovoltaics.

  15. An algorithm for circular test and improved optical configuration by two-dimensional (2D) laser heterodyne interferometer

    Science.gov (United States)

    Tang, Shanzhi; Yu, Shengrui; Han, Qingfu; Li, Ming; Wang, Zhao

    2016-09-01

    Circular test is an important tactic to assess motion accuracy in many fields especially machine tool and coordinate measuring machine. There are setup errors due to using directly centring of the measuring instrument for both of contact double ball bar and existed non-contact methods. To solve this problem, an algorithm for circular test using function construction based on matrix operation is proposed, which is not only used for the solution of radial deviation (F) but also should be applied to obtain two other evaluation parameters especially circular hysteresis (H). Furthermore, an improved optical configuration with a single laser is presented based on a 2D laser heterodyne interferometer. Compared with the existed non-contact method, it has a more pure homogeneity of the laser sources of 2D displacement sensing for advanced metrology. The algorithm and modeling are both illustrated. And error budget is also achieved. At last, to validate them, test experiments for motion paths are implemented based on a gantry machining center. Contrast test results support the proposal.

  16. Near-infrared (NIR) monitoring of Nylon 6 during quenching studied by projection two-dimensional (2D) correlation spectroscopy

    Science.gov (United States)

    Shinzawa, Hideyuki; Mizukado, Junji

    2016-11-01

    Evolutionary change in supermolecular structure of Nylon 6 during its melt-quenched process was studied by Near-infrared (NIR) spectroscopy. Time-resolved NIR spectra was measured by taking the advantage of high-speed NIR monitoring based on an acousto-optic tunable filter (AOTF). Fine spectral features associated with the variation of crystalline and amorphous structure occurring in relatively short time scale were readily captured. For example, synchronous and asynchronous 2D correlation spectra reveal the initial decrease in the contribution of the NIR band at 1485 nm due to the amorphous structure, predominantly existing in the melt Nylon 6. This is then followed by the emerging contribution of the band intensity at 1535 nm associated with the crystalline structure. Consequently, the results clearly demonstrate a definite advantage of the high-speed NIR monitoring for analyzing fleeting phenomena.

  17. Two Dimensional Electrostrictive Field Effect Transistor (2D-EFET): A sub-60mV/decade Steep Slope Device with High ON current

    Science.gov (United States)

    Das, Saptarshi

    2016-01-01

    This article proposes a disruptive device concept which meets both low power and high performance criterion for post-CMOS computing and at the same time enables aggressive channel length scaling. This device, hereafter refer to as two-dimensional electrostrictive field effect transistor or 2D-EFET, allows sub-60 mV/decade subthreshold swing and considerably higher ON current compared to any state of the art FETs. Additionally, by the virtue of its ultra-thin body nature and electrostatic integrity, the 2D-EFET enjoys scaling beyond 10 nm technology node. The 2D-EFET works on the principle of voltage induced strain transduction. It uses an electrostrictive material as gate oxide which expands in response to an applied gate bias and thereby transduces an out-of-plane stress on the 2D channel material. This stress reduces the inter-layer distance between the consecutive layers of the semiconducting 2D material and dynamically reduces its bandgap to zero i.e. converts it into a semi-metal. Thus the device operates with a large bandgap in the OFF state and a small or zero bandgap in the ON state. As a consequence of this transduction mechanism, internal voltage amplification takes place which results in sub-60 mV/decade subthreshold swing (SS). PMID:27721489

  18. Two Dimensional Electrostrictive Field Effect Transistor (2D-EFET): A sub-60mV/decade Steep Slope Device with High ON current

    Science.gov (United States)

    Das, Saptarshi

    2016-10-01

    This article proposes a disruptive device concept which meets both low power and high performance criterion for post-CMOS computing and at the same time enables aggressive channel length scaling. This device, hereafter refer to as two-dimensional electrostrictive field effect transistor or 2D-EFET, allows sub-60 mV/decade subthreshold swing and considerably higher ON current compared to any state of the art FETs. Additionally, by the virtue of its ultra-thin body nature and electrostatic integrity, the 2D-EFET enjoys scaling beyond 10 nm technology node. The 2D-EFET works on the principle of voltage induced strain transduction. It uses an electrostrictive material as gate oxide which expands in response to an applied gate bias and thereby transduces an out-of-plane stress on the 2D channel material. This stress reduces the inter-layer distance between the consecutive layers of the semiconducting 2D material and dynamically reduces its bandgap to zero i.e. converts it into a semi-metal. Thus the device operates with a large bandgap in the OFF state and a small or zero bandgap in the ON state. As a consequence of this transduction mechanism, internal voltage amplification takes place which results in sub-60 mV/decade subthreshold swing (SS).

  19. Two-dimensional (2D) infrared correlation study of the structural characterization of a surface immobilized polypeptide film stimulated by pH

    Science.gov (United States)

    Chae, Boknam; Son, Seok Ho; Kwak, Young Jun; Jung, Young Mee; Lee, Seung Woo

    2016-11-01

    The pH-induced structural changes to surface immobilized poly (L-glutamic acid) (PLGA) films were examined by Fourier transform infrared (FTIR) spectroscopy and two-dimensional (2D) correlation analysis. Significant spectral changes were observed in the FTIR spectra of the surface immobilized PLGA film between pH 6 and 7. The 2D correlation spectra constructed from the pH-dependent FTIR spectra of the surface immobilized PLGA films revealed the spectral changes induced by the alternations of the protonation state of the carboxylic acid group in the PLGA side chain. When the pH was increased from 6 to 8, weak spectral changes in the secondary structure of the PLGA main chain were induced by deprotonation of the carboxylic acid side group.

  20. Two-dimensional isoelectric focusing OFFGEL and microfluidic lab-on-chip electrophoresis for assessing dissolved proteins in seawater.

    Science.gov (United States)

    García-Otero, Natalia; Peña-Vázquez, Elena; Barciela-Alonso, María Carmen; Bermejo-Barrera, Pilar; Moreda-Piñeiro, Antonio

    2013-06-18

    Dissolved proteins were assessed in surface and deep seawater by two-dimensional isoelectric focusing (IEF) OFFGEL-lab-on-chip (LOC) electrophoresis after tangential flow ultrafiltration followed by centrifugal ultrafiltration (preconcentration factor of 3000). Dissolved protein isolation was performed by treating the ultrafiltrated retentate with cold acetone and also with chloroform as precipitating reagents. The best electrophoretic behavior of the isolated proteins was obtained after protein precipitation with chloroform before different rinsing stages for removing methanol and water interferences. Metals bound to proteins in the different OFFGEL fractions were assessed by inductively coupled plasma-optical emission spectrometry and electrothermal atomic absorption spectrometry, under optimized operating conditions. Experiments regarding stability of the metal-binding proteins [superoxide dismutase (SOD) and alcohol dehydrogenase (ADH) as protein models] showed the integrity of the Zn-binding SOD/ADH under the OFFGEL electrophoretic conditions. However, stability of Cu bound to SOD is not guaranteed. The first electrophoretic dimension (IEF OFFGEL) showed that dissolved proteins in surface seawater exhibit alkaline isoelectric points (pIs of 8.10 and 8.37) and also acid Ips (4.82, 5.13, 5.43, and 5.73), while LOC showed that the isolated proteins exhibit a spread molecular weight range (within 15 - 63 kDa); although, high molecular weights were the most commonly found. Regarding deep seawater, isolated proteins were of acid Ips (from 3.30 to 4.22) and low molecular weight (within the 21-24 kDa range). Elements such as Cd, Cu, Mn, and Ni were mainly associated with dissolved proteins of alkaline pIs in surface seawater, while Zn was mainly associated to proteins of acid pIs. However, only Cu and Mn were found to be bound to dissolved proteins of higher Ips in deep seawater, and the amount of Mn (from 68 to 84 μg L(-1)) was higher than that found in dissolved

  1. Assessment of the red cell proteome of young patients with unexplained hemolytic anemia by two-dimensional differential in-gel electrophoresis (DIGE.

    Directory of Open Access Journals (Sweden)

    Katharina von Löhneysen

    Full Text Available Erythrocyte cytosolic protein expression profiles of children with unexplained hemolytic anemia were compared with profiles of close relatives and controls by two-dimensional differential in-gel electrophoresis (2D-DIGE. The severity of anemia in the patients varied from compensated (i.e., no medical intervention required to chronic transfusion dependence. Common characteristics of all patients included chronic elevation of reticulocyte count and a negative workup for anemia focusing on hemoglobinopathies, morphologic abnormalities that would suggest a membrane defect, immune-mediated red cell destruction, and evaluation of the most common red cell enzyme defects, glucose-6-phosphate dehydrogenase and pyruvate kinase deficiency. Based upon this initial workup and presentation during infancy or early childhood, four patients classified as hereditary nonspherocytic hemolytic anemia (HNSHA of unknown etiology were selected for proteomic analysis. DIGE analysis of red cell cytosolic proteins clearly discriminated each anemic patient from both familial and unrelated controls, revealing both patient-specific and shared patterns of differential protein expression. Changes in expression pattern shared among the four patients were identified in several protein classes including chaperons, cytoskeletal and proteasome proteins. Elevated expression in patient samples of some proteins correlated with high reticulocyte count, likely identifying a subset of proteins that are normally lost during erythroid maturation, including proteins involved in mitochondrial metabolism and protein synthesis. Proteins identified with patient-specific decreased expression included components of the glutathione synthetic pathway, antioxidant pathways, and proteins involved in signal transduction and nucleotide metabolism. Among the more than 200 proteins identified in this study are 21 proteins not previously described as part of the erythrocyte proteome. These results

  2. Linkage analysis by two-dimensional DNA typing

    NARCIS (Netherlands)

    te Meerman, G J; Mullaart, E; van der Meulen, M A; den Daas, J H; Morolli, B; Uitterlinden, A G; Vijg, J

    1993-01-01

    In two-dimensional (2-D) DNA typing, genomic DNA fragments are separated, first according to size by electrophoresis in a neutral polyacrylamide gel and second according to sequence by denaturing gradient gel electrophoresis, followed by hybridization analysis using micro- and minisatellite core pro

  3. Generalized two-dimensional (2D) linear system analysis metrics (GMTF, GDQE) for digital radiography systems including the effect of focal spot, magnification, scatter, and detector characteristics

    Science.gov (United States)

    Kuhls-Gilcrist, Andrew T.; Gupta, Sandesh K.; Bednarek, Daniel R.; Rudin, Stephen

    2010-01-01

    The MTF, NNPS, and DQE are standard linear system metrics used to characterize intrinsic detector performance. To evaluate total system performance for actual clinical conditions, generalized linear system metrics (GMTF, GNNPS and GDQE) that include the effect of the focal spot distribution, scattered radiation, and geometric unsharpness are more meaningful and appropriate. In this study, a two-dimensional (2D) generalized linear system analysis was carried out for a standard flat panel detector (FPD) (194-micron pixel pitch and 600-micron thick CsI) and a newly-developed, high-resolution, micro-angiographic fluoroscope (MAF) (35-micron pixel pitch and 300-micron thick CsI). Realistic clinical parameters and x-ray spectra were used. The 2D detector MTFs were calculated using the new Noise Response method and slanted edge method and 2D focal spot distribution measurements were done using a pin-hole assembly. The scatter fraction, generated for a uniform head equivalent phantom, was measured and the scatter MTF was simulated with a theoretical model. Different magnifications and scatter fractions were used to estimate the 2D GMTF, GNNPS and GDQE for both detectors. Results show spatial non-isotropy for the 2D generalized metrics which provide a quantitative description of the performance of the complete imaging system for both detectors. This generalized analysis demonstrated that the MAF and FPD have similar capabilities at lower spatial frequencies, but that the MAF has superior performance over the FPD at higher frequencies even when considering focal spot blurring and scatter. This 2D generalized performance analysis is a valuable tool to evaluate total system capabilities and to enable optimized design for specific imaging tasks. PMID:21243038

  4. Simultaneous immunoblotting analysis with activity gel electrophoresis and 2-D gel electrophoresis.

    Science.gov (United States)

    Lee, Der-Yen; Chang, Geen-Dong

    2015-01-01

    Diffusion blotting method can couple immunoblotting analysis with another biochemical technique in a single polyacrylamide gel, however, with lower transfer efficiency as compared to the conventional electroblotting method. Thus, with diffusion blotting, protein blots can be obtained from an SDS polyacrylamide gel for zymography assay, from a native polyacrylamide gel for electrophoretic mobility shift assay (EMSA) or from a 2-D polyacrylamide gel for large-scale screening and identification of a protein marker. Thereafter, a particular signal in zymography, electrophoretic mobility shift assay, and 2-dimensional gel can be confirmed or identified by simultaneous immunoblotting analysis with a corresponding antiserum. These advantages make diffusion blotting desirable when partial loss of transfer efficiency can be tolerated or be compensated by a more sensitive immunodetection reaction using enhanced chemiluminescence detection.

  5. Imaging of Selenium by Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) in 2-D Electrophoresis Gels and Biological Tissues.

    Science.gov (United States)

    Cruz, Elisa Castañeda Santa; Susanne Becker, J; Sabine Becker, J; Sussulini, Alessandra

    2018-01-01

    Selenium and selenoproteins are important components of living organisms that play a role in different biological processes. Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) is a powerful analytical technique that has been employed to obtain distribution maps of selenium in biological tissues in a direct manner, as well as in selenoproteins, previously separated by their molecular masses and isoelectric points using two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). In this chapter, we present the protocols to perform LA-ICP-MS imaging experiments, allowing the distribution visualization and determination of selenium and/or selenoproteins in biological systems.

  6. 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.

  7. 2d electrophoresis of bovine milk proteins and milk fermented drink

    OpenAIRE

    Damir Mogut; Anna Iwaniak; Monika Hrynkiewicz; Jerzy Dziuba

    2015-01-01

    The aim of the study was the analysis of milk and milk fermented drink proteomes with the use of 2D electrophoresis. The criteria of proteins separation were the values of their isoelectric points (pI) and molecular weights (MW). Our results showed that milk and milk fermented drink proteomes consisted of 118 and 121 spots, respectively. The computer analysis revealed the identity of 95 spots in both proteomes. Non-identical spots indicated the changes resulting from the action of bact...

  8. Two-dimensional correlation spectroscopy (2D-COS) variable selection for near-infrared microscopy discrimination of meat and bone meal in compound feed.

    Science.gov (United States)

    Lü, Chengxu; Chen, Longjian; Yang, Zengling; Liu, Xian; Han, Lujia

    2014-01-01

    This article presents a novel method for combining auto-peak and cross-peak information for sensitive variable selection in synchronous two-dimensional correlation spectroscopy (2D-COS). This variable selection method is then applied to the case of near-infrared (NIR) microscopy discrimination of meat and bone meal (MBM). This is of important practical value because MBM is currently banned in ruminate animal compound feed. For the 2D-COS analysis, a set of NIR spectroscopy data of compound feed samples (adulterated with varying concentrations of MBM) was pretreated using standard normal variate and detrending (SNVD) and then mapped to the 2D-COS synchronous matrix. For the auto-peak analysis, 12 main sensitive variables were identified at 6852, 6388, 6320, 5788, 5600, 5244, 4900, 4768, 4572, 4336, 4256, and 4192 cm(-1). All these variables were assigned their specific spectral structure and chemical component. For the cross-peak analysis, these variables were divided into two groups, each group containing the six sensitive variables. This grouping resulted in a correlation between the spectral variables that was in accordance with the chemical-component content of the MBM and compound feed. These sensitive variables were then used to build a NIR microscopy discrimination model, which yielded a 97% correct classification. Moreover, this method detected the presence of MBM when its concentration was less than 1% in an adulterated compound feed sample. The concentration-dependent 2D-COS-based variable selection method developed in this study has the unique advantages of (1) introducing an interpretive aspect into variable selection, (2) substantially reducing the complexity of the computations, (3) enabling the transferability of the results to discriminant analysis, and (4) enabling the efficient compression of spectral data.

  9. 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...

  10. Combining high-throughput MALDI-TOF mass spectrometry and isoelectric focusing gel electrophoresis for virtual 2D gel-based proteomics.

    Science.gov (United States)

    Lohnes, Karen; Quebbemann, Neil R; Liu, Kate; Kobzeff, Fred; Loo, Joseph A; Ogorzalek Loo, Rachel R

    2016-07-15

    The virtual two-dimensional gel electrophoresis/mass spectrometry (virtual 2D gel/MS) technology combines the premier, high-resolution capabilities of 2D gel electrophoresis with the sensitivity and high mass accuracy of mass spectrometry (MS). Intact proteins separated by isoelectric focusing (IEF) gel electrophoresis are imaged from immobilized pH gradient (IPG) polyacrylamide gels (the first dimension of classic 2D-PAGE) by matrix-assisted laser desorption/ionization (MALDI) MS. Obtaining accurate intact masses from sub-picomole-level proteins embedded in 2D-PAGE gels or in IPG strips is desirable to elucidate how the protein of one spot identified as protein 'A' on a 2D gel differs from the protein of another spot identified as the same protein, whenever tryptic peptide maps fail to resolve the issue. This task, however, has been extremely challenging. Virtual 2D gel/MS provides access to these intact masses. Modifications to our matrix deposition procedure improve the reliability with which IPG gels can be prepared; the new procedure is described. Development of this MALDI MS imaging (MSI) method for high-throughput MS with integrated 'top-down' MS to elucidate protein isoforms from complex biological samples is described and it is demonstrated that a 4-cm IPG gel segment can now be imaged in approximately 5min. Gel-wide chemical and enzymatic methods with further interrogation by MALDI MS/MS provide identifications, sequence-related information, and post-translational/transcriptional modification information. The MSI-based virtual 2D gel/MS platform may potentially link the benefits of 'top-down' and 'bottom-up' proteomics.

  11. Chemical profiling and adulteration screening of Aquilariae Lignum Resinatum by Fourier transform infrared (FT-IR) spectroscopy and two-dimensional correlation infrared (2D-IR) spectroscopy.

    Science.gov (United States)

    Qu, Lei; Chen, Jian-Bo; Zhang, Gui-Jun; Sun, Su-Qin; Zheng, Jing

    2017-03-05

    As a kind of expensive perfume and valuable herb, Aquilariae Lignum Resinatum (ALR) is often adulterated for economic motivations. In this research, Fourier transform infrared (FT-IR) spectroscopy is employed to establish a simple and quick method for the adulteration screening of ALR. First, the principal chemical constituents of ALR are characterized by FT-IR spectroscopy at room temperature and two-dimensional correlation infrared (2D-IR) spectroscopy with thermal perturbation. Besides the common cellulose and lignin compounds, a certain amount of resin is the characteristic constituent of ALR. Synchronous and asynchronous 2D-IR spectra indicate that the resin (an unstable secondary metabolite) is more sensitive than cellulose and lignin (stable structural constituents) to the thermal perturbation. Using a certified ALR sample as the reference, the infrared spectral correlation threshold is determined by 30 authentic samples and 6 adulterated samples. The spectral correlation coefficient of an authentic ALR sample to the standard reference should be not less than 0.9886 (p=0.01). Three commercial adulterated ALR samples are identified by the correlation threshold. Further interpretation of the infrared spectra of the adulterated samples indicates the common adulterating methods - counterfeiting with other kind of wood, adding ingredient such as sand to increase the weight, and adding the cheap resin such as rosin to increase the content of resin compounds. Results of this research prove that FT-IR spectroscopy can be used as a simple and accurate quality control method of ALR.

  12. Near-infrared (NIR) imaging analysis of polylactic acid (PLA) nanocomposite by multiple-perturbation two-dimensional (2D) correlation spectroscopy

    Science.gov (United States)

    Shinzawa, Hideyuki; Murakami, Takurou N.; Nishida, Masakazu; Kanematsu, Wataru; Noda, Isao

    2014-07-01

    Multiple-perturbation two-dimensional (2D) correlation spectroscopy was applied to sets of near-infrared (NIR) imaging data of polylactic acid (PLA) nanocomposite samples undergoing UV degradation. Incorporation of clay nanoparticles substantially lowers the surface free energy barrier for the nucleation of PLA and eventually increases the frequency of the spontaneous nucleation of PLA crystals. Thus, when exposed to external stimuli such as UV light, PLA nanocomposite may show different structure alternation depending on the clay dispersion. Multiple-perturbation 2D correlation analysis of the PLA nanocomposite samples revealed different spatial variation between crystalline and amorphous structure of PLA, and the phenomenon especially becomes acute in the region where the clay particles are coagulated. The incorporation of the clay leads to the cleavage-induced crystallization of PLA when the sample is subjected to the UV light. The additional development of the ordered crystalline structure then works favorably to restrict the initial degradation of the polymer, providing the delay in the weight loss of the PLA.

  13. Chemical profiling and adulteration screening of Aquilariae Lignum Resinatum by Fourier transform infrared (FT-IR) spectroscopy and two-dimensional correlation infrared (2D-IR) spectroscopy

    Science.gov (United States)

    Qu, Lei; Chen, Jian-bo; Zhang, Gui-Jun; Sun, Su-qin; Zheng, Jing

    2017-03-01

    As a kind of expensive perfume and valuable herb, Aquilariae Lignum Resinatum (ALR) is often adulterated for economic motivations. In this research, Fourier transform infrared (FT-IR) spectroscopy is employed to establish a simple and quick method for the adulteration screening of ALR. First, the principal chemical constituents of ALR are characterized by FT-IR spectroscopy at room temperature and two-dimensional correlation infrared (2D-IR) spectroscopy with thermal perturbation. Besides the common cellulose and lignin compounds, a certain amount of resin is the characteristic constituent of ALR. Synchronous and asynchronous 2D-IR spectra indicate that the resin (an unstable secondary metabolite) is more sensitive than cellulose and lignin (stable structural constituents) to the thermal perturbation. Using a certified ALR sample as the reference, the infrared spectral correlation threshold is determined by 30 authentic samples and 6 adulterated samples. The spectral correlation coefficient of an authentic ALR sample to the standard reference should be not less than 0.9886 (p = 0.01). Three commercial adulterated ALR samples are identified by the correlation threshold. Further interpretation of the infrared spectra of the adulterated samples indicates the common adulterating methods - counterfeiting with other kind of wood, adding ingredient such as sand to increase the weight, and adding the cheap resin such as rosin to increase the content of resin compounds. Results of this research prove that FT-IR spectroscopy can be used as a simple and accurate quality control method of ALR.

  14. Effects on the Thermo-Mechanical and Crystallinity Properties of Nylon 6,6 Electrospun Fibres Reinforced with One Dimensional (1D and Two Dimensional (2D Carbon

    Directory of Open Access Journals (Sweden)

    Francisco Medellín-Rodríguez

    2013-08-01

    Full Text Available Electrospun one dimensional (1D and two dimensional (2D carbon based polymer nanocomposites are studied in order to determine the effect provided by the two differently structured nanofillers on crystallinity and thermo-mechanical properties of the nanofibres. The nanomaterials studied are pristine carbon nanotubes, oxidised carbon nanotubes, reduced graphene oxide and graphene oxide. Functional groups associated with the order structure of the polymers are analysed by infrared and Raman spectroscopies; the morphology is studied by scanning electron microscopy and the crystallinity properties are investigated by differential scanning calorimetry and X-ray diffraction. Differences in crystallisation behaviour between 1D and 2D carbon based nanofibres are shown by their crystallinity degree and their crystal sizes. The nanocomposite crystal sizes perpendicular to the plane (100 decrease with nanofiller content in all cases. The crystallinity trend and crystal sizes are in accordance with storage modulus response. The results also suggest that functionalisation favours interfacial bonding and dispersion of the nanomaterials within the polymer matrix. As a consequence the number of nucleating sites increases which in turn decreases the crystal size in the nanocomposites. These features explain the improved thermo-mechanical properties in the nanocomposites.

  15. 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.

  16. Proteomic Analyses of Agkistrodon contortrix contortrix Venom Using 2D Electrophoresis and MS Techniques.

    Science.gov (United States)

    Bocian, Aleksandra; Urbanik, Małgorzata; Hus, Konrad; Łyskowski, Andrzej; Petrilla, Vladimír; Andrejčáková, Zuzana; Petrillová, Monika; Legáth, Jaroslav

    2016-12-13

    Snake venom is a complex mixture of proteins and peptides which in the Viperidae is mainly hemotoxic. The diversity of these components causes the venom to be an extremely interesting object of study. Discovered components can be used in search for new pharmaceuticals used primarily in the treatment of diseases of the cardiovascular system. In order to determine the protein composition of the southern copperhead venom, we have used high resolution two dimensional electrophoresis and MALDI ToF/ToF MS-based identification. We have identified 10 groups of proteins present in the venom, of which phospholipase A₂ and metalloprotease and serine proteases constitute the largest groups. For the first time presence of 5'-nucleotidase in venom was found in this group of snakes. Three peptides present in the venom were also identified. Two of them as bradykinin-potentiating agents and one as an inhibitor.

  17. Proteomic Analyses of Agkistrodon contortrix contortrix Venom Using 2D Electrophoresis and MS Techniques

    Directory of Open Access Journals (Sweden)

    Aleksandra Bocian

    2016-12-01

    Full Text Available Snake venom is a complex mixture of proteins and peptides which in the Viperidae is mainly hemotoxic. The diversity of these components causes the venom to be an extremely interesting object of study. Discovered components can be used in search for new pharmaceuticals used primarily in the treatment of diseases of the cardiovascular system. In order to determine the protein composition of the southern copperhead venom, we have used high resolution two dimensional electrophoresis and MALDI ToF/ToF MS-based identification. We have identified 10 groups of proteins present in the venom, of which phospholipase A2 and metalloprotease and serine proteases constitute the largest groups. For the first time presence of 5′-nucleotidase in venom was found in this group of snakes. Three peptides present in the venom were also identified. Two of them as bradykinin-potentiating agents and one as an inhibitor.

  18. 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...

  19. 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.

  20. Comparison of ethanol-soluble proteins from different rye (Secale cereale) varieties by two-dimensional electrophoresis

    DEFF Research Database (Denmark)

    Radzikowski, Louise; Nesic, Ljiljana; Hansen, H.B.

    2002-01-01

    electrophoresis. The gels were scanned, compared using ImageMaster(R) software and the data sets were analyzed by principal component analysis (PCA) using THE UNSCRAMBLER software. Afterwards MATLAB was used to make a cluster analysis of the varieties based on PCA. The analysis of the gels showed...... characteristics showed that one protein spot was located close to the parameters bread volume and bread height....

  1. 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

    Separation of proteins on either carrier ampholyte-based or immobilized pH gradient-based two-dimensional (2-D) gels gives rise to electrophoretic patterns that are difficult to compare visually. In this paper we have used matrix-assisted laser desorption/ionization mass spectrometry (MALDI......-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......-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...

  2. Haptic-2D: A new haptic test battery assessing the tactual abilities of sighted and visually impaired children and adolescents with two-dimensional raised materials.

    Science.gov (United States)

    Mazella, Anaïs; Albaret, Jean-Michel; Picard, Delphine

    2016-01-01

    To fill an important gap in the psychometric assessment of children and adolescents with impaired vision, we designed a new battery of haptic tests, called Haptic-2D, for visually impaired and sighted individuals aged five to 18 years. Unlike existing batteries, ours uses only two-dimensional raised materials that participants explore using active touch. It is composed of 11 haptic tests, measuring scanning skills, tactile discrimination skills, spatial comprehension skills, short-term tactile memory, and comprehension of tactile pictures. We administered this battery to 138 participants, half of whom were sighted (n=69), and half visually impaired (blind, n=16; low vision, n=53). Results indicated a significant main effect of age on haptic scores, but no main effect of vision or Age × Vision interaction effect. Reliability of test items was satisfactory (Cronbach's alpha, α=0.51-0.84). Convergent validity was good, as shown by a significant correlation (age partialled out) between total haptic scores and scores on the B101 test (rp=0.51, n=47). Discriminant validity was also satisfactory, as attested by a lower but still significant partial correlation between total haptic scores and the raw score on the verbal WISC (rp=0.43, n=62). Finally, test-retest reliability was good (rs=0.93, n=12; interval of one to two months). This new psychometric tool should prove useful to practitioners working with young people with impaired vision.

  3. Analysis of rRNA Gene Methylation in Arabidopsis thaliana by CHEF-Conventional 2D Gel Electrophoresis.

    Science.gov (United States)

    Mohannath, Gireesha; Pikaard, Craig S

    2016-01-01

    Contour-clamped homogenous electric field (CHEF) gel electrophoresis, a variant of Pulsed-field gel electrophoresis (PFGE), is a powerful technique for resolving large fragments of DNA (10 kb-9 Mb). CHEF has many applications including the physical mapping of chromosomes, artificial chromosomes, and sub-chromosomal DNA fragments, etc. Here, we describe the use of CHEF and two-dimensional gel electrophoresis to analyze rRNA gene methylation patterns within the two ~4 million base pair nucleolus organizer regions (NORs) of Arabidopsis thaliana. The method involves CHEF gel electrophoresis of agarose-embedded DNA following restriction endonuclease digestion to cut the NORs into large but resolvable segments, followed by digestion with methylation-sensitive restriction endonucleases and conventional (or CHEF) gel electrophoresis, in a second dimension. Resulting products are then detected by Southern blotting or PCR analyses capable of discriminating rRNA gene subtypes.

  4. 2d electrophoresis of bovine milk proteins and milk fermented drink

    Directory of Open Access Journals (Sweden)

    Damir Mogut

    2015-09-01

    Full Text Available The aim of the study was the analysis of milk and milk fermented drink proteomes with the use of 2D electrophoresis. The criteria of proteins separation were the values of their isoelectric points (pI and molecular weights (MW. Our results showed that milk and milk fermented drink proteomes consisted of 118 and 121 spots, respectively. The computer analysis revealed the identity of 95 spots in both proteomes. Non-identical spots indicated the changes resulting from the action of bacterial proteinases on milk proteins during the production of milk fermented drink. Proteolytic starter cultures applied to produce the milk fermented drink led to a partial hydrolysis of milk proteins to peptides and free amino acid residues. Results obtained led to confirm the suitability of 2D electrophoresis to observe the changes in the proteomes of milk products, as well as other food products after the application of technological processes. The development of the methods of proteomic analysis will let, in the future, eliminate the artefacts, which may limit the possibility of errors during proteins’ identification.

  5. 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; 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......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...

  6. Two-dimensional separation of ionic species by hyphenation of capillary ion chromatography × capillary electrophoresis-mass spectrometry.

    Science.gov (United States)

    Beutner, Andrea; Kochmann, Sven; Mark, Jonas Josef Peter; Matysik, Frank-Michael

    2015-03-17

    The separation of complex mixtures such as biological or environmental samples requires high peak capacities, which cannot be established with a single separation technique. Therefore, multidimensional systems are in demand. In this work, we present the hyphenation of the two most important (orthogonal) techniques in ion analysis, namely, ion chromatography (IC) and capillary electrophoresis (CE), in combination with mass spectrometry. A modulator was developed ensuring a well-controlled coupling of IC and CE separations. Proof-of-concept measurements were performed using a model system consisting of nucleotides and cyclic nucleotides. The data are presented in a multidimensional contour plot. Analyte stacking in the CE separation could be exploited on the basis of the fact that the suppressed IC effluent is pure water.

  7. Two-dimensional polyacrylamide gel electrophoresis with immobilized pH gradients in the first dimension (IPG-Dalt): the state of the art and the controversy of vertical versus horizontal systems.

    Science.gov (United States)

    Görg, A; Boguth, G; Obermaier, C; Posch, A; Weiss, W

    1995-07-01

    After having established the basic protocol of two-dimensional electrophoresis with immobilized pH gradients in the first dimension (IPG-Dalt) in 1988 (A. Görg et al., Electrophoresis 1988, 9, 531-546), some critical parameters of the actual IPG-Dalt protocols as well as the results obtained with horizontal and vertical second-dimensional sodium dodecyl sulfate-electrophoresis are demonstrated and discussed.

  8. On-line two-dimensional capillary electrophoresis with mass spectrometric detection using a fully electric isolated mechanical valve.

    Science.gov (United States)

    Kohl, Felix J; Montealegre, Cristina; Neusüß, Christian

    2016-04-01

    CE is becoming more and more important in many fields of bioanalytical chemistry. Besides optical detection, hyphenation to ESI-MS detection is increasingly applied for sensitive identification purposes. Unfortunately, many CE techniques and methods established in research and industry are not compatible to ESI-MS since essential components of the background electrolyte interfere in ES ionization. In order to identify unknown peaks in established CE methods, here, a heart-cut 2D-CE separation system is introduced using a fully isolated mechanical valve with an internal loop of only 20 nL. In this system, the sample is separated using potentially any non-ESI compatible method in the first separation dimension. Subsequently, the portion of interest is cut by the internal sample loop of the valve and reintroduced to the second dimension where the interfering compounds are removed, followed by ESI-MS detection. When comparing the separation efficiency of the system with the valve to a system using a continuous capillary only a slight increase in peak width is observed. Ultraviolet/visible detection is integrated in the first dimension for switching time determination, enabling reproducible cutting of peaks of interest. The feasibility of the system is successfully demonstrated by a 2D analysis of a BSA tryptic digest sample using a nonvolatile (phosphate based) background electrolyte in the first dimension.

  9. Optimization of Large Gel 2D Electrophoresis for Proteomic Studies of Skeletal Muscle

    Science.gov (United States)

    Reed, Patrick W.; Densmore, Allison; Bloch, Robert J.

    2013-01-01

    We describe improved methods for large format, 2-dimensional gel electrophoresis (2-DE) that improve protein solubility and recovery, minimize proteolysis, and reduce the loss of resolution due to contaminants and manipulations of the gels, and thus enhance quantitative analysis of protein spots. Key modifications are: (i) the use of 7M urea + 2 M thiourea, instead of 9M urea, in sample preparation and in the tops of the gel tubes; (ii) standardized deionization of all solutions containing urea with a mixed bed ion exchange resin and removal of urea from the electrode solutions; and (iii) use of a new gel tank and cooling device that eliminate the need to run two separating gels in the SDS dimension. These changes make 2D-GE analysis more reproducible and sensitive, with minimal artifacts. Application of this method to the soluble fraction of muscle tissues reliably resolves ~1800 protein spots in adult human skeletal muscle and over 2800 spots in myotubes. PMID:22589104

  10. Two-dimensional gel electrophoresis analysis of mycelial cells treated with Tween 80: differentially expressed protein related to enhanced metabolite production.

    Science.gov (United States)

    Zhang, Bo-Bo; Chen, Lei; Cheung, Peter C K

    2012-10-24

    Two-dimensional gel electrophoresis identified 40 differentially expressed proteins which explained the mechanisms underlying the stimulatory effect of Tween 80 for exopolysaccharide production in the mycelium of an edible mushroom Pleurotus tuber-regium. The up-regulation of fatty acid synthase alpha subunit FasA might promote the synthesis of long-chain fatty acids and their incorporation into the mycelial cell membranes, increasing the membrane permeability. A down-regulation of Phospholipase D1 and an up-regulation of Hypothetical protein PGUG_02954 might mediate signal transduction between the mycelial cells and the extracellular stimulus (Tween 80). The down-regulated ATP-binding cassette transporter protein might function as pumps to extrude exopolysaccharide out of the cells that lead to a significant increase in its production. The present results explained how stimulatory agents like Tween 80 can increase mycelial cell membrane permeability to enhance the production of useful extracellular metabolites by submerged fermentation.

  11. Evaluating two-dimensional electrophoresis profiles of the protein phaseolin as markers of genetic differentiation and seed protein quality in common bean (Phaseolus vulgaris L.).

    Science.gov (United States)

    López-Pedrouso, María; Bernal, Javier; Franco, Daniel; Zapata, Carlos

    2014-07-23

    High-resolution two-dimensional electrophoresis (2-DE) profiles of the protein phaseolin, the major seed storage protein of common bean, display great number of spots with differentially glycosylated and phosphorylated α- and β-type polypeptides. This work aims to test whether these complex profiles can be useful markers of genetic differentiation and seed protein quality in bean populations. The 2-DE phaseolin profile and the amino acid composition were examined in bean seeds from 18 domesticated and wild accessions belonging to the Mesoamerican and Andean gene pools. We found that proteomic distances based on 2-DE profiles were successful in identifying the accessions belonging to each gene pool and outliers distantly related. In addition, accessions identified as outliers from proteomic distances showed the highest levels of methionine content, an essential amino acid deficient in bean seeds. These findings suggest that 2-DE phaseolin profiles provide valuable information with potential of being used in common bean genetic improvement.

  12. Two-dimensional gel electrophoresis data in support of leaf comparative proteomics of two citrus species differing in boron-tolerance

    Directory of Open Access Journals (Sweden)

    Wen Sang

    2015-09-01

    Full Text Available Here, we provide the data from a comparative proteomics approach used to investigate the response of boron (B-tolerant ‘Xuegan’ (Citrus sinensis and B-intolerant ‘Sour pummelo’ (Citrus grandis leaves to B-toxicity. Using two-dimensional gel electrophoresis (2-DE technique, we identified 50 and 45 protein species with a fold change of more than 1.5 and a P-value of less than 0.05 from B-toxic C. sinensis and C. grandis leaves. These B-toxicity-responsive protein species were mainly involved in carbohydrate and energy metabolism, antioxidation and detoxification, stress responses, coenzyme biosynthesis, protein and amino acid metabolism, signal transduction, cell transport, cytoskeleton, nucleotide metabolism, and cell cycle and DNA processing. A detailed analysis of this data may be obtained from Sang et al. (J. Proteomics 114 (2015[1].

  13. Evaluation of an effective sample prefractionation method for the proteome analysis of breast cancer tissue using narrow range two-dimensional gel electrophoresis.

    Science.gov (United States)

    Lee, KiBeom

    2008-06-01

    One method of improving the protein profiling of complex mammalian proteomes is the use of prefractionation followed by application of narrow pH range two dimensional (2-D) gels. The success of this strategy relies on sample solubilization; poor solubilization has been associated with missing protein fractions and diffuse, streaked, and/or trailing protein spots. In this study, I sought to optimize the solubilization of prefractionated human cancer cell samples using isoelectric focusing (IEF) rehydration buffers containing a variety of commercially available reducing agents, detergents, chaotropes, and carrier ampholytes. The solubilized proteins were resolved on 2-D gels and compared. Among five tested IEF rehydration buffers, those containing 3-[(3-cholamidopropyl)dimethylamino]-1-propane sulfonate (CHAPS) and dithiothreitol (DTT) provided superior resolution, while that containing Nonidet P-40 (NP-40) did not significantly affect protein resolution, and the tributyl phosphine (TBP)-containing buffer yielded consistently poor results. In addition, I found that buffers containing typically high urea and ampholyte levels generated sharper 2-D gels. Using these optimized conditions, I was able to apply 2-D gel analysis successfully to fractionated proteins from human breast cancer tissue MCF-7, across a pH range of 4-6.7.

  14. Detection of seminal fluid proteins in the bed bug, Cimex lectularius, using two-dimensional gel electrophoresis and mass spectrometry.

    Science.gov (United States)

    Reinhardt, K; Wong, C H; Georgiou, A S

    2009-03-01

    The global increase of the human parasite, the common bed bug Cimex lectularius, calls for specific pest control target sites. The bed bug is also a model species for sexual conflict theory which suggests that seminal fluids may be highly diverse. The species has a highly unusual sperm biology and seminal proteins may have unique functions. One-dimensional PAGE gels showed 40-50% band sharing between C. lectularius and another cimicid species, Afrocimex constrictus. However, adult, sexually rested C. lectularius males were found to store 5-7 microg of seminal protein and with only 60 microg of protein we obtained informative 2-D PAGE gels. These showed 79% shared protein spots between 2 laboratory populations, and more than half of the shared protein spots were detected in the mated female. Further analysis using liquid chromatography electrospray ionization tandem mass spectrometry revealed that 26.5% of the proteins had matches among arthropods in databases and 14.5% matched Drosophila proteins. These included ubiquitous proteins but also those more closely associated with reproduction such as moj 29, ubiquitin, the stress-related elongation factor EF-1 alpha, a protein disulfide isomerase and an antioxidant, Peroxiredoxin 6.

  15. Diagonal two-dimensional electrophoresis (D-2DE): a new approach to study the effect of osmotic stress induced by polyethylene glycol in durum wheat (Triticum durum Desf.).

    Science.gov (United States)

    Kacem, N S; Mauro, S; Muhovski, Y; Delporte, F; Renaut, J; Djekoun, A; Watillon, B

    2016-09-01

    Acclimatization to stress is associated with profound changes in proteome composition. The use of plant cell and tissue culture offers a means to investigate the physiological and biochemical processes involved in the adaptation to osmotic stress. We employed a new proteomic approach to further understand the response of calli to dehydration induced by polyethylene glycol (PEG6000). Calli of three durum wheat genotypes Djenah Khetifa, Oued Zenati and Waha were treated with two concentrations of polyethylene glycol to mimic osmotic stress. Changes in protein relative abundance were analyzed using a new electrophoretic approach named diagonal two-dimensional electrophoresis (D-2DE), combined with mass spectrometry. Total proteins were extracted from 30-day-old calli from three durum wheat genotypes that showed contrasting levels of drought stress tolerance in the field. The combination of one-dimensional electrophoresis and D-2DE gave a specific imprint of the protein extracts under osmotic stress, as well as characterizing and identifying individual target proteins. Of the variously expressed proteins, three were selected (globulin, GAPDH and peroxidase) and further analyzed using qRT-PCR at the transcriptome level in order to compare the results with the proteomic data. Western blot analysis was used to further validate the differences in relative abundance pattern. The proteins identified through this technique provide new insights as to how calli respond to osmotic stress. Our method of study provides an original and relevant approach of analyzing the osmotic-responsive mechanisms at the cellular level of durum wheat with agronomic perspectives.

  16. Two-dimensional electrophoresis analysis of the protein expression of dental pulp in different conditions%不同状态下牙髓组织蛋白质表达的二维电泳分析

    Institute of Scientific and Technical Information of China (English)

    林晨; 聂敏; 张露; 陈智

    2008-01-01

    目的 利用蛋白质组技术探讨牙髓对中龋和热刺激的反应.方法 用双向电泳得到牙髓在中龋和热刺激状态下的二维电泳图谱,对差异点进行质谱鉴定.结果 经Image Master2-D Platinum 5.0软件分析显示,正常牙髓和中龋牙髓的蛋白表达无显著差异;热损伤牙髓有2个蛋白点缺失,8个蛋白点下调.质谱分析鉴定了7种蛋白质.结论 本实验条件下,中龋牙髓的蛋白质表达与正常牙髓无显著差异,热刺激可造成部分蛋白表达的下调.%Objective To analyze the different responses of dental pulp to moderate caries and thermal stimulation by proteomies.Methods Two-dimensional electrophoresis(2-DE)was performed to obtain the 2-D gel electrophoresis patterns of dental pulp.Mass spectrometry(MS)was used to analyze several different selected spots in the expression proteins.Results No significant difference in protein expression was found between normal and moderate carious dental.Two protein spots were absent in heatdamaged group and 8 spots showed significantly down-regulated.Seven proteins were identified by MS.Conclusions In the present study,no significant difference in the pulp protein expression was detected between the healthy and moderate carious pulp tissues.However,down-regulation of pulp protein in thermal stimulation was observed.

  17. Proteome analysis of human colorectal cancer tissue using 2-D ...

    African Journals Online (AJOL)

    Jane

    2010-10-11

    Oct 11, 2010 ... Laser capture microdissection and two-dimensional difference gel electrophoresis were used to establish ... As a technique with high-flux and high resolution, pro- teomics ... in which the protein sample was labeled before 2-D.

  18. Two-dimensional capillary zone electrophoresis-mass spectrometry for the characterization of intact monoclonal antibody charge variants, including deamidation products.

    Science.gov (United States)

    Jooß, Kevin; Hühner, Jens; Kiessig, Steffen; Moritz, Bernd; Neusüß, Christian

    2017-08-12

    Capillary zone electrophoresis (CZE) is a powerful tool that is progressively being applied for the separation of monoclonal antibody (mAb) charge variants. Mass spectrometry (MS) is the desired detection method concerning identification of mAb variants. In biopharmaceutical applications, there exist optimized and validated electrolyte systems for mAb variant quantification. However, these electrolytes interfere greatly with the electrospray ionization (ESI) process. Here, a heart-cut CZE-CZE-MS setup with an implemented mechanical four-port valve interface was developed that used a generic ε-aminocaproic acid based background electrolyte in the first dimension and acetic acid in the second dimension. Interference-free, highly precise mass data (deviation less than 1 Da) of charge variants of trastuzumab, acting as model mAb system, were achieved. The mass accuracy obtained (low parts per million range) is discussed regarding both measured and calculated masses. Deamidation was detected for the intact model antibody, and related mass differences were significantly confirmed on the deglycosylated level. The CZE-CZE-MS setup is expected to be applicable to a variety of antibodies and electrolyte systems. Thus, it has the potential to become a compelling tool for MS characterization of antibody variants separated in ESI-interfering electrolytes. Graphical Abstract Two-dimensional capillary zone electrophoresis mass spectrometry for the characterization of intact monoclonal antibody (mAb) charge variants. A generic, but highly electrospray-interfering electrolyte system was used as first dimension for mAb charge variant separation and coupled to a volatile electrolyte system as second dimension via a four-port nanoliter valve. In this way, interference-free and precise mass spectrometric data of separated mAb charge variants, including deamidation products, were obtained.

  19. Two dimensional electrophoresis of the exo-proteome produced from community acquired methicillin resistant Staphylococcus aureus belonging to clonal complex 80.

    Science.gov (United States)

    Enany, Shymaa; Yoshida, Yutaka; Magdeldin, Sameh; Bo, Xu; Zhang, Ying; Enany, Mohamed; Yamamoto, Tadashi

    2013-10-01

    Two-dimensional electrophoresis (2DE) combined with mass spectrometry was used to characterize the exo-proteome secreted by two strains (ER13 and ER21) representing community acquired methicillin resistant Staphylococcus aureus (CA-MRSA) belonging to clonal complex 80 (CC80). Common spots were detected between the 2 gels using the Progenesis SameSpots software. Two hundred and fifty-one and 312 spots from the exo-proteome of ER13 and ER21 were resolved, respectively. 2DE overlap comparison showed that 59 spots were shared. LC-MS/MS analysis identified 57 proteins from these spots comprising about 21% extracellular, 48% cytoplasmic, 2% cytoplasmic membrane, 2% cell wall, and 26% with unknown localization. The identified proteins were classified with respect to their Gene Ontology (GO) annotation as ∼24% virulence determinants and toxins, ∼17% involved in carbohydrate metabolism, ∼14% involved in environmental stress, and ∼12% associated with cell division. The identification of the enterotoxin B from the exo-products of both strains used in our study, as belonging to CC80 was interesting. Copyright © 2013 Elsevier GmbH. All rights reserved.

  20. Optimization of an Efficient Protein Extraction Protocol Compatible with Two-Dimensional Electrophoresis and Mass Spectrometry from Recalcitrant Phenolic Rich Roots of Chickpea (Cicer arietinum L.

    Directory of Open Access Journals (Sweden)

    Moniya Chatterjee

    2012-01-01

    Full Text Available Two-dimensional electrophoresis and mass spectrometry are undoubtedly two essential tools popularly used in proteomic analyses. Utilization of these techniques however largely depends on efficient and optimized sample preparation, regarded as one of the most crucial steps for recovering maximum amount of reliable information. The present study highlights the optimization of an effective and efficient protocol, capable of extraction of root proteins from recalcitrant phenolic rich tissues of chickpea. The widely applicable TCA-acetone and phenol-based methods have been comparatively evaluated, amongst which the latter appeared to be better suited for the sample. The phenol extraction-based method further complemented with sodium dodecyl sulphate (SDS and pulsatory treatments proved to be the most suitable method represented by greatest spot number, good resolution, and spot intensities. All the randomly selected spots showed successful identification when subjected to further downstream MALDI-TOF and MS/MS analyses. Hence, the information obtained collectively proposes the present protein extraction protocol to be an effective one that could be applicable for recalcitrant leguminous root samples.

  1. Optimization of an Efficient Protein Extraction Protocol Compatible with Two-Dimensional Electrophoresis and Mass Spectrometry from Recalcitrant Phenolic Rich Roots of Chickpea (Cicer arietinum L.).

    Science.gov (United States)

    Chatterjee, Moniya; Gupta, Sumanti; Bhar, Anirban; Das, Sampa

    2012-01-01

    Two-dimensional electrophoresis and mass spectrometry are undoubtedly two essential tools popularly used in proteomic analyses. Utilization of these techniques however largely depends on efficient and optimized sample preparation, regarded as one of the most crucial steps for recovering maximum amount of reliable information. The present study highlights the optimization of an effective and efficient protocol, capable of extraction of root proteins from recalcitrant phenolic rich tissues of chickpea. The widely applicable TCA-acetone and phenol-based methods have been comparatively evaluated, amongst which the latter appeared to be better suited for the sample. The phenol extraction-based method further complemented with sodium dodecyl sulphate (SDS) and pulsatory treatments proved to be the most suitable method represented by greatest spot number, good resolution, and spot intensities. All the randomly selected spots showed successful identification when subjected to further downstream MALDI-TOF and MS/MS analyses. Hence, the information obtained collectively proposes the present protein extraction protocol to be an effective one that could be applicable for recalcitrant leguminous root samples.

  2. Molecular characterization, expression patterns, and polymorphism of a differentially expressed porcine gene (PYGM) isolated by suppression subtractive hybridization and two-dimensional gel electrophoresis analysis.

    Science.gov (United States)

    Xu, Yongjie; Yu, Wenmin; Feng, Xiaoting; Xie, Hongtao; Xiong, Yuanzhu

    2012-01-01

    Suppression subtractive hybridization was performed to detect the differences in gene expression of porcine longissimus dorsi muscles between Large White and Chinese Meishan pigs. An upregulated gene in Large White that shared high homology with human muscle glycogen phosphorylase (PYGM) was identified. The porcine PYGM gene contains an open reading frame encoding 842 amino acid residues with 26 and 283 nucleotides in the 5' and 3' untranslated regions, respectively. Tissue distribution analysis indicated that porcine PYGM mRNAs are highly expressed in all tissues. Expression pattern of PYGM was similar in the two breeds. Both breeds had the highest expression levels when 120 days old (p<0.01), and PYGM was upregulated during skeletal muscle development. A similar expression pattern of PYGM in protein level was also observed by differential proteome analysis of skeletal muscle development using two-dimensional gel electrophoresis and mass spectroscopy. The mRNA abundance of PYGM in Large White was higher than Meishan at all four stages (p<0.05). Moreover, a G/T mutation in exon 8 was identified and association analysis with meat quality traits showed that it was significantly associated with lean meat percentage (p<0.05). Our data may provide further insight into the molecular mechanisms responsible for breed-specific differences in porcine growth and meat quality.

  3. 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.

  4. Two-dimensional electrophoresis analysis of protein production during growth of Pseudomonas putida F1 on toluene, phenol, and their mixture.

    Science.gov (United States)

    Reardon, Kenneth F; Kim, Kee-Hong

    2002-07-01

    The protein profiles of Pseudomonas putida F1 during growth on toluene, phenol, and their mixture were examined by two-dimensional polyacrylamide gel electrophoresis. Although this bacterium uses the same catabolic pathway for both substrates, P. putida F1 produced specific sets of proteins in response to toluene and phenol as single or mixed substrates. Proteins associated with growth on these substrates could be classified into three categories: ten Group T proteins were associated with the degradation of toluene, seventeen Group P proteins were associated with the degradation of phenol, and one Group M protein was observed to be associated only with toluene-phenol mixture degradation. During growth on the mixture, the protein profile of the cells shifted from Group T proteins to Group P proteins. This correlated well with the substrate consumption pattern, in which toluene was consumed first and growth on phenol did not begin until the medium was nearly depleted of toluene. Individual Group T and Group P protein intracellular concentrations had different transients as the cells grew on the mixture; seven protein levels increased, four decreased, and sixteen reached a maximum and then declined. The Group M protein reached a concentration maximum near the time when growth on phenol began. Variations in the maintenance of these proteins were also noted. These results demonstrate that cells growing on a mixture of substrates undergo significant physiological changes. Further investigation of these changes is expected to shed light on the unusual biodegradation kinetics previously observed with this mixed-substrate system.

  5. Protein Extraction Methods for Two-Dimensional Electrophoresis from Baphicacanthus cusia (Nees) Bremek Leaves-A Medicinal Plant with High Contents of Interfering Compounds

    Institute of Scientific and Technical Information of China (English)

    XIANG Xiao-liang; NING Shu-ju; JIANG Xia; GONG Xiao-gui; ZHU Ren-lei; WEI Dao-zhi

    2010-01-01

    Protein extraction is a critical step for two-dimensional electrophoresis (2-DE). Different plant samples require different and adaptive protein extraction protocols. The leaves of medicinal plant, Baphicacanthus cusia (Nees) Bremek are notoriously recalcitrant to common protein extraction methods due to high levels of interfering compounds (especially the secondary metabolites and pigments). This study was aimed to establish a routine procedure for the proteomic analysis of B. cusia leaves, and a new protocol for the protein extraction was developed by optimizing tfichloroacetic acid (TCA)/acetone extraction method. The efficiency of this protocol was demonstrated by comparison with 3 published protein extraction methods (chloroform/acetone, Mg/NP-40, Tris-base/acetone). The results showed that the optimized TCA/acetone precipitation extraction method gave a relatively high protein yield (9.263 mg g fresh weight), high-resolution separation, clear protein profiles, the highest proteins spots (1 311 protein spots), and displayed less contamination in 2DE gels. Therefore, the results suggested that the optimized TCA/acetone method was the most effective among the 4 methods for B. cusia leaves.

  6. Detection of activity and mass spectrometric identification of mouse liver carboxylesterase and aldehyde dehydrogenase separated by non-denaturing two-dimensional electrophoresis after extraction with detergents.

    Science.gov (United States)

    Shimazaki, Youji; Manabe, Takashi

    2005-05-20

    To examine the activities and identity of enzymes associated with organelles such as microsomes and mitochondria, proteins from mouse liver were extracted using the non-ionic detergents Nonidet P-40 (NP-40), polyoxyethylene sorbitan monooleate (Tween 80), polyoxyethylene isooctylphenyl ester (Triton X), n-octyl beta-D-glucoside (octyl glycoside) or anionic detergent sodium dodecylsulfate (SDS) after the removal of cytosolic proteins. The proteins extracted by detergents were separated by non-denaturing two-dimensional electrophoresis (2-DE). The activities of esterase and aldehyde dehydrogenase were retained by non-denaturing 2-DE after treatment with each non-ionic detergent, but the activities were reduced or lost when the proteins were extracted with more than 0.5% SDS. For proteomic analysis of the organelle-associated proteins in mouse liver, proteins were separated by non-denaturing 2-DE and were identified using electrospray ionization tandem mass spectrometry (ESI-MS/MS) after the proteins were solubilized by octyl glycoside, NP-40 and 0.1% SDS. Several organelle-associated proteins such as carboxylesterase, aldehyde dehydrogenase, glucose regulated protein and HSP60 were identified. These results indicate that the activities and identity of detergent-soluble enzymes can be examined by this non-denaturing 2-DE and mass spectrometry.

  7. 未成熟与成熟猪囊尾蚴蛋白双向电泳的图谱分析%Total Protein Analysis of Immature and Mature Cysticerci of Taenia solium by Two-dimensional Electrophoresis

    Institute of Scientific and Technical Information of China (English)

    方文; 肖靓靓; 包怀恩; 牟荣

    2011-01-01

    为从蛋白质水平揭示猪带绦虫入侵中间宿主家猪的免疫逃避机制,应用双向电泳技术分析未成熟与成熟猪囊尾蚴蛋白质表达差异,进行双向电泳图像软件分析.结果表明:未成熟猪囊尾蚴与成熟猪囊尾蚴蛋白的双向电泳凝胶上分别有(217±13)个、(241±17)个蛋白斑点,未成熟猪囊尾蚴表达上调2倍以上的蛋白有6个,下调2倍以上的蛋白有2个.%In order to explore the immune-escape mechanisms of the T. solium cysticercus on the protein level, the differentially expressed proteins of the immature and mature T. solium cysticerci were separated by two-dimensional electrophoresis respectively and analyzed by ImageMaster 2D Plantinum 6. 0 software. The results showed that the immature and mature T. solium cysticerci have 217 13 and 241 17 protein spots respectively, the immature T. solium cysticerci have six proteins of more than two times upregulation and two proteins of more than two times downregulation compared to the mature T. solium cysticerci.

  8. 1-D and 2-D electrophoresis protein profiles of the scorpion venom from Brotheas amazonicus

    Energy Technology Data Exchange (ETDEWEB)

    Higa, A.M.; Noronha, M.D.N. [Universidade do Estado do Amazonas (UEA), Manaus, AM (Brazil). Rede Proteomica do Amazonas (Proteam). Lab. de Genomica e Proteomica; Rocha-Oliveira, F.; Lopez-Lozano, J.L.L. [Universidade Federal do Amazonas (UFAM), Manaus, AM (Brazil). Pos-Graduacao em Biotecnologia

    2008-07-01

    Full text: Introduction: Scorpions venoms show specific neurotoxins to insect or mammals. These toxins are very important molecular tools to development of news drugs or bioinsecticides. Brotheas amazonicus scorpion is an endemic specie in Amazonian Rain Forest, but your venom do not show toxicity in humans. Information about biological specific activity on insect of this venom is not known yet. Objectives: Molecular protein toxins profiles of the venom from Brotheas amazonicus scorpion by 1-D and 2-D electrophoresis methods to detected toxins with potential biotech applications. Results: Several spots 'families' with {approx} 60, 70 and 80 kDa were detected in gel acidic region with pI {approx} 4,5 - 6 range, in the same region 1-D zimography showed proteolytic activity on gelatin and fibrinogen and proteolytic activity was inhibited by PMSF, suggesting scorpion serine proteinases. 50 kDa proteins were detected with pI {approx} 6,5 - 7 range. In 23 - 50 kDa gel acid region were observed some proteins. In 23 - 14 kDa gel acidic region were detected proteins with pI 4 - 7 range. 1-D Tris-tricine gel showed proteins with {approx} 7 kDa, suggesting scorpion neurotoxins. In gel basic region only 14 kDa proteins were observed with pI {approx} 9 - 10 range. Conclusion: Molecular profile of the scorpion venom from B. amazonicus showed proteins with high and low molecular masses, mainly with acidic pI. Proteolytic activity suggest serine proteinases with high molecular masses and 7 kDa proteins in B. amazonicus venom suggest scorpion neurotoxins. Purification and molecular characterization of these toxins are in course.

  9. Two-dimensional HRCT for monitoring postoperative results of the anterior cruciate ligament reconstruction. Zweidimensionale (2-D) CT-Arthrotomographie zur postoperativen Kontrolle einer neuen vorderen Kreuzbandplastik

    Energy Technology Data Exchange (ETDEWEB)

    Tosch, U.; Witt, H. (Freie Univ. Berlin (Germany, F.R.). Roentgendiagnostisches Zentralinstitut); Hertel, P.; Lais, E. (Freie Univ. Berlin (Germany, F.R.). Unfallchirurgische Klinik)

    1989-11-01

    Fifty-eight patients underwent intraarticular reconstruction of the anterior cruciate ligament. This was performed by using an autogenous transplant from the mid portion of the patellar ligament with a proximal and distal bone block, as described by Hertel. For comparison with the conventional X-ray examination, HRCT was performed to study the early postoperative results. In four patients (7%) dislocation of the bone block in the femoral condyle was seen. Two-dimensional reconstruction proved to be a satisfactory method for demonstration of the exact position of the autogenous transplant in both coronary and sagittal planes. (orig.).

  10. An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results

    Directory of Open Access Journals (Sweden)

    Arthur John

    2004-01-01

    Full Text Available Abstract Background Many proteomics initiatives require a seamless bioinformatics integration of a range of analytical steps between sample collection and systems modeling immediately assessable to the participants involved in the process. Proteomics profiling by 2D gel electrophoresis to the putative identification of differentially expressed proteins by comparison of mass spectrometry results with reference databases, includes many components of sample processing, not just analysis and interpretation, are regularly revisited and updated. In order for such updates and dissemination of data, a suitable data structure is needed. However, there are no such data structures currently available for the storing of data for multiple gels generated through a single proteomic experiments in a single XML file. This paper proposes a data structure based on XML standards to fill the void that exists between data generated by proteomics experiments and storing of data. Results In order to address the resulting procedural fluidity we have adopted and implemented a data model centered on the concept of annotated gel (AG as the format for delivery and management of 2D Gel electrophoresis results. An eXtensible Markup Language (XML schema is proposed to manage, analyze and disseminate annotated 2D Gel electrophoresis results. The structure of AG objects is formally represented using XML, resulting in the definition of the AGML syntax presented here. Conclusion The proposed schema accommodates data on the electrophoresis results as well as the mass-spectrometry analysis of selected gel spots. A web-based software library is being developed to handle data storage, analysis and graphic representation. Computational tools described will be made available at http://bioinformatics.musc.edu/agml. Our development of AGML provides a simple data structure for storing 2D gel electrophoresis data.

  11. In-Depth Characterization of the Phaseolin Protein Diversity of Common Bean (Phaseolus vulgaris L. Based on Two-Dimensional Electrophoresis and Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    María López-Pedrouso

    2012-01-01

    Full Text Available Phaseolin is the major seed storage protein of common bean. It comprises a complex set of glycoproteins heterogeneous in their polypeptide composition that is encoded by a gene family. Analyses of phaseolin banding patterns by one-dimensional electrophoresis (SDS-PAGE have been central to the current understanding of the diversity of wild and cultivated common beans. In this work, we have carried out a detailed description and interpretation of phaseolin diversity in cultivated common beans of different geographic origins (Mesoamerican and Andean gene pools based on the current two-dimensional electrophoresis (2-DE technology and mass spectrometry (MS. High-quality 2-DE gel images revealed very complex phaseolin patterns across the studied cultivars. Specifically, patterns of phaseolin within cultivars were organized in a horizontal string of multiple isospot pairs varying in isoelectric point and molecular mass. The degree of similarity among phaseolin patterns was estimated from the percentage of spots shared between pairs of cultivars. Analyses of proteomic distances between phaseolin types by non-metrical multidimensional scaling revealed that 2-DE phaseolin profiles are more similar among cultivars belonging to the same gene pool. However, higher differentiation was found among cultivars of the Andean gene pool. Analysis of genetic variations of the PCR-based SCAR marker of phaseolin seed protein was in general agreement with 2-DE phaseolin patterns, but provided supplementary information regarding diversity among cultivars. Furthermore, the molecular basis responsible for the complexity of 2-DE phaseolin patterns was investigated. Thus, identification of phaseolin spots from 2-DE gels by MALDI-TOF and MALDI-TOF/TOF MS showed that each single isospot pair contained only one type (α or β of phaseolin polypeptide, but pairs with higher and lower molecular mass corresponded to α- and β-type polypeptides, respectively. In addition, partial

  12. ProteomeGRID: towards a high-throughput proteomics pipeline through opportunistic cluster image computing for two-dimensional gel electrophoresis.

    Science.gov (United States)

    Dowsey, Andrew W; Dunn, Michael J; Yang, Guang-Zhong

    2004-12-01

    The quest for high-throughput proteomics has revealed a number of critical issues. Whilst improved two-dimensional gel electrophoresis (2-DE) sample preparation, staining and imaging issues are being actively pursued by industry, reliable high-throughput spot matching and quantification remains a significant bottleneck in the bioinformatics pipeline, thus restricting the flow of data to mass spectrometry through robotic spot excision and protein digestion. To this end, it is important to establish a full multi-site Grid infrastructure for the processing, archival, standardisation and retrieval of proteomic data and metadata. Particular emphasis needs to be placed on large-scale image mining and statistical cross-validation for reliable, fully automated differential expression analysis, and the development of a statistical 2-DE object model and ontology that underpins the emerging HUPO PSI GPS (Human Proteome Organization Proteomics Standards Initiative General Proteomics Standards). The first step towards this goal is to overcome the computational and communications burden entailed by the image analysis of 2-DE gels with Grid enabled cluster computing. This paper presents the proTurbo framework as part of the ProteomeGRID, which utilises Condor cluster management combined with CORBA communications and JPEG-LS lossless image compression for task farming. A novel probabilistic eager scheduler has been developed to minimise make-span, where tasks are duplicated in response to the likelihood of the Condor machines' owners evicting them. A 60 gel experiment was pair-wise image registered (3540 tasks) on a 40 machine Linux cluster. Real-world performance and network overhead was gauged, and Poisson distributed worker evictions were simulated. Our results show a 4:1 lossless and 9:1 near lossless image compression ratio and so network overhead did not affect other users. With 40 workers a 32x speed-up was seen (80% resource efficiency), and the eager scheduler reduced the

  13. An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results

    OpenAIRE

    Arthur John; Swartz Martha; Jiang Liu; Stanislaus Romesh; Almeida Jonas S

    2004-01-01

    Abstract Background Many proteomics initiatives require a seamless bioinformatics integration of a range of analytical steps between sample collection and systems modeling immediately assessable to the participants involved in the process. Proteomics profiling by 2D gel electrophoresis to the putative identification of differentially expressed proteins by comparison of mass spectrometry results with reference databases, includes many components of sample processing, not just analysis and inte...

  14. JAC2D: A two-dimensional finite element computer program for the nonlinear quasi-static response of solids with the conjugate gradient method; Yucca Mountain Site Characterization Project

    Energy Technology Data Exchange (ETDEWEB)

    Biffle, J.H.; Blanford, M.L.

    1994-05-01

    JAC2D is a two-dimensional finite element program designed to solve quasi-static nonlinear mechanics problems. A set of continuum equations describes the nonlinear mechanics involving large rotation and strain. A nonlinear conjugate gradient method is used to solve the equations. The method is implemented in a two-dimensional setting with various methods for accelerating convergence. Sliding interface logic is also implemented. A four-node Lagrangian uniform strain element is used with hourglass stiffness to control the zero-energy modes. This report documents the elastic and isothermal elastic/plastic material model. Other material models, documented elsewhere, are also available. The program is vectorized for efficient performance on Cray computers. Sample problems described are the bending of a thin beam, the rotation of a unit cube, and the pressurization and thermal loading of a hollow sphere.

  15. High Blood Pressure Effects on the Blood to Cerebrospinal Fluid Barrier and Cerebrospinal Fluid Protein Composition: A Two-Dimensional Electrophoresis Study in Spontaneously Hypertensive Rats

    Directory of Open Access Journals (Sweden)

    Ibrahim González-Marrero

    2013-01-01

    Full Text Available The aim of the present work is to analyze the cerebrospinal fluid proteomic profile, trying to find possible biomarkers of the effects of hypertension of the blood to CSF barrier disruption in the brain and their participation in the cholesterol and β-amyloid metabolism and inflammatory processes. Cerebrospinal fluid (CSF is a system linked to the brain and its composition can be altered not only by encephalic disorder, but also by systemic diseases such as arterial hypertension, which produces alterations in the choroid plexus and cerebrospinal fluid protein composition. 2D gel electrophoresis in cerebrospinal fluid extracted from the cistern magna before sacrifice of hypertensive and control rats was performed. The results showed different proteomic profiles between SHR and WKY, that α-1-antitrypsin, apolipoprotein A1, albumin, immunoglobulin G, vitamin D binding protein, haptoglobin and α-1-macroglobulin were found to be up-regulated in SHR, and apolipoprotein E, transthyretin, α-2-HS-glycoprotein, transferrin, α-1β-glycoprotein, kininogen and carbonic anhidrase II were down-regulated in SHR. The conclusion made here is that hypertension in SHR produces important variations in cerebrospinal fluid proteins that could be due to a choroid plexus dysfunction and this fact supports the close connection between hypertension and blood to cerebrospinal fluid barrier disruption.

  16. The new horizon in 2D electrophoresis: new technology to increase resolution and sensitivity.

    Science.gov (United States)

    Moche, Martin; Albrecht, Dirk; Maaß, Sandra; Hecker, Michael; Westermeier, Reiner; Büttner, Knut

    2013-06-01

    A principally new type of an electrophoresis setup for the second dimension of 2DE named HPE (high performance electrophoresis) has recently become available that provides excellent reproducibility much superior to traditional 2DE. It takes up ideas from early beginnings of 2DE which could not be satisfactory realized at that time. The new HPE system is in contrast to all other established systems a horizontal electrophoresis that employs a new type of precast polyacrylamide gels on film-backing and runs on a multilevel flatbed electrophoresis apparatus. In a systematic approach we compared its features to traditional 2DE for the cytosolic proteome of Bacillus subtilis. Not only the reproducibility is enhanced, but also nearly all qualitative parameters as resolution, sensitivity, the number of protein spots (25% more), and the number of different proteins (also additional 25%) are markedly increased. More than 200 proteins were exclusively found in HPE. This new electrophoresis system does not use buffer tanks. No glass plates are needed. Therefore handling of gels is greatly facilitated and very simple to use even for personnel with low technical skills. The new HPE system is technically at the beginnings and further development with increased performance can be expected.

  17. Evaluation of protein pattern changes in roots and leaves of Zea mays plants in response to nitrate availability by two-dimensional gel electrophoresis analysis

    Directory of Open Access Journals (Sweden)

    Cocucci Maurizio

    2009-08-01

    Full Text Available Abstract Background Nitrogen nutrition is one of the major factors that limit growth and production of crop plants. It affects many processes, such as development, architecture, flowering, senescence and photosynthesis. Although the improvement in technologies for protein study and the widening of gene sequences have made possible the study of the plant proteomes, only limited information on proteome changes occurring in response to nitrogen amount are available up to now. In this work, two-dimensional gel electrophoresis (2-DE has been used to investigate the protein changes induced by NO3- concentration in both roots and leaves of maize (Zea mays L. plants. Moreover, in order to better evaluate the proteomic results, some biochemical and physiological parameters were measured. Results Through 2-DE analysis, 20 and 18 spots that significantly changed their amount at least two folds in response to nitrate addition to the growth medium of starved maize plants were found in roots and leaves, respectively. Most of these spots were identified by Liquid Chromatography Electrospray Ionization Tandem Mass Spectrometry (LC-ESI-MS/MS. In roots, many of these changes were referred to enzymes involved in nitrate assimilation and in metabolic pathways implicated in the balance of the energy and redox status of the cell, among which the pentose phosphate pathway. In leaves, most of the characterized proteins were related to regulation of photosynthesis. Moreover, the up-accumulation of lipoxygenase 10 indicated that the leaf response to a high availability of nitrate may also involve a modification in lipid metabolism. Finally, this proteomic approach suggested that the nutritional status of the plant may affect two different post-translational modifications of phosphoenolpyruvate carboxylase (PEPCase consisting in monoubiquitination and phosphorylation in roots and leaves, respectively. Conclusion This work provides a first characterization of the proteome

  18. Proteomic analysis of copper-binding proteins in excess copper-stressed rice roots by immobilized metal affinity chromatography and two-dimensional electrophoresis.

    Science.gov (United States)

    Song, Yufeng; Zhang, Hongxiao; Chen, Chen; Wang, Guiping; Zhuang, Kai; Cui, Jin; Shen, Zhenguo

    2014-04-01

    Copper (Cu) is an essential micronutrient required for plant growth and development. However, excess Cu can inactivate and disturb protein structure as a result of unavoidable binding to proteins. To understand better the mechanisms involved in Cu toxicity and tolerance in plants, we developed a new immobilized metal affinity chromatography (IMAC) method for the separation and isolation of Cu-binding proteins extracted from roots of rice seedling exposed to excess Cu. In our method, IDA-Sepharose or EDDS-Sepharose column (referred as pre-chromatography) and Cu-IDA-Sepharose column (referred as Cu-IMAC) were connected in tandem. Namely, protein samples were pre-chromatographed with IDA-Sepharose column to removal metal ions, then protein solution was flowed into Cu-IMAC column for enriching Cu-binding proteins in vitro. Compared with the control (Cu-IMAC without any pre-chromatography), IDA-Sepharose pre-chromatography method markedly increased yield of the Cu-IMAC-binding proteins, and number of protein spots and the abundance of 40 protein spots on two-dimensional electrophoresis (2-DE) gels. Thirteen protein spots randomly selected from 2-DE gel and 11 proteins were identified using MALDI-TOF-TOF MS. These putative Cu-binding proteins included those involved in antioxidant defense, carbohydrate metabolism, nucleic acid metabolism, protein folding and stabilization, protein transport and cell wall synthesis. Ten proteins contained one or more of nine putative metal-binding motifs reported by Smith et al. (J Proteome Res 3:834-840, 2004) and seven proteins contained one or two of top six motifs reported by Kung et al. (Proteomics 6:2746-2758, 2006). Results demonstrated that more proteins specifically bound with Cu-IMAC could be enriched through removal of metal ions from samples by IDA-Sepharose pre-chromatography. Further studies are needed on metal-binding characteristics of these proteins in vivo and the relationship between Cu ions and protein biological

  19. Altered expression of several genes in IIIManL-defective mutants of Streptococcus salivarius demonstrated by two-dimensional gel electrophoresis of cytoplasmic proteins.

    Science.gov (United States)

    Lapointe, R; Frenette, M; Vadeboncoeur, C

    1993-05-01

    Mannose, glucose and fructose are transported in Streptococcus salivarius by a phosphoenolpyruvate:mannose phosphotransferase system (PTS) which consists of a membrane-bound Enzyme II (EII) and two forms of IIIMan having molecular weights of 38,900 (IIIManH) and 35,200 (IIIManL), respectively. We have previously reported the isolation of spontaneous mutants lacking IIIManL and showed that they exhibit higher beta-galactosidase activity than the parental strain after growth on glucose, and that some of them constitutively express a fructose PTS which is induced by fructose in the parental strain. In an attempt to determine whether the expression of other genes is affected by the mutation and what the physiological link is between them, we examined three S. salivarius IIIManL-defective mutants (strains A37, B31 and G29) and the parental strain using two-dimensional gel electrophoresis after growth of the cells on a variety of sugars. After growth on glucose, five new proteins were detected in the cytoplasm of the three mutants. Two of these proteins were induced in the parental strain by galactose or oligosaccharides containing galactose, and one was specifically induced by melibiose. The other two proteins were not detected in the parental strain under any of the growth conditions tested. Two other proteins were only detected in glucose-grown cells of mutant A37, and a protein associated with the metabolism of fructose was constitutively expressed in mutants B31 and G29. Moreover, we have found that under identical growth conditions the amounts of several other proteins which were detected in the parental strain were either increased or decreased in the mutants. Globally, our results have indicated that (1) the expression of several genes was affected in the spontaneous IIIManL-defective mutants; (2) some of the proteins abnormally produced in the mutants were specifically induced in the parental strain by sugars; (3) the phenotypic modifications observed in the

  20. The Goat (Capra hircus) Mammary Gland Mitochondrial Proteome: A Study on the Effect of Weight Loss Using Blue-Native PAGE and Two-Dimensional Gel Electrophoresis

    Science.gov (United States)

    Cugno, Graziano; Parreira, José R.; Ferlizza, Enea; Hernández-Castellano, Lorenzo E.; Carneiro, Mariana; Renaut, Jenny; Castro, Noemí; Arguello, Anastasio; Capote, Juan

    2016-01-01

    Seasonal weight loss (SWL) is the most important limitation to animal production in the Tropical and Mediterranean regions, conditioning producer’s incomes and the nutritional status of rural communities. It is of importance to produce strategies to oppose adverse effects of SWL. Breeds that have evolved in harsh climates have acquired tolerance to SWL through selection. Most of the factors determining such ability are related to changes in biochemical pathways as affected by SWL. In this study, a gel based proteomics strategy (BN: Blue-Native Page and 2DE: Two-dimensional gel electrophoresis) was used to characterize the mitochondrial proteome of the secretory tissue of the goat mammary gland. In addition, we have conducted an investigation of the effects of weight loss in two goat breeds with different levels of adaptation to nutritional stress: Majorera (tolerant) and Palmera (susceptible). The study used Majorera and Palmera dairy goats, divided in 4 sets, 2 for each breed: underfed group fed on wheat straw (restricted diet, so their body weight would be 15–20% reduced by the end of experiment), and a control group fed with an energy-balanced diet. At the end of the experimental period (22 days), mammary gland biopsies were obtained for all experimental groups. The proteomic analysis of the mitochondria enabled the resolution of a total of 277 proteins, and 148 (53%) were identified by MALDI-TOF/TOF mass spectrometry. Some of the proteins were identified as subunits of the glutamate dehydrogenase complex and the respiratory complexes I, II, IV, V from mitochondria, as well as numerous other proteins with functions in: metabolism, development, localization, cellular organization and biogenesis, biological regulation, response to stimulus, among others, that were mapped in both BN and 2DE gels. The comparative proteomics analysis enabled the identification of several proteins: NADH-ubiquinone oxidoreductase 75 kDa subunit and lamin B1 mitochondrial (up

  1. Influence of one- and two-dimensional gel electrophoresis procedure on metal-protein bindings examined by electrospray ionization mass spectrometry, inductively coupled plasma mass spectrometry, and ultrafiltration.

    Science.gov (United States)

    Schmidt, Anne-Christine; Störr, Bianca; Kummer, Nicolai-Alexeji

    2011-08-15

    Three independent methods, (i) electrospray ionization mass spectrometry (ESI-MS), (ii) carrying out the complete protein preparation procedure required for protein gel electrophoresis (GE) including extraction, precipitation, washing, and desalting with subsequent microwave digestion of the produced protein fractions for metal content quantification, and (iii) ultrafiltration for separating protein-bound and unbound metal fractions, were employed to elucidate the influences of protein sample preparation and GE running conditions on metal-protein bindings. A treatment of the protein solution with acetone instead of trichloroacetic acid or ammonium sulfate for precipitate formation led to a strongly enhanced metal binding capacity. The desalting step of the resolubilized protein sample caused a metal loss between 10 and 35%. The omission of some extraction buffer additives led to a diminished metal binding capacity of protein fractions obtained from the sample preparation procedure for GE, whereas a tenside addition to the protein solution inhibited metal-protein bindings. The binding stoichiometry of Cu and Zn-protein complexes determined by ESI-MS was influenced by the type of the metal salt which was applied to the protein solution. A higher pH value of the sample solution promoted the metal ion complexation by the proteins. Ultrafiltration experiments revealed a higher Cu- and Zn-binding capacity of the model protein lysozyme in both resolubilization buffers for 1D- and 2D-GE compared to the protein extraction buffer. Strongly diminished metal binding capacities of lysozyme were recorded in the running buffer of 1D-GE and in the gel staining solutions.

  2. Phenols content and 2-D electrophoresis protein pattern: a promising tool to monitor Posidonia meadows health state

    Directory of Open Access Journals (Sweden)

    Randazzo Davide

    2007-07-01

    Full Text Available Abstract Background The endemic seagrass Posidonia oceanica (L. Delile colonizes soft bottoms producing highly productive meadows that play a crucial role in coastal ecosystems dynamics. Human activities and natural events are responsible for a widespread meadows regression; to date the identification of "diagnostic" tools to monitor conservation status is a critical issue. In this study the feasibility of a novel tool to evaluate ecological impacts on Posidonia meadows has been tested. Quantification of a putative stress indicator, i.e. phenols content, has been coupled to 2-D electrophoretic protein analysis of rhizome samples. Results The overall expression pattern from Posidonia rhizome was determined using a preliminary proteomic approach, 437 protein spots were characterized by pI and molecular weight. We found that protein expression differs in samples belonging to sites with high or low phenols: 22 unique protein spots are peculiar of "low phenols" and 27 other spots characterize "high phenols" samples. Conclusion Posidonia showed phenols variations within the meadow, that probably reflect the heterogeneity of environmental pressures. In addition, comparison of the 2-D electrophoresis patterns allowed to highlight qualitative protein expression differences in response to these pressures. These differences may account for changes in metabolic/physiological pathways as adaptation to stress. A combined approach, based on phenols content determination and 2-D electrophoresis protein pattern, seems a promising tool to monitor Posidonia meadows health state.

  3. 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.

  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. 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.

  6. Establishment of two-dimensional electrophoresis system for proteome of Coelomactra antiquata mantle%西施舌外套膜蛋白质组双向电泳体系的构建

    Institute of Scientific and Technical Information of China (English)

    田美; 申欣; 程汉良; 孟学平

    2009-01-01

    Coelomactra antiquata is a high value economic shellfish which is famous treasure feast food and medical care of aquaculture consumption.The border cells of C.antiquata mantle can secrete calcium carbonate to form shells.By comparing the experimental analysis of different pH gradient strips,the optimal conditions of hydration,and different staining methods on the impact of the results of two-dimensional gel electrophoresis,we established the mantle proteome two-dimensional gel electrophoresis system of C.antiquata,which provide the basis to study the protein composition of formation of C.antiquata mantle from the protein level case.The results showed that:using pH 4~7 with the non-linear strip,the inclusion of hydration desalting step,staining method using silver nitrate staining,can obtain the two-dimensional gel electrophoresis map with a high-resolution and high reproducibility which laid the foundation for further research the protein composition of C.antiquata mantle.%建立了西施舌(Coelomactra antiquata)外套膜蛋白质组的双向凝胶电泳体系,比较分析了不同pH梯度胶条、水化条件的优化及不同染色方法对双向电泳结果的影响.结果表明:用pH 4~7的非线性胶条,水化时加上除盐步骤,采用硝酸银染色,即可获得高分辨率、高重现性的双向电泳图谱,为进一步研究西施舌外套膜蛋白质的组成奠定了基础.

  7. 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.

  8. 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.

  9. 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

    Analysis of cellular protein patterns by computer-aided 2-dimensional gel electrophoresis together with recent advances in protein sequence analysis have made possible the establishment of comprehensive 2-dimensional gel protein databases that may link protein and DNA information and that offer a...

  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 ...

  11. MALDI-TOF MS applied to apoC-III glycoforms of patients with congenital disorders affecting O-glycosylation. Comparison with two-dimensional electrophoresis

    NARCIS (Netherlands)

    Yen-Nicolay, S.; Boursier, C.; Rio, M. del; Lefeber, D.J.; Pilon, A.; Seta, N.; Bruneel, A.

    2015-01-01

    PURPOSE: The O-glycan abnormalities accompanying some congenital disorders of glycosylation, namely conserved oligomeric Golgi-congenital disorders of glycosylation (COG-CDGs) and ATP6V0A2-CDGs, are mainly detected using electrophoresis methods applied to circulating apolipoprotein C-III. The object

  12. Comparative Analysis of the Endosperm Proteins Separated by 2-D Electrophoresis for Two Cultivars of Hybrid Rice (Oryza sativa L.)

    Institute of Scientific and Technical Information of China (English)

    Pingfang Yang; Shihua Shen; Tingyun Kuang

    2006-01-01

    Liangyoupeijiu is a two-parental-line, and Shanyou63 is a three-parental-line hybrid rice (Oryza sativa L.).Although both belong to the indica subspecies, they have obvious differences with respect to morphology,physiology and grain quality. Variations in endosperm protein compositions were studied by comparing the 2-D electrophoresis (2-DE) maps for these two cultivars of hybrid rice. After matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF/MS) analysis, a 21-kDa precursor of 19-kDa globulin was identified as the major storage protein for both cultivars. Some isoforms of peroxiredoxin and seed maturation protein were found to only exist in Shanyou63, whereas aldose reductase and starch granule-bound starch synthase were only detected in Liangyoupeijiu. These data might provide a foundation for further comparative studies of these two cultivars of hybrid rice.

  13. Isolation, identification and characterisation of starch-interacting proteins by 2-D affinity electrophoresis.

    Science.gov (United States)

    Kosar-Hashemi, Behjat; Irwin, Jennifer A; Higgins, Jody; Rahman, Sadequr; Morell, Matthew K

    2006-05-01

    A 2-D affinity electrophoretic technique (2-DAE) has been used to isolate proteins that interact with various starch components from total barley endosperm extracts. In the first dimension, proteins are separated by native PAGE. The second-dimensional gel contains polysaccharides such as amylopectin and glycogen. The migration of starch-interacting proteins in this dimension is determined by their affinity towards a particular polysaccharide and these proteins are therefore spatially separated from the bulk of proteins in the crude extract. Four distinct proteins demonstrate significant affinity for amylopectin and have been identified as starch branching enzyme I (SBEI), starch branching enzyme IIa (SBEIIa), SBEIIb and starch phosphorylase using polyclonal antibodies and zymogram activity analysis. In the case of starch phosphorylase, a protein spot was excised from a 2-DAE polyacrylamide gel and analysed using Q-TOF MS/MS, resulting in the alignment of three internal peptide sequences with the known sequence of the wheat plastidic starch phosphorylase isoform. This assignment was confirmed by the determination of the enzyme's function using zymogram analysis. Dissociation constants (Kd) were calculated for the three enzymes at 4 degrees C and values of 0.20, 0.21 and 1.3 g/L were determined for SBEI, SBEIIa and starch phosphorylase, respectively. Starch synthase I could also be resolved from the other proteins in the presence of glycogen and its identity was confirmed using a polyclonal antibody and by activity analysis. The 2-DAE method described here is simple, though powerful, enabling protein separation from crude extracts on the basis of function.

  14. 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...

  15. Topological defects in two-dimensional crystals

    OpenAIRE

    Chen, Yong; Qi, Wei-Kai

    2008-01-01

    By using topological current theory, we study the inner topological structure of the topological defects in two-dimensional (2D) crystal. We find that there are two elementary point defects topological current in two-dimensional crystal, one for dislocations and the other for disclinations. The topological quantization and evolution of topological defects in two-dimensional crystals are discussed. Finally, We compare our theory with Brownian-dynamics simulations in 2D Yukawa systems.

  16. 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

    Analysis of cellular protein patterns by computer-aided 2-dimensional gel electrophoresis together with recent advances in protein sequence analysis have made possible the establishment of comprehensive 2-dimensional gel protein databases that may link protein and DNA information and that offer...... 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...... partial protein sequence to genes for which the full DNA sequence and the chromosome location is known, and to study the regulatory properties and function of groups of proteins that are coordinately expressed in a given biological process. Human 2-dimensional gel protein databases are becoming...

  17. Comparison of protein expression profiles between three Perkinsus spp., protozoan parasites of molluscs, through 2D electrophoresis and mass spectrometry.

    Science.gov (United States)

    Fernández-Boo, S; Chicano-Gálvez, E; Alhama, J; Barea, J L; Villalba, A; Cao, A

    2014-05-01

    The genus Perkinsus includes protozoan parasites of a wide range of marine molluscs worldwide, some of which have been responsible for heavy mollusc mortalities and dramatic economic losses. This study was performed with the aim of increasing the knowledge of Perkinsus spp. proteome. Proteins extracted from in vitro cultured cells of three species of this genus, P. marinus, P. olseni and P. chesapeaki, were analysed using 2D electrophoresis. Four gels from each species were produced. Qualitative and quantitative comparisons among gels were performed with Proteamweaver software. Cluster analysis grouped the four gels of each Perkinsus sp.; furthermore, P. marinus and P. olseni gels were grouped in a cluster different from P. chesapeaki. Around 2000 spots of each species were considered, from which 213 spots were common to the 3 species; P. chesapeaki and P. marinus shared 310 spots, P. chesapeaki and P. olseni shared 315 spots and P. marinus and P. olseni shared 242 spots. A number of spots were exclusive of each Perkinsus species: 1161 spots were exclusive of P. chesapeaki, 1124 of P. olseni and 895 of P. marinus. A total of 84 spots, including common and species-specific ones, were excised from the gels and analysed using MALDI-TOF and nESI-IT (MS/MS) techniques. Forty-two spots were successfully sequenced, from which 28 were annotated, most of them clustered into electron transport, oxidative stress and detoxification, protein synthesis, carbohydrate metabolism, signal transduction, metabolic process and proteolysis.

  18. Two-dimensional Electrophoresis Analysis of Proteins in Response to Cold Stress in Extremely Cold-resistant Winter Wheat Dongnongdongmai 1 Tillering Nodes

    Institute of Scientific and Technical Information of China (English)

    Cang Jing; Yu Jing; Liu Li-jie; Yang Yang; Cui Hong; Hao Zai-bin; Li Zhuo-fu

    2012-01-01

    The overwintering survival ratio of the cultivar Dongnongdongmai 1 with strong cold-resistance in paramos of Heilongjiang Province in China are over 85%. The tillering nodes are the most important organs for overwintering survival of winter wheat, because there are more substances associated with cold resistance in tillering nodes than those in leaves and roots. Proteins in the tillering nodes of the cold-resistant cultivar Dongnongdongmai 1 grown under field conditions with or without any lowtemperature stress were analyzed by 2-dimensional electrophoresis and identified by mass spectrometry. In the range of pH 4-7, the expression of 37 proteins showed obvious difference (±more than two fold) in the proteomic maps of cold-stressed and non-stressed tillering nodes, including a new protein spot. All proteins exhibiting the difference in expression were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, followed by a database search for protein identification and function prediction. Five groups of proteins were confirmed, namely stress-related proteins (22%), metabolism-associated proteins (35%), and signaling molecules (24%), cell wall-binding proteins (5%), unclear proteins (14%). This indicated that tillering node cells supported the energy requirements of plant growth and stress resistance by signal transduction adapting to metabolism and structure.

  19. Analysis of cerebrospinal fluid protein expression in Parkinson's disease by two-dimensional difference gel electrophoresis%应用DIGE测定帕金森病脑脊液中蛋白变化

    Institute of Scientific and Technical Information of China (English)

    王尔松; 高翔; 周嘉伟; 胡杰; 夏鹰; 郭继光; 呼建文; 江澄川

    2008-01-01

    Objective To identify differentially expressed proteins in cerebrospinal fluid (CSF) of Parkinson's disease (PD), so as to provide clues for investigating PD biomarkers. Methods Two-dimensional difference gel electrophoresis (2D DIGE) technique, in combination with matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), was used to determine the differentially expressed CSF proteins in PD patients in comparison with control subjects. Results The levels of 20 protein spots were significantly altered in PD CSF. Of them, 11 spots were up-regulated and 9 spots were down-regulated. Of the 8 proteins identified in the profile of differentially expressed protein spots between patients and controls, an isoform of apolipoprotein A-I, myosin phosphatase target subunit 1 (MYPT1), and 3 unknown proteins were down-regulated, whereas an apolipoprotein A-I isoform, proapolipoprotein, and lipoprotein were up-regulated. Conclusions MYPT1 is related with synapse function and proapolipoprotein, lipoprotein and apo A-I are associated with cholesterol metabolism. These proteins may have links with the pathogenesis of PD and may be identified as CSF biomarks in PD.%目的 测定帕金森病(PD)脑脊液中蛋白的变化,为进一步探索PD的生物标记物提供线索.方法 采用荧光差异凝胶电泳技术分离并筛选PD和正常对照者脑脊液中差异表达蛋白质,用基质辅助激光解吸电离飞行时间质谱(MALDI-TOF MS)或串联质谱技术进行鉴定并分析.结果 共发现20个明显的差异蛋白点,其中11个点在PD中上调,9个点下调.共鉴定出8个蛋白质,其中有3个未知蛋白,均表现为下调.蛋白MYPT1出现明显下调,载脂蛋白原、脂蛋白发生明显上调,载脂蛋白A-I的一个异构体发生上调,一个异构体发生下调.结论 MYPT1与突触功能有关,载脂蛋白原、脂蛋白、载脂蛋白A-I与胆固醇代谢有关,这些蛋白与PD发生有一定关联,有可能成为PD的生物标记物.

  20. Assessment of Protein Binding of 5-Hydroxythalidomide Bioactivated in Humanized Mice with Human P450 3A-Chromosome or Hepatocytes by Two-Dimensional Electrophoresis/Accelerator Mass Spectrometry.

    Science.gov (United States)

    Yamazaki, Hiroshi; Suemizu, Hiroshi; Kazuki, Yasuhiro; Oofusa, Ken; Kuribayashi, Shunji; Shimizu, Makiko; Ninomiya, Shinichi; Horie, Toru; Shibata, Norio; Guengerich, F Peter

    2016-08-15

    Bioactivation of 5-hydroxy-[carbonyl-(14)C]thalidomide, a known metabolite of thalidomide, by human artificial or native cytochrome P450 3A enzymes, and nonspecific binding in livers of mice was assessed using two-dimensional electrophoresis combined with accelerator mass spectrometry. The apparent major target proteins were liver microsomal cytochrome c oxidase subunit 6B1 and ATP synthase subunit α in mice containing humanized P450 3A genes or transplanted humanized liver. Liver cytosolic retinal dehydrogenase 1 and glutathione transferase A1 were targets in humanized mice with P450 3A and hepatocytes, respectively. 5-Hydroxythalidomide is bioactivated by human P450 3A enzymes and trapped with proteins nonspecifically in humanized mice.

  1. Comparative fluorescence two-dimensional gel electrophoresis using a gel strip sandwich assembly for the simultaneous on-gel generation of a reference protein spot grid.

    Science.gov (United States)

    Ackermann, Doreen; Wang, Weiqun; Streipert, Benjamin; Geib, Birgit; Grün, Lothar; König, Simone

    2012-05-01

    The comparison of proteins separated on 2DE is difficult due to gel-to-gel variability. Here, a method named comparative fluorescence gel electrophoresis (CoFGE) is presented, which allows the generation of an artificial protein grid in parallel to the separation of an analytical sample on the same gel. Different fluorescent stains are used to distinguish sample and marker on the gel. The technology combines elements of 1DE and 2DE. Special gel combs with V-shaped wells are placed in a stacking gel above the pI strip. Proteins separated on the pI strip are electrophoresed at the same time as marker proteins (commercially available purified protein of different molecular weight) placed in V-wells. In that way, grids providing approximately 100 nodes as landmarks for the determination of protein spot coordinates are generated. Data analysis is possible with commercial 2DE software capable of warping. The method improves comparability of 2DE protein gels, because they are generated in combination with regular in-gel anchor points formed by protein standards. This was shown here for two comparative experiments with three gels each using Escherichia coli lysate. For a set of 47 well-defined samples spots, the deviation of the coordinates was improved from 7% to less than 1% applying warping using the marker grid. Conclusively, as long as the same protein markers, the same size of pI-strips and the same technology are used, gel matching is reproducibly possible. This is an important advancement for projects involving comparison of 2DE-gels produced over several years and in different laboratories. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. An efficient and rapid method for enrichment of lipophilic proteins from Mycobacterium tuberculosis H37Rv for two-dimensional gel electrophoresis.

    Science.gov (United States)

    Sharma, Divakar; Bisht, Deepa

    2016-05-01

    Lipophilic proteome profiling is crucial because they have an anticipated role in biological processes and pathogenesis of Mycobacterium tuberculosis. These lipophilic proteins might be used as potential targets for the development of newer diagnostic markers and drug targets due to their association with membranes and drugs. We developed an efficient and rapid method to enrich the lipophilic proteins extraction from M. tuberculosis H37Rv for 2DE. In the extraction of lipophilic proteins, nonionic detergent (Triton X-100) was added in sonication buffer that augmented the solubilization of the proteins at the time of sonication. Enriched whole cell lysate was subjected to direct phase separation using Triton X-114, without the need for preisolation of membranes. In this study, we report that our optimized extraction buffer increased the lipophilic proteins extraction and their improved resolution on 2D gel up to two- to threefolds (quantitatively and qualitatively) as compared to standard extraction buffer. Some proteins were identified by MALDI-TOF/MS. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. The human keratinocyte two-dimensional gel protein database (update 1995): mapping components of signal transduction pathways

    DEFF Research Database (Denmark)

    Celis, J E; Rasmussen, H H; Gromov, P

    1995-01-01

    The master two-dimensional (2-D) gel database of human keratinocytes currently lists 3154 cellular proteins (2224 isoelectric focusing, IEF; and 930 nonequilibrium pH gradient electrophoresis, NEPHGE), many of which correspond to post-translational modifications. 1082 polypeptides have been ident...

  4. 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.

  5. 关节滑液双向凝胶电泳预处理方案的评估%Assessment of synovial fluid preparation for two-dimensional gel electrophoresis

    Institute of Scientific and Technical Information of China (English)

    廖伟雄; 李众利; 王杰; 王鸿丽; 傅仰木; 白晓伟

    2013-01-01

    目的:评估膝关节骨性关节炎(knee osteoarthritis,KOA)患者关节滑液双向凝胶电泳几种预处理方案的优劣。方法收集2012年1月-2012年3月在解放军总医院行关节镜诊治KOA患者关节滑液样本8例,混合均匀并等分为36份。9份不进行任何处理,9份用透明质酸酶处理,9份采用亲和层析法除高丰度蛋白,9份用透明质酸酶联合亲和层析法进行处理,对36份滑液进行双向凝胶电泳,比较未处理组与处理组以及处理组之间电泳图谱的差异并确定最佳预处理方案,采用最佳方案对12例不同严重程度KOA患者关节滑液进行预处理,分析寻找差异蛋白点并用质谱定性。结果采用透明质酸酶联合亲和层析法对样本进行预处理后获得的电泳图谱质量最佳。用此法进行预处理的12例不同严重程度KOA患者滑液,鉴定出了载脂蛋白、纤维蛋白原D片段等与关节疾病相关的蛋白因子。结论透明质酸酶联合亲和层析预处理方案能获得高质量的电泳图谱,可作为蛋白质组学研究中优先选取的样本预处理方案。%Objective To assess the advantages and disadvantages of several synovial fluid preparation methods for two-dimensional gel electrophoresis in patients with knee osteoarthritis (KOA). Methods Eight synovial fluid samples from KOA patients admitted to our hospital from January 2012 to March 2012 for arthroscopic diagnosis and treatment were mixed up and divided into 36 equal shares. Of which, 9 were not pretreated, 9 were treated with hyaluronidase, 9 with affinity chromatography to deplete high-abundance proteins, and 9 with combined hyaluronidase and affinity chromatography. The 36 equal sample shares were treated by two-dimensional gel electrophoresis. Different gel electrophoresis images of the treated and untreated samples were compared to determine the optimal pretreatment plan which was used in pretreatment of synovial fluid from 12

  6. Two-Dimensional Planetary Surface Lander

    Science.gov (United States)

    Hemmati, H.; Sengupta, A.; Castillo, J.; McElrath, T.; Roberts, T.; Willis, P.

    2014-06-01

    A systems engineering study was conducted to leverage a new two-dimensional (2D) lander concept with a low per unit cost to enable scientific study at multiple locations with a single entry system as the delivery vehicle.

  7. 不同地域东亚钳蝎蝎毒的双向电泳鉴定%Identification of Scorpion Venom in Buthus Martensii Karsch from Different Regions by Two-dimensional Gel Electrophoresis (2-DE)

    Institute of Scientific and Technical Information of China (English)

    倪伊婷; 郭美华; 王君德; 刘赟; 辛毅; 吴大畅

    2012-01-01

    Objective To identify qualitatively and analyze the activity of scorpion venom in Buthus Martensii Karsch from different regions by two-dimensional gel electrophoresis (2-DE),and investigate the protein composition and function differences of scorpion venom. Methods Quantitive identification and content determination of proteins in scorpion venom were performed following preconditions including dissolution, desalting and condensing of the freeze-drying scorpion venom powder. The proteins in scorpion venom were separated by pH gradient isoeleciric focusing and SUS-PAGE gel eledrophoresis. The two-dimensional electrophoresis gel map was captured via gel imaging system after staining. The special different proteins were determined and comparatively analyzed through PD Quesl. Image analysis software,and thus the scorpion venom from different regions was qualitatively identified. Results Protein fingerprints were acquired from three samples. Total protein spots were 80,69,77,and the distinctive number of which were 56,46,55 , successively. Conclusion Scorpion venom in Buthus Martensii Karsch from diffe.re.nt regions separated with 2-DE show obviously diverse protein distributions.%目的 利用蛋白质组学中双向电泳技术,定性鉴定、分析不同地域东亚钳蝎蝎毒活性的差别,探索不同产地蝎毒的蛋白质组成及功能差异.方法 将不同产地的冷冻干燥蝎毒粉经溶解、除盐、浓缩后测定蝎毒蛋白质含量,进行定量的蝎毒鉴定.采用pH梯度等电聚焦和SDS-PAGE凝胶电泳技术分离蝎毒蛋白质.银染后通过凝胶成像系统获 得双向电泳凝胶图谱,用PD Quest图像分析软件比较分析,确定差异的特征蛋白点,从而定性鉴定不同产地蝎毒.结果 获得3个样品的蛋白质指纹图谱.分别检测出80,69和77个点,特征差异蛋白点依次为56,46和55个.结论 不同产地的东亚钳蝎蝎毒通过双向电泳分离蛋白后,表现出明显不同的蛋白点分布.

  8. 适于双向电泳分析的酵母胞外蛋白提取方法%Procedure to Prepare Samples for Two-dimensional Electrophoresis of Secreted Proteins from Saccharomyces cerevisiae

    Institute of Scientific and Technical Information of China (English)

    杜维; 朴永哲; 黄玮; 谷月; 赵长新

    2015-01-01

    Saccraomyces cerevsiae FFC2144 was cultured in nitrogen base medium without protein. The secretory proteins of yeasts were extracted by ammonium sulfate precipitation, ultrafiltration and lyophilization-phenol extraction respectively. Extraction rates by 3 methods were calculated and the proteins were separated by two-dimensional electrophoresis. The proteins isolated were confirmed by MALDI-TOF-MS. The extraction rate by lyophilization-phenol method was 73.67% and 114 protein spots were obtained with the most protein spots and clearest electrophoretogram. Lyophilization-phenol method could be an ideal separation method for studying secretory proteomics.%采用了无蛋白酵母培养基培养FFC2144酵母细胞,用硫铵沉淀法、超滤法、冻干酚提等方法提取酵母胞外蛋白,计算3种方法的提取率并分别用双向电泳的方法对提取到的蛋白样品进行分离,同时运用质谱鉴定分离后蛋白.其中冻干-平衡酚法提取后得到114个蛋白点,提取率为73.67%,图谱识别的蛋白点最多图谱最清晰,是研究分泌类蛋白质组学理想的分离方法.

  9. 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.

  10. Two-dimensional gel electrophoresis and its application in vaccine research,development and production%双向电泳技术及其在疫苗研究开发与生产中的应用

    Institute of Scientific and Technical Information of China (English)

    李爱灵; 王辉; 刘保奎

    2009-01-01

    双向电泳技术已广泛用于蛋白质组学研究,该技术除了在农业和基础医学领域中有着广泛的应用外,还在疫苗的研究、开发和生产中具有重要的应用前景.此文就双向电泳技术在疫苗抗原及疫苗候选菌株的筛选、基因工程疫苗的研究、抗原呈递及免疫应答机制的研究和疫苗生产过程中批间一致性分析等方面的应用进行了综述.%Two-dimensional gel electrophoresis has been widely used in proteomics research.The technology has a wide range of applications in the fields of agriculture and basic medicine,and has important application prospects in the area of vaccine research,development and production.This review summarizes the application of the technology in the area of vaccine research,development and production,including antigen screening,selection of candidate vaccine strain,research on genetic engineering vaccine,antigen-presenting and immune response mechanisms,and inter-batch consistency analysis in the process of vaccine production.

  11. 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.

  12. 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.

  13. Optimization of Two-Dimensional Electrophoresis Conditions for Proteome Analysis of Peach Fruit%桃果实总蛋白质双向电泳优化体系的建立

    Institute of Scientific and Technical Information of China (English)

    张丽; 姜丽; 石韵; 康若祎; 王利斌; 郁志芳

    2013-01-01

    An effective two -dimensional electrophoresis system was developed to determine the total protein from "huiyulu" peach fruit in this study. The optimum conditions for total protein detection were listed as follows: phenol extraction,800 μg protein sample, 17 cm IPG strip with pH 4-7,and finally detecting proteins with modified colloidal coomassie brilliant blue G-250 staining. With the optimum conditions,a high quality 2-DE map with low background was achieved.%以“晖雨露”水蜜桃为试验材料,建立了一种适用于桃果实总蛋白质的双向电泳体系.最终试验确定采用酚抽法提取桃果实蛋白质,采用17 cm,pH 4~7的线性IPG胶条,800 μg蛋白质上样,并用考马斯亮蓝G-250胶体考染,可以得到背景清晰、分辨率高的双向电泳图谱.对影响双向电泳图谱质量的因素进行了讨论分析.

  14. 用于双向凝胶电泳分析的奶牛乳清蛋白样品制备方法的比较%Comparison of Bovine Whey Protein Preparation Methods for Two-Dimensional Gel Electrophoresis Analysis

    Institute of Scientific and Technical Information of China (English)

    边艳杰; 李庆章; 张岚; 郭洪波; 吕英

    2011-01-01

    为建立适用于双向凝胶电泳分析的奶牛乳清蛋白的制备方法,分别比较了直接裂解法、三氯乙酸-丙酮法,Trizol法和2-D clean up kit法对奶牛乳清蛋白提取效率和双向凝胶电泳图谱的影响.用2-D Quant Kit试剂盒测定蛋白浓度,分别用十二烷基磺酸钠.聚丙烯酰胺凝胶电泳和双向凝胶电泳进行奶牛乳清蛋白的分离.蛋白定量结果表明,2-D clean up kit法产率最高,直接裂解法、三氯乙酸一丙酮法次之,trizol法产率最低;十二烷基磺酸钠-聚丙烯酰胺凝胶电泳结果表明,2-D clean up kit法提取的蛋白质量最高;双向电泳图谱分析表明,2-D clean up kit法得到的蛋白图谱与另外3种方法相比,检测到的蛋白点最多,图谱背景清晰,分辨率最高.结果提示,2-D clean-up法相对最适合于双向凝胶电泳分析奶牛乳清蛋白样品的制备,尤其对一些低丰度高分子量蛋白的分离效果较为明显.%Bovine whey contains many kinds of high-abundance proteins and varied interferential impurity, so it' s hard to obtain satisfied protein images of bovine whey in two dimensional electrophoresis (2-DE). Protein extraction from bovine whey is a key step to achieve high-resolution protein separation in 2-DE. Four routine total protein extraction methods were compared in order to determine an optimal one in 2-DE analysis for bovine whey. Bovine whey protein were extracted by direct schizolysis, TCA-acetone, trizol precipitation and 2-D clean up kit. The concentration of total protein was measured by 2-D quant kit, bovine whey protein were separated using SDS-PAGE and 2-DE. The data showed that use of 2-D clean up kit gave maximum protein yield, and the use of trizol gave the lowest. The result of SDSPAGE showed that use of 2-D clean up kit generated the highest-quality protein among these four methods. The result of 2-DE gels showed that 238 protein spots were detected on the 2-DE gel using 2-D clean up kit, and the gel

  15. Position Analysis of Three Recombinant Proteins of Echinococcus granulosus Protoscolex with Two-dimensional Electrophoresis%细粒棘球蚴原头节3种重组抗原的双向电泳定位分析

    Institute of Scientific and Technical Information of China (English)

    朱明星; 李君良; 巨艳; 高鹏; 赵巍

    2013-01-01

    Objective To obtain specific antibodies of the three recombinant antigens obtained previously,rEgZW-5,rEg14-3-3 and rEgP-29,for identifiying the corresponding proteins in two-dimensional electrophoretogram of Echinococcus granulosus protoscolex.Methods The distribution of proteins from E.granulosus protoscoleces was judged by SDS-PAGE previously.Two-dimensional electrophoresis was used to separate proteins from E.granulosus protoscoleces,and the result was scanned and analyzed by the PDquest software to get the information about the quantity of proteins as well as their isoelectric point (IP) and relative molecular mass (Mr).Rabbits were immunized with the 3 recombinant antigens and antibodies were purified from antisera.Western blotting was used to identify the protein as marker in two-dimensional electrophoretogram of protoscolex.Results SDS-PAGE displayed that the proteins separated from Echinococcus granulosus protoscoleces mainly distributed in the Mr region of 18 000-90000.240proteins were obtained by two-dimensional electrophoresis with Mr 15790-117050 and IP 4.0-9.5,and 85.8% (206/241) of the proteins showed the IP ranged from 5 to 9.Western blotting showed that the specific antibody of rEg14-3-3 identified the 14-3-3 protein in two-dimensional electrophoretogram of protoscolex with Mr 33 000 and IP 4.86,the specific antibody of rEgZW-5 identified the ZW-5 protein with Mr 23 000 and IP 4.98,and the specific antibody of rEg P-29 identified the P-29 protein with Mr 29 000 and IP 5.65.Conclusion The antibodies against the three recombinant proteins from Echinococcus granulosus protoscoleces can identify corresponding proteins in the two-dimensional electrophotoregrams.%目的 利用已有的细粒棘球蚴(Echinococcus granulosus)原头节3种重组抗原rEgZW-5、rEg14-3-3和rEgP-29获得特异性抗体,以识别双向电泳图谱中相应的蛋白位点. 方法 十二烷基硫酸钠-聚丙烯酰胺凝胶电泳(SDS-PAGE)初步分离细粒棘球蚴原头节

  16. Si-B-C陶瓷涂敷2D C/SiC复合材料的抗氧化性能%Oxidation resistance of two dimensional C/SiC composite coated with Si-B-C ceramic

    Institute of Scientific and Technical Information of China (English)

    左新章; 张立同; 刘永胜; 成来飞; 龚慧灵

    2013-01-01

    Two dimensional C/SiC composite coated with Si-B-C ceramic was prepared via chemical vapor deposition (CVD).Properties and structure evolution and self-healing mechanisms of the C/SiC composite were studied after oxidation for 10 h during 700-1200 ℃.At the same time,the evolution of morphologies,composition and phase for Si-B-C ceramic were also investigated.The experimental results show that the oxidation of Si-B-C ceramic accelerates with the temperature increasing,however,the oxidation scale is shallow and no more than 7 μm.With the temperature increasing,viscosity of borosilicate glass oxidized from Si-B-C ceramic reduces but volatilization accelerates.When the temperature increases to 1200 ℃,SiO2 crystallizes from borosilicate glass.C/SiC composite coated with Si-B-C ceramic shows an excellent oxidation resistance.Mass loss increases with temperature increasing,which is only 0.47% after oxidation for 10 h at 1200 ℃.Furthermore,the strength retention ratio is 91.6% at 1000 ℃,higher than that at other temperatures.The main mechanisms for excellent oxidation resistance of C/SiC composite is that borosilicatc glass oxidized from Si-B-C ceramic can seal cracks in composite effectively.%利用化学气相沉积(CVD)法制备了Si-B-C陶瓷涂敷改性的2D C/SiC复合材料,研究了其在700~1200℃氧化10 h性能和结构的演变规律以及自愈合机制,同时获得了Si-B-C涂层在不同温度氧化后的形貌、组分和物相转变规律.结果表明:涂敷在复合材料表面的Si-B-C陶瓷随温度的升高氧化加快,但氧化程度较低,不深于7μm;随温度的升高,氧化形成的硅硼玻璃黏度降低,挥发增强;当温度达到1200℃时,硅硼玻璃析出SiO2晶体;Si-B-C陶瓷涂敷改性的C/SiC具有优良的抗氧化性能,随氧化温度的升高,复合材料失重率增加,但在1200℃氧化10h后失重率仅为0.47%;此外材料在1000℃氧化后的强度保持率最高,达到91.6%,Si-B-C陶瓷氧化形

  17. Total Protein Analysis by Two-dimensional Electrophoresis in Cysticerci of Taenia solium and Taenia asiatica%猪带绦虫囊尾蚴与亚洲带绦虫囊尾蚴蛋白双向电泳图谱分析

    Institute of Scientific and Technical Information of China (English)

    方文; 肖靓靓; 包怀恩; 牟荣

    2011-01-01

    Two 20-day-old three-way crossed hybrid pigs were infected with 80 000 Taenia solium or T. Asiatica eggs, respectively. Immature cysticerci of the two species in liver were collected at 40 days after infection. The total proteins were separated by two-dimensional electrophoresis, and differentially expressed proteins were analyzed by Image-Master 2D Plantinum 6.0 software. The results showed that there were (236±12) and (231 ±14) protein spots in 2D electrophoresis gel images of T. Solium and T. Asiatica, respectively, with 3 proteins up-regulated and 7 proteins down-lated in T- scutum rt-Tir^rrus iiy 2-fold or more compared with those in T. Asioiica cystirercua-%将2头20日龄三元杂交乳猪分别感染猪带绦虫虫卵和亚洲带绦虫虫卵,8×104个/头.感染后40 d分别收集寄生在肝脏的未成熟猪带绦虫囊尾蚴(简称猪囊尾蚴)和亚洲带绦虫囊尾蚴,制备囊尾蚴蛋白,并进行蛋白双向电泳分析,用ImageMaster 2D Plantinum 6.0软件分析差异表达蛋白.结果显示,感染后40 d肝脏寄生的未成熟猪囊尾蚴和亚洲带绦虫囊尾蚴蛋白的双向电泳凝胶上分别有(236±12)和(231±14)个蛋白斑点,差异表达2倍以上的蛋白共10个,其中猪囊尾蚴表达上调的蛋白3个,下调的蛋白7个.

  18. Two-dimensional cubic convolution.

    Science.gov (United States)

    Reichenbach, Stephen E; Geng, Frank

    2003-01-01

    The paper develops two-dimensional (2D), nonseparable, piecewise cubic convolution (PCC) for image interpolation. Traditionally, PCC has been implemented based on a one-dimensional (1D) derivation with a separable generalization to two dimensions. However, typical scenes and imaging systems are not separable, so the traditional approach is suboptimal. We develop a closed-form derivation for a two-parameter, 2D PCC kernel with support [-2,2] x [-2,2] that is constrained for continuity, smoothness, symmetry, and flat-field response. Our analyses, using several image models, including Markov random fields, demonstrate that the 2D PCC yields small improvements in interpolation fidelity over the traditional, separable approach. The constraints on the derivation can be relaxed to provide greater flexibility and performance.

  19. Two-dimensional subwavelength plasmonic lattice solitons

    CERN Document Server

    Ye, F; Hu, B; Panoiu, N C

    2010-01-01

    We present a theoretical study of plasmonic lattice solitons (PLSs) formed in two-dimensional (2D) arrays of metallic nanowires embedded into a nonlinear medium with Kerr nonlinearity. We analyze two classes of 2D PLSs families, namely, fundamental and vortical PLSs in both focusing and defocusing media. Their existence, stability, and subwavelength spatial confinement are studied in detai

  20. 双向电泳分析鸢尾绿白嵌合叶片的蛋白质%Two-Dimensional Polyacrylamide Gel Electrophoresis Analysis of Proteins from Albino-Green Chimeric Leaves of Iris japonica

    Institute of Scientific and Technical Information of China (English)

    胡金勇; 曾英; 桑玉英

    2002-01-01

    Proteins extracted from albino-green chimeric leave s of Iris japonica were separated by two-dimensional polyacrylamide gel ele ctrophoresis and relative molecular weights and isoelectric points were determin ed.Approximately 400 protein spots were identified in each 2-D PAGE gel.Altered expression was apparent for at least 13 proteins.The results showed that protein expression patterns changed obviously in the green and white leaf strips.In com parison with the 2-D PAGE map from Arabidopsis thaliana in SWISS-2DPAGE data base, it revealed that the expression pattern of large subunit of RuBisCO and the proteins labeled W and T was closely related to the mechanism involved in chimeric variations of Iris japonic.%利用双向聚丙烯酰胺凝胶电泳对鸢尾(Iris japonica )绿白嵌合叶片的蛋白质进行分离,并初步鉴定了蛋白质的相对分子量和等电点.每个电泳图谱共检测到400余个蛋白点,其中至少13个蛋白的表达变化明显;结果表明,嵌合叶片的绿色与白色叶组织具有明显不同的蛋白质双向电泳图谱.与数据库中拟南芥双向电泳图谱相比较,发现Rubisco大亚基、标记为W和T蛋白的表达变化与产生绿白嵌合叶片的表型密切相关.

  1. Local doping of two-dimensional materials

    Science.gov (United States)

    Wong, Dillon; Velasco, Jr, Jairo; Ju, Long; Kahn, Salman; Lee, Juwon; Germany, Chad E.; Zettl, Alexander K.; Wang, Feng; Crommie, Michael F.

    2016-09-20

    This disclosure provides systems, methods, and apparatus related to locally doping two-dimensional (2D) materials. In one aspect, an assembly including a substrate, a first insulator disposed on the substrate, a second insulator disposed on the first insulator, and a 2D material disposed on the second insulator is formed. A first voltage is applied between the 2D material and the substrate. With the first voltage applied between the 2D material and the substrate, a second voltage is applied between the 2D material and a probe positioned proximate the 2D material. The second voltage between the 2D material and the probe is removed. The first voltage between the 2D material and the substrate is removed. A portion of the 2D material proximate the probe when the second voltage was applied has a different electron density compared to a remainder of the 2D material.

  2. Network generation enhances interpretation of proteomics data sets by a combination of two-dimensional polyacrylamide gel electrophoresis and matrix-assisted laser desorption/ionization-time of flight mass spectrometry.

    Science.gov (United States)

    Wang, Xijun; Zhang, Aihua; Sun, Hui; Wu, Gelin; Sun, Wenjun; Yan, Guangli

    2012-10-21

    Recent advances in proteomic technologies have enabled us to create detailed protein-protein interaction maps in diseases. As the size of the interaction dataset increases, powerful computational methods are required in order to effectively interpret network models from large scale interactome data. In this study, we carried out comparative proteomics to construct and identify the proteins networks associated with hepatic injury (HI) which are largely unknown, as a case study. All proteins expressed were separated and identified by two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time-of-flight-time-of-flight mass spectrometry (MALDI-TOF/TOF MS). Protein-interacting networks and pathways were mapped using STRING analysis program. We have performed for the first time a comprehensive profiling of changes in protein expression of HI rats, to uncover the networks altered by treated with CCl(4). Identification of fifteen spots (seven over-expressed and eight under-expressed) were established by MALDI-TOF/TOF MS. These proteins were subjected to functional pathway analysis using STRING software for better understanding of the biological context of the identified proteins. It suggested that modulation of multiple vital physiological pathways including DNA repair process, cell apoptosis, oxidation reduction, signal transduction, metabolic process, intracellular signaling cascade, regulation of biological processes, cell communication, regulation of cellular process, and molecular transport. In summary, the present study provides the first protein-interacting network maps and novel insights into the biological responses and potential pathways of HI. The generation of protein interaction networks clearly enhances the interpretation of proteomic data, particularly in respect of understanding molecular mechanisms of panel protein biomarkers.

  3. Binding energy of two-dimensional biexcitons

    DEFF Research Database (Denmark)

    Singh, Jai; Birkedal, Dan; Vadim, Lyssenko;

    1996-01-01

    Using a model structure for a two-dimensional (2D) biexciton confined in a quantum well, it is shown that the form of the Hamiltonian of the 2D biexciton reduces into that of an exciton. The binding energies and Bohr radii of a 2D biexciton in its various internal energy states are derived...... analytically using the fractional dimension approach. The ratio of the binding energy of a 2D biexciton to that of a 2D exciton is found to be 0.228, which agrees very well with the recent experimental value. The results of our approach are compared with those of earlier theories....

  4. Two-Dimensional Gel Electrophoresis Analyses of pH-Dependent Protein Expression in Facultatively Alkaliphilic Bacillus pseudofirmus OF4 Lead to Characterization of an S-Layer Protein with a Role in Alkaliphily

    Science.gov (United States)

    Gilmour, Raymond; Messner, Paul; Guffanti, Arthur A.; Kent, Rebecca; Scheberl, Andrea; Kendrick, Nancy; Krulwich, Terry Ann

    2000-01-01

    The large majority of proteins of alkaliphilic Bacillus pseudofirmus OF4 grown at pH 7.5 and 10.5, as studied by two-dimensional gel electrophoresis analyses, did not exhibit significant pH-dependent variation. A new surface layer protein (SlpA) was identified in these studies. Although the prominence of some apparent breakdown products of SlpA in gels from pH 10.5-grown cells led to discovery of the alkaliphile S-layer, the largest and major SlpA forms were present in large amounts in gels from pH 7.5-grown cells as well. slpA RNA abundance was, moreover, unchanged by growth pH. SlpA was similar in size to homologues from nonalkaliphiles but contained fewer Arg and Lys residues. An slpA mutant strain (RG21) lacked an exterior S-layer that was identified in the wild type by electron microscopy. Electrophoretic analysis of whole-cell extracts further indicated the absence of a 90-kDa band in the mutant. This band was prominent in wild-type extracts from both pH 7.5- and 10.5-grown cells. The wild type grew with a shorter lag phase than RG21 at either pH 10.5 or 11 and under either Na+-replete or suboptimal Na+ concentrations. The extent of the adaptation deficit increased with pH elevation and suboptimal Na+. By contrast, the mutant grew with a shorter lag and faster growth rate than the wild type at pH 7.5 under Na+-replete and suboptimal Na+ conditions, respectively. Logarithmically growing cells of the two strains exhibited no significant differences in growth rate, cytoplasmic pH regulation, starch utilization, motility, Na+-dependent transport of α-aminoisobutyric acid, or H+-dependent synthesis of ATP. However, the capacity for Na+-dependent pH homeostasis was diminished in RG21 upon a sudden upward shift of external pH from 8.5 to 10.5. The energy cost of retaining the SlpA layer at near-neutral pH is apparently adverse, but the constitutive presence of SlpA enhances the capacity of the extremophile to adjust to high pH. PMID:11029415

  5. 上槽缓冲容量不足导致双向电泳纵向拖尾原因初探%Insufficient buffer capacity in up chamber leads to vertical streaking of two-dimensional electrophoresis

    Institute of Scientific and Technical Information of China (English)

    金科华

    2011-01-01

    Objective To study the effect of buffer capacity in up chamber on vertical streaking (VSTK) of two-dimensional electrophoresis. Methods The same buffer volume was kept in up chamber, VSTK was compared by running two SDS gels or single one in 1×Laemmli buffer (buffer), or two ones in 1. 5× , 2× and 3× buffer in up chamber respectively. Results VSTK appeared severely when two gels were run in 1× buffer, while disappeared when one did When two gels were run in 1. 5 × buffer, VSTK only existed in the region of high molecular weight, and protein spots in the region of medium and low molecular weight were round without streaking. When two gels were run in 2× buffer, compared with 1. 5× buffer, the VSTK in the region of high molecular weight was further improved, and the round protein spots in the region of medium and low molecular weight increased. VSTK disappeared completely when two gels were run in 3× buffer. Conclusion Insufficient buffer capacity in up chamber may lead to vertical streaking.%目的 探讨上槽缓冲容量对双向电泳纵向拖尾的影响.方法 保持上槽缓冲液体积不变,分别采用1×buffer电泳2块或1块SDS胶,或1.5×、2×、3×buffer电泳2块胶,比较纵向拖尾情况.结果 1×buffer电泳2块胶,整块胶出现严重纵向拖尾,电泳1块胶时无纵向拖尾.1.5×buffer电泳2块胶,纵向拖尾只存在于高分子量区,中低分子量区蛋白点呈圆形,无拖尾.2×buffer电泳2块胶,高分子量区纵向拖尾较1.5×buffer进一步减少,中低分子量区圆形蛋白点增多.3×buffer电泳2块胶时,纵向拖尾完全消除.结论 上槽缓冲液缓冲容量不足导致双向电泳纵向拖尾.

  6. 茭白总蛋白质双向电泳技术体系的建立%Establishment of Two-Dimensional Electrophoresis Conditions for Proteomic Analysis of Zizania latifolia

    Institute of Scientific and Technical Information of China (English)

    罗海波; 陈伟; 周静峰; 宋慧波; 郁志芳

    2013-01-01

    In order to establish the two-dimensional electrophoresis (2-DE) conditions of Zizania latifolia,the effects of different protein extraction methods,loading amount,pH ranges of IPG strip and gel concentration,etc,on 2-DE maps were investigated.The results showed that the modified phenol extraction protocol is more suitable for total protein extraction of Z.latifolia compared with TCA/acetone protocol.And a high quality 2-DE map with more protein spots,clear background and high protein point resolution was obtained using the following optimized procedure:loading 1.0mg protein sample on 17 cm IPG strip with pH 4-7,SDS-PAGE with 12 g/dL gel concentration,and finally detecting proteins with coomassie brilliant blue G250 staining.The research provides a basis for further study of the Z.latifolia proteomics.%为建立茭白总蛋白质双向电泳技术体系,研究了TCA/丙酮沉淀法和改良酚抽法两种不同总蛋白质提取方法、蛋白质上样量、pH值范围及凝胶质量浓度等条件对2-DE的影响.结果表明,改良酚抽法更适合茭白总蛋白质的提取,采用17 cm、pH 4~7的胶条、1.0 mg的蛋白质上样量、12 g/dL的凝胶浓度、考马斯亮蓝G-250胶体考染法染色,最终可获得蛋白质点较多,背景清晰,分辨率较高的2-DE图谱,为进一步开展茭白差异蛋白质组学研究奠定了基础.

  7. 蕨菜总蛋白质双向电泳技术体系的建立%Research on Two-Dimensional Electrophoresis Conditions for Proteomic Analysis of Pteridium aquilinum

    Institute of Scientific and Technical Information of China (English)

    黄劲松; 姜丽; 石韵; 宦晨; 郁志芳

    2013-01-01

    为了建立蕨菜中总蛋白质的双向电泳技术体系,作者以新鲜蕨菜为实验材料,分别比较了不同蛋白提取方法,不同上样量以及不同pH范围IPG胶条对2-DE图谱的影响.结果表明,采用TCA-丙酮结合酚抽法提取蕨菜中的蛋白质,采用IPG胶条pH5-8、蛋白质的上样量为1200μg、考马斯亮蓝G-250胶体考染法进行染色.在此条件下进行蕨菜全蛋白质的双向电泳所得到的图谱蛋白质点多达719个,且蛋白质点分布均匀、背景清晰、分辨率较高.%In order to establish two-dimensional electrophoresis technology system of total proteins of Pteridium aquilinum,2-DE maps was compared with protein extraction method,loading amount and pH ranges of IPG strips The results showed that phenol extraction protocol combined with TCA/ acetone was more favorable for total protein extraction from fresh Pteridium aquilinum.A high quality 2-DE map with more protein spots,better dispersion,clearer background and higher protein point resolution were acquired by using the following optimized parameters:loading 1200μg protein sample on 17cm IPG strip with pH 5-8,and finally detecting proteins with Coomassie brilliant blue G250 staining.Under above experimental conditions,the total number of protein spots is 719,this experimental results provides a basis for further study of post-harvested Pteridium aquilinum proteomics.

  8. Low-cost two-dimensional gel densitometry.

    Science.gov (United States)

    Levenson, R M; Maytin, E V; Young, D A

    1986-11-01

    A major obstacle to full utilization of the powerful technique of two-dimensional (2-D) gel electrophoresis is the expense and complexity of quantifying the results. Using an analog-to-digital converter already present in the widely available Commodore 64 or Commodore 128 microcomputer, we have developed a 2-D gel densitometer (GELSCAN) which adds only $20.00 to the cost of the Commodore system (currently around $700.00). The system is designed to work with autoradiograms of 2-D gels. Spots of interest are identified visually and then positioned manually over a light source. A pinhole photoelectric sensor mounted in a hand-held, Plexiglas holder, or "mouse," is briefly rubbed over each spot. Maximum density of the spot is determined and its value is converted to counts per minute via an internal calibration curve which corrects for the nonlinear response of film to radiation. Local spot backgrounds can be subtracted and values can be normalized between gels to adjust for variation in amount of radioactivity applied or in exposure time. Reproducibility is excellent and the technique has some practical as well as theoretical advantages over other more complicated approaches to 2-D gel densitometry. In addition, the GELSCAN system can also be used for scanning individual bands in 1-D gels, quantitation of "dot-blot" autoradiograms and other tasks involving transmission densitometry.

  9. Two-dimensional photonic crystal surfactant detection.

    Science.gov (United States)

    Zhang, Jian-Tao; Smith, Natasha; Asher, Sanford A

    2012-08-07

    We developed a novel two-dimensional (2-D) crystalline colloidal array photonic crystal sensing material for the visual detection of amphiphilic molecules in water. A close-packed polystyrene 2-D array monolayer was embedded in a poly(N-isopropylacrylamide) (PNIPAAm)-based hydrogel film. These 2-D photonic crystals placed on a mirror show intense diffraction that enables them to be used for visual determination of analytes. Binding of surfactant molecules attaches ions to the sensor that swells the PNIPAAm-based hydrogel. The resulting increase in particle spacing red shifts the 2-D diffracted light. Incorporation of more hydrophobic monomers increases the sensitivity to surfactants.

  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. Determining the cleavage site for the mature antimicrobial peptide of Nile tilapia β-defensin using 2D electrophoresis, western blot, and mass spectrometry analysis.

    Science.gov (United States)

    Chang, Chin-I; Chen, Li-Hao; Hu, Yeh-Fang; Wu, Chia-Che; Tsai, Jyh-Ming

    2017-03-01

    Several proteomic techniques were used to determine the cleavage site of the mature antimicrobial peptide of Nile tilapia β-defensin. The computer-predicted Nile tilapia β-defensin ((25)ASFPWSCLSLSGVCRKVCLPTELFFGPLGCGKGSLCCVSHFL(66)) composed of 42 amino acids was chemically synthesized and prepared to produce an antibody for Western blotting. Total proteins from the skin of the Nile tilapia were separated on two-dimensional electrophoresis, and the spot of Nile tilapia β-defensin was recognized using Western blot analysis. It was then excised and extracted from the gel. The precise molecular mass of this spot was determined by LC-MS/MS spectrometry. Four major peptides were discovered, with molecular weights of 4293.2 Da, 4306.5 Da, 4678.9 Da, and 4715.0 Da. The calculated mass of the 40-amino-acid sequence ((27)FPWSCLSLSGVCRKVCLPTELFFGPLGCGKGSLCCVSHFL(66)) of Nile tilapia β-defensin starting from Phe27 and ending with Leu66 was 4293.18 Da, which completely matched the 4293.2 Da peptide that was obtained from the mass spectrometry analysis. This result confirmed that the cleavage site for the mature C-terminal Nile tilapia β-defensin is at residue Ser26-Phe27, not at Ala24-25 as predicted by computer analysis. This study provides a simple but reliable model to determine the cleavage site for a mature antimicrobial peptide. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. 应用双向电泳和质谱联用技术研究乳源蛋白的差异性%Analysis of milk protein by two-dimensional electrophoresis combined with mass spectrometry

    Institute of Scientific and Technical Information of China (English)

    向明霞; 王丽娜; 李昀锴; 李子超; 成希飞; 徐明芳

    2012-01-01

    Two-dimensional electrophoresiscotnbined with mass spectrometry was used for the analysis of the differences of milk proteins. 21 differential proteins which mainly distributed in areas of low abundance existed only in water buffalo milk were identified according to comparing the profiles of caseins matched with software of ImageMaster 2D Platinum. And 24 differential whey proteins only in water buffalo milk were identified. Four casein fractions belonged to water buffalo milk casein and two new fractions which were high homology components with water buffalo milk casein were determined with the further analysis by mass spectrometry( MS). Four casein fractions belonged to water buffalo milk whey and two new fractions which were high homology components with water buffalo milk whey using were also determined by the same method.%应用双向电泳和质谱联用技术,对不同乳源蛋白的差异性进行了研究.根据ImageMaster 2 DPlatinum图像分析软件对不同乳源酪蛋白和乳清蛋白的双向电泳(2-DE)图谱进行蛋白斑点的匹配分析,获得21个存在于水牛奶中主要分布在低丰度蛋白区的酪蛋白差异蛋白点和24个存在于水牛奶中乳清蛋白差异蛋白点.这些差异蛋白点经质谱鉴定分析,得到4个属于水牛奶酪蛋白的主要组分和2个与水牛奶中酪蛋白有较高同源性的新组分,同时获得4个属于水牛奶乳清蛋白的主要组分和3个与水牛奶中乳清蛋白有较高同源性的组分.

  13. Two-dimensional Kagome photonic bandgap waveguide

    DEFF Research Database (Denmark)

    Nielsen, Jens Bo; Søndergaard, Thomas; Libori, Stig E. Barkou;

    2000-01-01

    The transverse-magnetic photonic-bandgap-guidance properties are investigated for a planar two-dimensional (2-D) Kagome waveguide configuration using a full-vectorial plane-wave-expansion method. Single-moded well-localized low-index guided modes are found. The localization of the optical modes...... is investigated with respect to the width of the 2-D Kagome waveguide, and the number of modes existing for specific frequencies and waveguide widths is mapped out....

  14. Piezoelectricity in Two-Dimensional Materials

    KAUST Repository

    Wu, Tao

    2015-02-25

    Powering up 2D materials: Recent experimental studies confirmed the existence of piezoelectricity - the conversion of mechanical stress into electricity - in two-dimensional single-layer MoS2 nanosheets. The results represent a milestone towards embedding low-dimensional materials into future disruptive technologies. © 2015 Wiley-VCH Verlag GmbH & Co. KGaA.

  15. A two-dimensional Dirac fermion microscope

    DEFF Research Database (Denmark)

    Bøggild, Peter; Caridad, Jose; Stampfer, Christoph

    2017-01-01

    in the solid state. Here we provide a perspective view on how a two-dimensional (2D) Dirac fermion-based microscope can be realistically implemented and operated, using graphene as a vacuum chamber for ballistic electrons. We use semiclassical simulations to propose concrete architectures and design rules of 2...

  16. Two-dimensional calculus

    CERN Document Server

    Osserman, Robert

    2011-01-01

    The basic component of several-variable calculus, two-dimensional calculus is vital to mastery of the broader field. This extensive treatment of the subject offers the advantage of a thorough integration of linear algebra and materials, which aids readers in the development of geometric intuition. An introductory chapter presents background information on vectors in the plane, plane curves, and functions of two variables. Subsequent chapters address differentiation, transformations, and integration. Each chapter concludes with problem sets, and answers to selected exercises appear at the end o

  17. Two dimensional vernier

    Science.gov (United States)

    Juday, Richard D. (Inventor)

    1992-01-01

    A two-dimensional vernier scale is disclosed utilizing a cartesian grid on one plate member with a polar grid on an overlying transparent plate member. The polar grid has multiple concentric circles at a fractional spacing of the spacing of the cartesian grid lines. By locating the center of the polar grid on a location on the cartesian grid, interpolation can be made of both the X and Y fractional relationship to the cartesian grid by noting which circles coincide with a cartesian grid line for the X and Y direction.

  18. 亚洲带绦虫囊尾蚴特异性抗原筛选和鉴定%Screen and detection of specific antigens of Taenia asiatica cysticercus with two dimensional electrophoresis, western blotting and MS/MS spectrometry

    Institute of Scientific and Technical Information of China (English)

    方文; 肖靓靓; 包怀恩; 牟荣

    2011-01-01

    Objective To screen and identify specific antigens of Taenia asiatica cysticercus and to predict the function of target proteins using bioinformatics method. Methods Six three-way cross hybrid pigs were randomly divided into experimental group and control group and each experimental pig was infected with 84 000 eggs. Serum samples were collected 40 days after the infection. The total protein of Taenia asiatica cysticercus was separated by two dimensional electrophoresis and western blotting was performed to find out distinct antigens. Proteins from the two groups were identified by electrospray ion trap mass spectrometry(ESI-Trap MS). Results Totally 204 ± 11 spots were detected through Coomassie brilliant blue stained gels with relative molecular weight( Mr) of 14 400 -94 000 kDa and isoelectric point(pl) of 3. 0 - 10. 0. Western-blotting showed 6 specific antigen spots with pool sera of infected pigs. Two of the 6 antigens with known functions were ascribed to ATPase family gene 3-like protein 2 and ATP synthase beta subunit. Conclusion Two specific antigens of Taenia asiatica cysticercus have been identified.%目的 对亚洲带绦虫囊尾蚴的特异性抗原进行筛选、鉴定和生物信息学分析.方法 6头20d龄三元杂交乳猪随机分为实验组和对照组,实验组每头灌胃亚洲带绦虫虫卵悬液8.4万个;20 d后,分别制备实验组及对照组心脏血混合血清;收集、制备实验组亚洲带绦虫囊尾蚴蛋白并进行双向电泳分析,将凝胶蛋白斑点转移至聚偏氟乙烯膜,用实验组及对照组混合血清(均为1∶10)为一抗,羊抗猪辣根过氧化物酶- IgG(1∶200)为二抗,进行蛋白质印迹分析和质谱鉴定.结果 双向电泳凝胶共检测到( 204±11)个蛋白质斑点,相对分子质量为14 400 ~94 000 kPa,等电点(pI)为3.0~10.0;筛选出6个特异性抗原,经质谱鉴定出其中2个蛋白,分别为ATP酶管家基因3-类蛋白2(AT-Pase family gene 3-like protein 2)

  19. 日本血吸虫虫卵、童虫和雌雄成虫膜蛋白的双向电泳%Analysis of membrane proteins from egg, schistosomulum, adult male and female worm of Schistosoma japonicum by two dimensional electrophoresis

    Institute of Scientific and Technical Information of China (English)

    程国锋; 冯新港; 林矫矫; 石耀军; 陆柯; 周元聪; 蔡幼民

    2005-01-01

    Membrane proteins were extracted from eggs, schistosomulum, adult male and female worms of Schistosoma japonicum in order to analyze the differently expressed profile by two dimensional electrophoresis. Schistosomulum and adult worms were obtained from rabbits infected with 1 500 cercariaes on 14 and 42 days after challenge, respectively. Adult male and female worms on 42 days were manually detached and stored into liquid nitrogen until use. Eggs were collected by PercollTM from the liver of rabbits. ProteoPrep Membrane Extraction KitTM was employed to extracted membrane proteins by reducing and alkylating with TBP and iodoacetamide from 200mg of eggs, schistosomulums, adult male worm and female worms, respectively. Immobilized pH gradient strips with a linear pH range of 3-10(130mm) were rehydrated together with membrane proteins (30μg) in 250μl solution containing 7mol urea, 2mol thiourea, 2% SB3-10, 4% CHAPS, 40mmol Tris, 30mmol DTT, then separated on 12.5% SDS polyacrylamide gel for the second dimensional electrophoresis. Gels were stained with silver, scanned by Labscan, and analyzed using ImageMasterTM Analysis software. The 2D maps of egg, schistosomulum, adult female worm and male worm were showed 78±3, 67±3, 108±4 and 122±4 spots respectively. There were 35±1 spots which showed specific expression in female worm as compared with male worm, but 45±2 spots were in male worms. Most differently expressed spots between male and female worms were located in the area of 40-70kD and pI 4-7. The large number of unique spots from sehistosomulum was located in the area of alkalescence. The 2D map of for adult male worms uniquely showed 5 spots as compared with that of schistosomulum and female worm. The female worm showed 4 unique spots as compared with that of schistosomulum, egg and male worm. The unique spots between male and female worms were identified by the database of SWISS 2D-PAGE according to the molecular weight and isoelectronic point

  20. Two-dimensional heterostructures for energy storage

    Science.gov (United States)

    Pomerantseva, Ekaterina; Gogotsi, Yury

    2017-07-01

    Two-dimensional (2D) materials provide slit-shaped ion diffusion channels that enable fast movement of lithium and other ions. However, electronic conductivity, the number of intercalation sites, and stability during extended cycling are also crucial for building high-performance energy storage devices. While individual 2D materials, such as graphene, show some of the required properties, none of them can offer all properties needed to maximize energy density, power density, and cycle life. Here we argue that stacking different 2D materials into heterostructured architectures opens an opportunity to construct electrodes that would combine the advantages of the individual building blocks while eliminating the associated shortcomings. We discuss characteristics of common 2D materials and provide examples of 2D heterostructured electrodes that showed new phenomena leading to superior electrochemical performance. We also consider electrode fabrication approaches and finally outline future steps to create 2D heterostructured electrodes that could greatly expand current energy storage technologies.

  1. Two-dimensional x-ray diffraction

    CERN Document Server

    He, Bob B

    2009-01-01

    Written by one of the pioneers of 2D X-Ray Diffraction, this useful guide covers the fundamentals, experimental methods and applications of two-dimensional x-ray diffraction, including geometry convention, x-ray source and optics, two-dimensional detectors, diffraction data interpretation, and configurations for various applications, such as phase identification, texture, stress, microstructure analysis, crystallinity, thin film analysis and combinatorial screening. Experimental examples in materials research, pharmaceuticals, and forensics are also given. This presents a key resource to resea

  2. Two-dimensional optical spectroscopy

    CERN Document Server

    Cho, Minhaeng

    2009-01-01

    Discusses the principles and applications of two-dimensional vibrational and optical spectroscopy techniques. This book provides an account of basic theory required for an understanding of two-dimensional vibrational and electronic spectroscopy.

  3. Two-Dimensional Electrons.

    Science.gov (United States)

    2014-09-26

    Isihara and Y. Nalane, Elementary Excitations and Energy Dispersion in TTF-TCNQ;Proc. Internat. Conf. on Phys. and Chem. of Low-Dimen. Syn. Conductors ...Abano Terme, Molec. Crys. Liq. Crys. 120, 85 (1984). One-dimensiona4 conductors such as TTF-TCNQ are attracting considerable attention for their...A. Isihara and Y. Nakane; Magnetoconductivity of 2D Conductors ; Proc. Internat. Conf. on Phys. and Chem. of Low-Dimen. Syn. Conductors , Abano Terme

  4. Establishment and optimization of two-dimensional electrophoresis for myocardial proteomes of mice%小鼠心肌蛋白质组双向电泳技术的建立及其优化

    Institute of Scientific and Technical Information of China (English)

    刘明; 王慧君; 李学锋; 金贺; 康伟

    2006-01-01

    BACKGROUND: Two-dimensional electrophoresis (2-DE) is precise and effective for the isolation and analysis of complex protein mixtures, has become one of valuable key techniques for proteome. Mice models were as research subjects to model human disease status, one of important methods for cardiovascular disease. The establishment and optimization of 2-DE for proteomes of mice myocardium will provide basis for heart disease.OBJECTIVE: To establish and optimize a stable technique of 2-DE for proteomic analysis of mice myocardium.DESIGN: Mice were used as research subjects, observational comparative study.SETTING: Department of Pathology, Nanfang Hospital Affiliated to Southern Medical University.PARTICIPANTS: The experiment was performed at the Department of Pathology, Nanfang Hospital Affiliated to Southern Medical University between February and September 2004. Totally 12 male BABL/c mice of 4-5 weeks without special-pathogen free with the body mass of 12-15 g were selected, which was provided by the Experimental Animal Center of Southern Medical University.METHODS: The mice were put to death by dislocation of cervical vertebra under drugged state to obtain heart. Various protein extraction method,loading sampling buffer, strip range of IPG, sampling volume of protein,staining method and so on were compared, analyzed, scanned and digilized,and then performing image analysis. Each link in the study was established and optimized.MAIN OUTCOME MEASURES: Resolution of protein and reproducibility of the trial.RESULTS: A method that was optimal for cardiac tissue can isolate about a total of 910 protein spots on pH 4-7 gel strips. 200 μg was fit for silver stain while 1000 μg was for Coomassie stains. It was found that in the myocardium of normal mice about (920±30) protein spots were obtained in 17 em pH 3-10 L gel strip, while around (880±30) were gained in the pH 4-7 L gel strip. The mean matching rate achieves to 86. 9%.CONCLUSION: The findings of the trial showed

  5. Analysis of directional dependence of the two-dimensional array of detectors 2D array seven 29 implications in the planning system; Analisis de la dependencia direcccional de la matriz bidimensional de detectores 2D array seven29. Implicaciones en el sistema de planificacion

    Energy Technology Data Exchange (ETDEWEB)

    Mora Melendez, R.; Seguro Fernandez, A.; Iborra Oquendo, M.; Urena Llinares, A.

    2013-07-01

    The main objective of our study is to find correction factors dependent on the 2D array incidence angles, and to give account of the phenomenon, allowing the Planner to faithfully reproduce data and curves measured experimentally. (Author)

  6. Metal imaging in non-denaturating 2D electrophoresis gels by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) for the detection of metalloproteins.

    Science.gov (United States)

    Becker, J Susanne; Lobinski, Ryszard; Becker, J Sabine

    2009-01-01

    Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) was developed as a powerful analytical technique for metal imaging of 2D gels for the detection of metalloproteins in rat kidney after electrophoretic separation. Protein complexes, extracted with water, were separated in their native state in the first and second dimension by blue native gel electrophoresis (BN-PAGE). Essential and toxic metals, such as zinc, copper, iron, manganese and lead, were monitored by LA-ICP-MS after gel ablation by a focused laser beam in a way that the total surface of a selected fragment of the gel was totally ablated. The metal distribution of this part of the gel was then constructed by plotting the metal (isotope) signal intensity as a function of the x,y (isoelectric point, molecular mass) coordinates of the gel. The proteins at locations rich in metals were cut out, digested with trypsin and analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS).

  7. Comparative analysis between two-dimensional (2D) and three-dimensional (3D) MRI acquisitions - clinical applications for the evaluation of the knees in juvenile rheumatoid arthritis (JRA); Analise comparativa entre aquisicao tri (3D) e bidimensional (2D) em ressonancia magnetica - aplicabilidade clinica em joelhos em artrite reumatoide juvenil (ARJ)

    Energy Technology Data Exchange (ETDEWEB)

    Doria, Andre S. [Hospital das Clinicas, Sao Paulo, SP (Brazil). Inst. de Radiologia; Rebelo, Marina de Sa [Hospital das Clinicas, Sao Paulo, SP (Brazil). Instituto do Coracao. Servico de Informatica; Castro, Claudio Campi de [Hospital das Clinicas, Sao Paulo, SP (Brazil). Instituto do Coracao. Servico de Ressonancia Magnetica] [and others

    2000-06-01

    In this cross-sectional study in patients with juvenile rheumatoid arthritis the authors compare two-dimensional evaluation of the maximum synovial diameter on post-contrast axial T1-weighted SE (spin-echo) sequences with volumetric (three-dimensional assessment) on post-contrast axial T1-weighted SPIR (spectral presaturation with inversion recovery) SE sequences. With the aim of determining their cost-effectiveness these two methods of assessment were compared to clinical and laboratorial parameters, as well as the presence of synovial enhancement seen on magnetic resonance imaging. (author)

  8. Two-dimensional effects in nonlinear Kronig-Penney models

    DEFF Research Database (Denmark)

    Gaididei, Yuri Borisovich; Christiansen, Peter Leth; Rasmussen, Kim

    1997-01-01

    An analysis of two-dimensional (2D) effects in the nonlinear Kronig-Penney model is presented. We establish an effective one-dimensional description of the 2D effects, resulting in a set of pseudodifferential equations. The stationary states of the 2D system and their stability is studied...

  9. A two-dimensional Dirac fermion microscope

    Science.gov (United States)

    Bøggild, Peter; Caridad, José M.; Stampfer, Christoph; Calogero, Gaetano; Papior, Nick Rübner; Brandbyge, Mads

    2017-06-01

    The electron microscope has been a powerful, highly versatile workhorse in the fields of material and surface science, micro and nanotechnology, biology and geology, for nearly 80 years. The advent of two-dimensional materials opens new possibilities for realizing an analogy to electron microscopy in the solid state. Here we provide a perspective view on how a two-dimensional (2D) Dirac fermion-based microscope can be realistically implemented and operated, using graphene as a vacuum chamber for ballistic electrons. We use semiclassical simulations to propose concrete architectures and design rules of 2D electron guns, deflectors, tunable lenses and various detectors. The simulations show how simple objects can be imaged with well-controlled and collimated in-plane beams consisting of relativistic charge carriers. Finally, we discuss the potential of such microscopes for investigating edges, terminations and defects, as well as interfaces, including external nanoscale structures such as adsorbed molecules, nanoparticles or quantum dots.

  10. A two-dimensional Dirac fermion microscope.

    Science.gov (United States)

    Bøggild, Peter; Caridad, José M; Stampfer, Christoph; Calogero, Gaetano; Papior, Nick Rübner; Brandbyge, Mads

    2017-06-09

    The electron microscope has been a powerful, highly versatile workhorse in the fields of material and surface science, micro and nanotechnology, biology and geology, for nearly 80 years. The advent of two-dimensional materials opens new possibilities for realizing an analogy to electron microscopy in the solid state. Here we provide a perspective view on how a two-dimensional (2D) Dirac fermion-based microscope can be realistically implemented and operated, using graphene as a vacuum chamber for ballistic electrons. We use semiclassical simulations to propose concrete architectures and design rules of 2D electron guns, deflectors, tunable lenses and various detectors. The simulations show how simple objects can be imaged with well-controlled and collimated in-plane beams consisting of relativistic charge carriers. Finally, we discuss the potential of such microscopes for investigating edges, terminations and defects, as well as interfaces, including external nanoscale structures such as adsorbed molecules, nanoparticles or quantum dots.

  11. Mobility anisotropy of two-dimensional semiconductors

    CERN Document Server

    Lang, Haifeng; Liu, Zhirong

    2016-01-01

    The carrier mobility of anisotropic two-dimensional (2D) semiconductors under longitudinal acoustic (LA) phonon scattering was theoretically studied with the deformation potential theory. Based on Boltzmann equation with relaxation time approximation, an analytic formula of intrinsic anisotropic mobility was deduced, which shows that the influence of effective mass to the mobility anisotropy is larger than that of deformation potential constant and elastic modulus. Parameters were collected for various anisotropic 2D materials (black phosphorus, Hittorf's phosphorus, BC$_2$N, MXene, TiS$_3$, GeCH$_3$) to calculate their mobility anisotropy. It was revealed that the anisotropic ratio was overestimated in the past.

  12. 2D-electrophoresis and multiplex immunoassay proteomic analysis of different body fluids and cellular components reveal known and novel markers for extended fasting

    Directory of Open Access Journals (Sweden)

    Evelo Chris T

    2011-03-01

    Full Text Available Abstract Background Proteomic technologies applied for profiling human biofluids and blood cells are considered to reveal new biomarkers of exposure or provide insights into novel mechanisms of adaptation. Methods Both a non-targeted (classical 2D-electrophoresis combined with mass spectrometry as well as a targeted proteomic approach (multiplex immunoassay were applied to investigate how fasting for 36 h, as compared to 12 h, affects the proteome of platelets, peripheral blood mononuclear cells (PBMC, plasma, urine and saliva collected from ten healthy volunteers. Results Between-subject variability was highest in the plasma proteome and lowest in the PBMC proteome. Random Forests analysis performed on the entire dataset revealed that changes in the level of the RhoGDI2 protein in PBMC and plasma ApoA4 levels were the two most obvious biomarkers of an extended fasting. Random Forests (RF analysis of the multiplex immunoassay data revealed leptin and MMP-3 as biomarkers for extended fasting. However, high between-subject variability may have masked the extended fasting effects in the proteome of the biofluids and blood cells. Conclusions Identification of significantly changed proteins in biofluids and blood cells using a non-targeted approach, together with the outcome of targeted analysis revealed both known and novel markers for a 36 h fasting period, including the cellular proteins RhoGDI2 and CLIC1, and plasma proteins ApoA4, leptin and MMP-3. The PBMC proteome exhibited the lowest between-subject variability and therefore these cells appear to represent the best biosamples for biomarker discovery in human nutrigenomics.

  13. Nonlocal bottleneck effect in two-dimensional turbulence

    CERN Document Server

    Biskamp, D; Schwarz, E

    1998-01-01

    The bottleneck pileup in the energy spectrum is investigated for several two-dimensional (2D) turbulence systems by numerical simulation using high-order diffusion terms to amplify the effect, which is weak for normal diffusion. For 2D magnetohydrodynamic (MHD) turbulence, 2D electron MHD (EMHD) turbulence and 2D thermal convection, which all exhibit direct energy cascades, a nonlocal behavior is found resulting in a logarithmic enhancement of the spectrum.

  14. Rationally synthesized two-dimensional polymers.

    Science.gov (United States)

    Colson, John W; Dichtel, William R

    2013-06-01

    Synthetic polymers exhibit diverse and useful properties and influence most aspects of modern life. Many polymerization methods provide linear or branched macromolecules, frequently with outstanding functional-group tolerance and molecular weight control. In contrast, extending polymerization strategies to two-dimensional periodic structures is in its infancy, and successful examples have emerged only recently through molecular framework, surface science and crystal engineering approaches. In this Review, we describe successful 2D polymerization strategies, as well as seminal research that inspired their development. These methods include the synthesis of 2D covalent organic frameworks as layered crystals and thin films, surface-mediated polymerization of polyfunctional monomers, and solid-state topochemical polymerizations. Early application targets of 2D polymers include gas separation and storage, optoelectronic devices and membranes, each of which might benefit from predictable long-range molecular organization inherent to this macromolecular architecture.

  15. Two-Dimensional Mesoscale-Ordered Conducting Polymers

    NARCIS (Netherlands)

    Liu, Shaohua; Zhang, Jian; Dong, Renhao; Gordiichuk, Pavlo; Zhang, Tao; Zhuang, Xiaodong; Mai, Yiyong; Liu, Feng; Herrmann, Andreas; Feng, Xinliang

    2016-01-01

    Despite the availability of numerous two-dimensional (2D) materials with structural ordering at the atomic or molecular level, direct construction of mesoscale-ordered superstructures within a 2D monolayer remains an enormous challenge. Here, we report the synergic manipulation of two types of assem

  16. Two-Dimensional Mesoscale-Ordered Conducting Polymers

    NARCIS (Netherlands)

    Liu, Shaohua; Zhang, Jian; Dong, Renhao; Gordiichuk, Pavlo; Zhang, Tao; Zhuang, Xiaodong; Mai, Yiyong; Liu, Feng; Herrmann, Andreas; Feng, Xinliang

    2016-01-01

    Despite the availability of numerous two-dimensional (2D) materials with structural ordering at the atomic or molecular level, direct construction of mesoscale-ordered superstructures within a 2D monolayer remains an enormous challenge. Here, we report the synergic manipulation of two types of

  17. Forensic potential of comprehensive two-dimensional gas chromatography

    NARCIS (Netherlands)

    Sampat, A.; Lopatka, M.; Sjerps, M.; Vivo-Truyols, G.; Schoenmakers, P.; van Asten, A.

    2016-01-01

    In this study, the application of comprehensive two-dimensional (2D) gas chromatography (GC × GC) in forensic science is reviewed. The peer-reviewed publications on the forensic use of GC × GC and 2D gas chromatography with mass spectrometric detection (GC × GC-MS) have been studied in detail, not o

  18. Forensic potential of comprehensive two-dimensional gas chromatography

    NARCIS (Netherlands)

    Sampat, A.; Lopatka, M.; Sjerps, M.; Vivo-Truyols, G.; Schoenmakers, P.; van Asten, A.

    2016-01-01

    In this study, the application of comprehensive two-dimensional (2D) gas chromatography (GC × GC) in forensic science is reviewed. The peer-reviewed publications on the forensic use of GC × GC and 2D gas chromatography with mass spectrometric detection (GC × GC-MS) have been studied in detail, not o

  19. TreePM Method for Two-Dimensional Cosmological Simulations

    Indian Academy of Sciences (India)

    Suryadeep Ray

    2004-09-01

    We describe the two-dimensional TreePM method in this paper. The 2d TreePM code is an accurate and efficient technique to carry out large two-dimensional N-body simulations in cosmology. This hybrid code combines the 2d Barnes and Hut Tree method and the 2d Particle–Mesh method. We describe the splitting of force between the PM and the Tree parts. We also estimate error in force for a realistic configuration. Finally, we discuss some tests of the code.

  20. Approach for in vivo protein binding of 5-n-butyl-pyrazolo[1,5-a]pyrimidine bioactivated in chimeric mice with humanized liver by two-dimensional electrophoresis with accelerator mass spectrometry.

    Science.gov (United States)

    Yamazaki, Hiroshi; Kuribayashi, Shunji; Inoue, Tae; Tateno, Chise; Nishikura, Yasufumi; Oofusa, Ken; Harada, Daisuke; Naito, Shinsaku; Horie, Toru; Ohta, Shigeru

    2010-01-01

    Drug development of a potential analgesic agent 5-n-butyl-7-(3,4,5-trimethoxybenzoylamino)pyrazolo[1,5-a]pyrimidine was withdrawn because of its limited hepatotoxic effects in humans that could not be predicted from regulatory animal or in vitro studies. In vivo formation of glutathione conjugates and covalent binding of a model compound 5-n-butyl-pyrazolo[1,5-a]pyrimidine were investigated in the present study after intravenous administration to chimeric mice with a human or rat liver because of an interesting capability of human cytochrome P450 1A2 in forming a covalently bound metabolite in vitro. Rapid distribution and elimination of radiolabeled 5-n-butyl-pyrazolo[1,5-a]pyrimidine in plasma or liver fractions were seen in chimeric mice after intravenous administration. However, similar covalent binding in liver was detected over 0.17-24 h after intravenous administration. Radio-LC analyses revealed that the chimeric mice with humanized liver preferentially gave the 3-hydroxylated metabolite and its glutathione conjugate in the plasma and liver. On the contrary, chimeric mice with a rat liver had some rat-specific metabolites in vivo. Analyses by electrophoresis with accelerator mass spectrometry of in vivo radiolabeled liver proteins in chimeric mice revealed that bioactivated 5-n-butyl-pyrazolo[1,5-a]pyrimidine bound nonspecifically to a variety of microsomal proteins including human P450 1A2 as well as cytosolic proteins in the livers from chimeric mice with humanized liver. These results suggest that the hepatotoxic model compound 5-n-butyl-pyrazolo[1,5-a]pyrimidine was activated by human liver microsomal P450 1A2 to reactive intermediate(s) in vivo in humanized chimeric mice and could relatively nonspecifically bind to biomolecules such as P450 1A2 and other proteins.

  1. Theory of two-dimensional transformations

    OpenAIRE

    Kanayama, Yutaka J.; Krahn, Gary W.

    1998-01-01

    The article of record may be found at http://dx.doi.org/10.1109/70.720359 Robotics and Automation, IEEE Transactions on This paper proposes a new "heterogeneous" two-dimensional (2D) transformation group ___ to solve motion analysis/planning problems in robotics. In this theory, we use a 3×1 matrix to represent a transformation as opposed to a 3×3 matrix in the homogeneous formulation. First, this theory is as capable as the homogeneous theory, Because of the minimal size, its implement...

  2. Predicting Two-Dimensional Silicon Carbide Monolayers.

    Science.gov (United States)

    Shi, Zhiming; Zhang, Zhuhua; Kutana, Alex; Yakobson, Boris I

    2015-10-27

    Intrinsic semimetallicity of graphene and silicene largely limits their applications in functional devices. Mixing carbon and silicon atoms to form two-dimensional (2D) silicon carbide (SixC1-x) sheets is promising to overcome this issue. Using first-principles calculations combined with the cluster expansion method, we perform a comprehensive study on the thermodynamic stability and electronic properties of 2D SixC1-x monolayers with 0 ≤ x ≤ 1. Upon varying the silicon concentration, the 2D SixC1-x presents two distinct structural phases, a homogeneous phase with well dispersed Si (or C) atoms and an in-plane hybrid phase rich in SiC domains. While the in-plane hybrid structure shows uniform semiconducting properties with widely tunable band gap from 0 to 2.87 eV due to quantum confinement effect imposed by the SiC domains, the homogeneous structures can be semiconducting or remain semimetallic depending on a superlattice vector which dictates whether the sublattice symmetry is topologically broken. Moreover, we reveal a universal rule for describing the electronic properties of the homogeneous SixC1-x structures. These findings suggest that the 2D SixC1-x monolayers may present a new "family" of 2D materials, with a rich variety of properties for applications in electronics and optoelectronics.

  3. 双向凝胶电泳在先天性肛门直肠畸形中的初步应用%Proteome Analysis of Anorectal malformations by Two-dimensional Electrophoresis

    Institute of Scientific and Technical Information of China (English)

    王建尧; 刘磊; 姚君; 叶明; 王斌; 叶晓硕; 冯奇; 宋雪倩; 邹沙芹

    2013-01-01

    目的:寻找先天性肛门直肠畸形患儿直肠末端组织中异常表达的蛋白质.方法:通过二维凝胶电泳分离先天性肛门直肠畸形患儿直肠末端组织及正常新生儿直肠末端组织,用Image Master2D Platium 6.0软件比较电泳图谱中的异常蛋白质点.结果:筛选出19个表达差异的蛋白质点,其中有12个蛋白质点表达上调,7个蛋白质点表达下调,差异具有统计学意义.结论:先天性肛门直肠畸形可以导致血清中多种蛋白的异常表达.这些差异表达的蛋白可以为先天性肛门直肠畸形的进一步研究提供了依据.

  4. Comparative proteomics and metallomics studies in Arabidopsis thaliana leaf tissues: evaluation of the selenium addition in transgenic and nontransgenic plants using two-dimensional difference gel electrophoresis and laser ablation imaging.

    Science.gov (United States)

    Maciel, Bruna C M; Barbosa, Herbert S; Pessôa, Gustavo S; Salazar, Marcela M; Pereira, Gonçalo A G; Gonçalves, Danieli C; Ramos, Carlos H I; Arruda, Marco A Z

    2014-04-01

    The main goal of this work is to evaluate some differential protein species in transgenic (T) and nontransgenic (NT) Arabidopsis thaliana plants after their cultivation in the presence or absence of sodium selenite. The transgenic line was obtained through insertion of CaMV 35S controlling nptII gene. Comparative proteomics through 2D-DIGE is carried out in four different groups (NT × T; NT × Se-NT (where Se is selenium); Se-NT × Se-T, and T × Se-T). Although no differential proteins are achieved in the T × Se-T group, for the others, 68 differential proteins (by applying a regulation factor ≥1.5) are achieved, and 27 of them accurately characterized by ESI-MS/MS. These proteins are classified into metabolism, energy, signal transduction, disease/defense categories, and some of them are involved in the glycolysis pathway-Photosystems I and II and ROS combat. Additionally, laser ablation imaging is used for evaluating the Se and sulfur distribution in leaves of different groups, corroborating some results obtained and related to proteins involved in the glycolysis pathway. From these results, it is possible to conclude that the genetic modification also confers to the plant resistance to oxidative stress.

  5. FACE RECOGNITION USING TWO DIMENSIONAL LAPLACIAN EIGENMAP

    Institute of Scientific and Technical Information of China (English)

    Chen Jiangfeng; Yuan Baozong; Pei Bingnan

    2008-01-01

    Recently,some research efforts have shown that face images possibly reside on a nonlinear sub-manifold. Though Laplacianfaces method considered the manifold structures of the face images,it has limits to solve face recognition problem. This paper proposes a new feature extraction method,Two Dimensional Laplacian EigenMap (2DLEM),which especially considers the manifold structures of the face images,and extracts the proper features from face image matrix directly by using a linear transformation. As opposed to Laplacianfaces,2DLEM extracts features directly from 2D images without a vectorization preprocessing. To test 2DLEM and evaluate its performance,a series of ex-periments are performed on the ORL database and the Yale database. Moreover,several experiments are performed to compare the performance of three 2D methods. The experiments show that 2DLEM achieves the best performance.

  6. The Rare Two-Dimensional Materials with Dirac Cones

    OpenAIRE

    Wang, Jinying; Deng, Shibin; Liu, Zhongfan; Liu, Zhirong

    2014-01-01

    Inspired by the great development of graphene, more and more works have been conducted to seek new two-dimensional (2D) materials with Dirac cones. Although 2D Dirac materials possess many novel properties and physics, they are rare compared with the numerous 2D materials. To provide explanation for the rarity of 2D Dirac materials as well as clues in searching for new Dirac systems, here we review the recent theoretical aspects of various 2D Dirac materials, including graphene, silicene, ger...

  7. Two-dimensional signal analysis

    CERN Document Server

    Garello, René

    2010-01-01

    This title sets out to show that 2-D signal analysis has its own role to play alongside signal processing and image processing.Concentrating its coverage on those 2-D signals coming from physical sensors (such as radars and sonars), the discussion explores a 2-D spectral approach but develops the modeling of 2-D signals and proposes several data-oriented analysis techniques for dealing with them. Coverage is also given to potential future developments in this area.

  8. Characterization and comparison of mycobacterial antigens by two-dimensional immunoelectrophoresis.

    Science.gov (United States)

    Roberts, D B; Wright, G L; Affronti, L F; Reich, M

    1972-10-01

    Two-dimensional immunoelectrophoresis (2D-IEP), in which a complex of antigens is subjected to electrophoresis first through an agarose matrix in one direction and secondly through an antiserum-agarose matrix at right angles to the first direction, was evaluated as a tool for analysis of mycobacterial antigens. Cell extracts from four species of mycobacteria, Mycobacterium tuberculosis (four strains), M. bovis strain BCG, M. scrofulaceum, and M. phlei, were assayed by 2D-IEP with four anti-mycobacterial antisera. Besides displaying the precipitin curves in a more easily interpreted format than did conventional immunoelectrophoresis (IEP), 2D-IEP offered greater sensitivity in terms of numbers of precipitin curves when like reactions were compared with IEP patterns. As many as 60 immunoprecipitates were observed on 2D-IEP slides compared to 18 on comparable IEP plates. Technical reproducibility of patterns from run to run was excellent. Other parameters, such as the influence of using different batches of antigen on the pattern, are discussed. Each of the cell extract antigens gave a unique pattern of precipitin peaks which could be easily differentiated from the patterns given by the other mycobacterial cell extracts when reacted with any of the antisera in 2D-IEP. Since both the species and strains of mycobacteria could be easily and reproducibly differentiated solely on the basis of two-dimensional immunoelectrophoretic patterns obtained with any of the antisera employed in this study, it may be possible, by using IEP, to differentiate and identify all species and strains of mycobacteria with one standard, highly sensitive antiserum, rather than a battery of antisera.

  9. 二维电泳分析胎儿酒精综合征斑马鱼模型蛋白表达谱%Two-dimensional electrophoresis analysis for protein profile change in zebrafish alcohol syndrome model

    Institute of Scientific and Technical Information of China (English)

    钱林溪; 孙淑娜; 蔡威; 王跃祥; 蒋缪; 宋后燕

    2011-01-01

    Objective To study the putative mechanisms underlying fetal alcohol syndrome by comparative protein-profile analysis between normal and ethanol-treated zebrafish embryo with twodimensional electrophoresis (2-DE).Methods Zebrafish embryos were exposed in 400 mmol/L ethanol at dome stage for 3 hours,and then ethanol-induced abnormalities were observed.Proteomes of zebrafish embryos at early stages including zygote stage,dome stage,shield stage and 5-somite stage,were separated by 2-DE.The subtraction analysis method was applied to eliminate the interference from maternal derived proteins.The ethanol-treated embryos at 5-somite stage was analyzed by 2-DE,and the protein profile was compared with that generated from control embryos at the same stage.The data obtained from 2-DE analysis were verified by in-situ hybridization.Results 400 mmol/L ethanol treatment caused axial malformation (62%) and cyclopia (60%) in zebrafish embryos.The 2-DE analysis showed that the expression of Collagen2al (Col2a1) and TAR DNA binding protein (TDP) was decreased in 12 hours post fertilization (12 hpf) ethanol-treated embryos by 81% and 73%,respectively.The in-situ hybridization also demonstrated that the expression of Col2al in axial mesoderm was reduced by ethanol treatment at the same stage.But for 24 hpf ethanoltreated embryos,the expression of Col2al in axis recovered to a comparable level to that in control embryos,while the structure of neural tube was disrupted severely by ethanol exposure.Conclusions It is suggested that the expressions of Col2al and TDP were disrupted by ethanol during early stage,which might induce the zebrafish developmental abnormalities.The ethanol interference on early expression of Col2al is supposed to be one of the major reasons leading to later abnormalities of axis and neutral tube.%目的 利用二维电泳分析乙醇诱导斑马鱼胚胎发育畸形的可能分子机制.方法 采用400 mmol/L乙醇在斑马鱼胚胎圆顶期处理3 h,观察乙

  10. Two-dimensional liquid chromatography

    DEFF Research Database (Denmark)

    Græsbøll, Rune

    of this thesis is on online comprehensive two-dimensional liquid chromatography (online LC×LC) with reverse phase in both dimensions (online RP×RP). Since online RP×RP has not been attempted before within this research group, a significant part of this thesis consists of knowledge and experience gained...

  11. Establishment of Membrane Proteomics Platform with Two-dimensional Electrophoresis for Preparing Identifying Plasma Membrane Proteins from Atractylodes lancea%茅苍术质膜蛋白的制备及其双向电泳蛋白质组学平台的构建

    Institute of Scientific and Technical Information of China (English)

    陈飞; 周彤; 魏宇佳; 杨晶; 戴传超

    2016-01-01

    In order to understand related metabolic pathways of secondary metabolites and carry on metabolic regulation of active medical ingredients in endangered medicinal plant Atractylodes lancea,the method of plasma membrane proteomics was studied in this paper. Purified plasma membrane proteins were respectively extracted and purified from root,stem,and leaf of A. lancea using ultracentrifugation combined with aqueous two-phase partitioning. Moreover,the conditions for two-dimensional electrophoresis(2DE)analysis were optimized,and partial proteins in the latter were identified. The results showed that treating the ultra-centrifuged crude membrane compositions with the aqueous two-phase system of 6.4%,6.3%,and 6.1% Dextran T-500/PEG 3350(w/w)respectively,the high- purity plasma membrane proteins of 92.1%(root),91.5%(stem)and 90.8%(leaf)were obtained. The plasma membrane proteins were decomposed by 2% CHAPS and 2%Triton X-100 as the comprehensive detergents,loaded in the amount of 100 μg and resolved by IEF of 80 000 Vhs and 12.5%-15% SDS-PAGE gradient gel,and total 267,297 and 248 protein spots in the plasma membrane protein profiles of root,stem and leave respectively were detected by the Image Master 2D Platinum 7.0 software. And similarities and differences of 3 tissue proteins were further comparatively analyzed.At last,5 proteins were selected and successfully identified by MALDI-TOF-MS. Conclusively,a complete proteomics technology platform for preparing high-purity plasma membrane proteins from varied tissues of root,stem and leave of A. lancea and identifying the mass spectrometry of membrane protein is established.%探讨濒危药用植物茅苍术的质膜蛋白质组方法,旨在达到了解其次级代谢物的代谢途径,并对相关药用活性成分进行代谢调控的目的。以茅苍术的根、茎、叶为实验材料,确定了超速离心结合双水相法作为提取、纯化其质膜蛋白的方法;进而对这些质膜蛋白的双向

  12. Proteome analysis of round-headed and normal spermatozoa by 2-D fluorescence difference gel electrophoresis and mass spectrometry%以荧光差异凝胶双向电泳和质谱技术对圆头精子和正常精子的蛋白质组学分析

    Institute of Scientific and Technical Information of China (English)

    Ting-Ting Liao; Zhen Xiang; Wen-Bing Zhu; Li-Qing Fan

    2009-01-01

    Globozoospermia is a severe form of teratozoospermia characterized by round-headed spermatozoa with an absent acrosome, an aberrant nuclear membrane and midpiece defects. Globozoospermia is diagnosed by the presence of 100% round-headed spermatozoa on semen analysis, and patients with this condition are absolutely infertile. The objective of this study was to investigate the differences in protein expression between human round-headed and normal spermatozoa. Two-dimensional (2-D) fluorescence difference gel electrophoresis (DIGE) coupled with mass spectrometry (MS) was used in this study. Over 61 protein spots were analysed in each paired normal/round-headed comparison, using DIGE technology along with an internal standard. In total, 35 protein spots identified by tandem mass spectrometry (MS/MS) exhibited significant changes (paired t-test, P < 0.05) in the expression level between normal and round-headed spermatozoa. A total of nine proteins were found to be upregulated and 26 proteins were found to be downregulated in round-headed spermatozoa compared with normal spermatozoa. The differentially expressed proteins that we identified may have important roles in a variety of cellular processes and structures, including spermatogenesis, cell skeleton, metabolism and spermatozoa motility.

  13. Graphene and Two-Dimensional Materials for Optoelectronic Applications

    Directory of Open Access Journals (Sweden)

    Andreas Bablich

    2016-03-01

    Full Text Available This article reviews optoelectronic devices based on graphene and related two-dimensional (2D materials. The review includes basic considerations of process technology, including demonstrations of 2D heterostructure growth, and comments on the scalability and manufacturability of the growth methods. We then assess the potential of graphene-based transparent conducting electrodes. A major part of the review describes photodetectors based on lateral graphene p-n junctions and Schottky diodes. Finally, the progress in vertical devices made from 2D/3D heterojunctions, as well as all-2D heterostructures is discussed.

  14. Establishment and optimization of two-dimensional gel electrophoresis for proteomics research of sperm protein of varicocele patients%精索静脉曲张不育患者精子蛋白组双向电泳技术的建立与优化

    Institute of Scientific and Technical Information of China (English)

    何犇; 唐伟; 罗华铭; 郭毅; 李跃华

    2012-01-01

    目的:建立与优化精索静脉曲张不育患者精子蛋白质组双向凝胶电泳技术.方法:采取Percoll密度梯度离心法提取精索静脉曲张不育患者精子,比较不同精子蛋白样品制备方法、不同胶条、不同上样量和不同水化方式对双向凝胶电泳结果的影响.结果:使用clean-up kit法对样品进行预处理,选取pH 5~8的固相化pH梯度胶条,采用250 μg的上样量和主动水化方式能获得背景干净、分辨率高的双向电泳(Two-dimensional electrophoresis,2-DE)图谱.结论:成功建立了精索静脉曲张不育患者精子蛋白双向凝胶电泳平台,所获2-DE图谱的分辨率高、重复性好,为进一步探讨精索静脉曲张导致不育的分子机制奠定了技术基础.%Objective:To establish and optimize a set of two-dimensional gel electrophoresis(2-DE) techniques for proteomic research of sperm protein of varicocele patients. Methods: Spermatozoa in the semen were purified by Percoll gradient technique. The effects of different sample preparation methods,different gels,different amount of protein loads and different rehydration methods to the 2-DE maps were compared. Results:After the sample was treated with clean-up kit,a high resolution and clear 2-DE map for sperm protein of varicocele patients was obtained with pH 5~8 gel, 250 μg protein loads and initiative rehydration method. Conclusion:The 2-DE map of sperm protein of varicocele patients is successfully obtained with good repeatability and high resolution, which paves the way for the further proteomic research of infertility caused by varicocele.

  15. Two dimensional unstable scar statistics.

    Energy Technology Data Exchange (ETDEWEB)

    Warne, Larry Kevin; Jorgenson, Roy Eberhardt; Kotulski, Joseph Daniel; Lee, Kelvin S. H. (ITT Industries/AES Los Angeles, CA)

    2006-12-01

    This report examines the localization of time harmonic high frequency modal fields in two dimensional cavities along periodic paths between opposing sides of the cavity. The cases where these orbits lead to unstable localized modes are known as scars. This paper examines the enhancements for these unstable orbits when the opposing mirrors are both convex and concave. In the latter case the construction includes the treatment of interior foci.

  16. Two-Dimensional Vernier Scale

    Science.gov (United States)

    Juday, Richard D.

    1992-01-01

    Modified vernier scale gives accurate two-dimensional coordinates from maps, drawings, or cathode-ray-tube displays. Movable circular overlay rests on fixed rectangular-grid overlay. Pitch of circles nine-tenths that of grid and, for greatest accuracy, radii of circles large compared with pitch of grid. Scale enables user to interpolate between finest divisions of regularly spaced rule simply by observing which mark on auxiliary vernier rule aligns with mark on primary rule.

  17. Photodetectors based on two dimensional materials

    Science.gov (United States)

    Zheng, Lou; Zhongzhu, Liang; Guozhen, Shen

    2016-09-01

    Two-dimensional (2D) materials with unique properties have received a great deal of attention in recent years. This family of materials has rapidly established themselves as intriguing building blocks for versatile nanoelectronic devices that offer promising potential for use in next generation optoelectronics, such as photodetectors. Furthermore, their optoelectronic performance can be adjusted by varying the number of layers. They have demonstrated excellent light absorption, enabling ultrafast and ultrasensitive detection of light in photodetectors, especially in their single-layer structure. Moreover, due to their atomic thickness, outstanding mechanical flexibility, and large breaking strength, these materials have been of great interest for use in flexible devices and strain engineering. Toward that end, several kinds of photodetectors based on 2D materials have been reported. Here, we present a review of the state-of-the-art in photodetectors based on graphene and other 2D materials, such as the graphene, transition metal dichalcogenides, and so on. Project supported by the National Natural Science Foundation of China (Nos. 61377033, 61574132, 61504136) and the State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences.

  18. Molecular assembly on two-dimensional materials

    Science.gov (United States)

    Kumar, Avijit; Banerjee, Kaustuv; Liljeroth, Peter

    2017-02-01

    Molecular self-assembly is a well-known technique to create highly functional nanostructures on surfaces. Self-assembly on two-dimensional (2D) materials is a developing field driven by the interest in functionalization of 2D materials in order to tune their electronic properties. This has resulted in the discovery of several rich and interesting phenomena. Here, we review this progress with an emphasis on the electronic properties of the adsorbates and the substrate in well-defined systems, as unveiled by scanning tunneling microscopy. The review covers three aspects of the self-assembly. The first one focuses on non-covalent self-assembly dealing with site-selectivity due to inherent moiré pattern present on 2D materials grown on substrates. We also see that modification of intermolecular interactions and molecule–substrate interactions influences the assembly drastically and that 2D materials can also be used as a platform to carry out covalent and metal-coordinated assembly. The second part deals with the electronic properties of molecules adsorbed on 2D materials. By virtue of being inert and possessing low density of states near the Fermi level, 2D materials decouple molecules electronically from the underlying metal substrate and allow high-resolution spectroscopy and imaging of molecular orbitals. The moiré pattern on the 2D materials causes site-selective gating and charging of molecules in some cases. The last section covers the effects of self-assembled, acceptor and donor type, organic molecules on the electronic properties of graphene as revealed by spectroscopy and electrical transport measurements. Non-covalent functionalization of 2D materials has already been applied for their application as catalysts and sensors. With the current surge of activity on building van der Waals heterostructures from atomically thin crystals, molecular self-assembly has the potential to add an extra level of flexibility and functionality for applications ranging

  19. 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.

  20. Two-dimensional fourier transform spectrometer

    Energy Technology Data Exchange (ETDEWEB)

    DeFlores, Lauren; Tokmakoff, Andrei

    2016-10-25

    The present invention relates to a system and methods for acquiring two-dimensional Fourier transform (2D FT) spectra. Overlap of a collinear pulse pair and probe induce a molecular response which is collected by spectral dispersion of the signal modulated probe beam. Simultaneous collection of the molecular response, pulse timing and characteristics permit real time phasing and rapid acquisition of spectra. Full spectra are acquired as a function of pulse pair timings and numerically transformed to achieve the full frequency-frequency spectrum. This method demonstrates the ability to acquire information on molecular dynamics, couplings and structure in a simple apparatus. Multi-dimensional methods can be used for diagnostic and analytical measurements in the biological, biomedical, and chemical fields.

  1. Two-dimensional fourier transform spectrometer

    Science.gov (United States)

    DeFlores, Lauren; Tokmakoff, Andrei

    2013-09-03

    The present invention relates to a system and methods for acquiring two-dimensional Fourier transform (2D FT) spectra. Overlap of a collinear pulse pair and probe induce a molecular response which is collected by spectral dispersion of the signal modulated probe beam. Simultaneous collection of the molecular response, pulse timing and characteristics permit real time phasing and rapid acquisition of spectra. Full spectra are acquired as a function of pulse pair timings and numerically transformed to achieve the full frequency-frequency spectrum. This method demonstrates the ability to acquire information on molecular dynamics, couplings and structure in a simple apparatus. Multi-dimensional methods can be used for diagnostic and analytical measurements in the biological, biomedical, and chemical fields.

  2. Effect of Isoelectrofocusing Intensity on Protein Separation of Cassava Leaves by Two-Dimensional Gel Electrophoresis%等电聚焦强度对木薯叶片蛋白质双向电泳分离结果的影响

    Institute of Scientific and Technical Information of China (English)

    王海燕; 王斌; 王丹; 王东阳; 王力敏; 王红岩; 王旭初; 田维敏

    2011-01-01

    To obtain high-resolution reference of two-dimensional gel electrophoresis (2-DE)profiles of proteins from cassava leaves, the parameters of isoelectro-focusing (IEF) intensity were optimized. Results showed that the quality of 2-DE profiles under 130 000 Vhs was better than that of those under other conditions. Seven proteins among the selected 10 proteins were positively identified by MALDI TOF MS, suggesting their MS compatibility. The identified proteins were mainly involved in energy metabolic pathway and some of which appeared only in the 2-DE profiles under 130 000 Vhs condition.%通过优化等电聚焦强度改良木薯叶片蛋白质双向电泳的分离效果.结果表明,13万Vhs等电聚焦强度能很好地分离木薯叶片蛋白质,且分离的蛋白质具有良好的质谱兼容性.质谱鉴定7个蛋白点,结果显示这些蛋白主要参与能量代谢,其中有些蛋白点是在13万Vhs聚焦强度下特异出现的.

  3. Divorticity and dihelicity in two-dimensional hydrodynamics

    DEFF Research Database (Denmark)

    Shivamoggi, B.K.; van Heijst, G.J.F.; Juul Rasmussen, Jens

    2010-01-01

    A framework is developed based on the concepts of divorticity B (≡×ω, ω being the vorticity) and dihelicity g (≡vB) for discussing the theoretical structure underlying two-dimensional (2D) hydrodynamics. This formulation leads to the global and Lagrange invariants that could impose significant...

  4. Zero sound in a two-dimensional dipolar Fermi gas

    NARCIS (Netherlands)

    Lu, Z.K.; Matveenko, S.I.; Shlyapnikov, G.V.

    2013-01-01

    We study zero sound in a weakly interacting two-dimensional (2D) gas of single-component fermionic dipoles (polar molecules or atoms with a large magnetic moment) tilted with respect to the plane of their translational motion. It is shown that the propagation of zero sound is provided by both mean-f

  5. On the continua in two-dimensional nonadiabatic magnetohydrodynamic spectra

    NARCIS (Netherlands)

    De Ploey, A.; Van der Linden, R. A. M.; Belien, A. J. C.

    2000-01-01

    The equations for the continuous subspectra of the linear magnetohydrodynamic (MHD) normal modes spectrum of two-dimensional (2D) plasmas are derived in general curvilinear coordinates, taking nonadiabatic effects in the energy equation into account. Previously published derivations of continuous sp

  6. Bounds on the capacity of constrained two-dimensional codes

    DEFF Research Database (Denmark)

    Forchhammer, Søren; Justesen, Jørn

    2000-01-01

    Bounds on the capacity of constrained two-dimensional (2-D) codes are presented. The bounds of Calkin and Wilf apply to first-order symmetric constraints. The bounds are generalized in a weaker form to higher order and nonsymmetric constraints. Results are given for constraints specified by run...

  7. Two-dimensional liquid chromatography

    DEFF Research Database (Denmark)

    Græsbøll, Rune

    Two-dimensional liquid chromatography has received increasing interest due to the rise in demand for analysis of complex chemical mixtures. Separation of complex mixtures is hard to achieve as a simple consequence of the sheer number of analytes, as these samples might contain hundreds or even...... dimensions. As a consequence of the conclusions made within this thesis, the research group has, for the time being, decided against further development of online LC×LC systems, since it was not deemed ideal for the intended application, the analysis of the polar fraction of oil. Trap-and...

  8. Protein expression profiles of human lymph and plasma mapped by 2D-DIGE and 1D SDS–PAGE coupled with nanoLC–ESI–MS/MS bottom-up proteomics

    OpenAIRE

    Clement, Cristina C.; Aphkhazava, David; Nieves, Edward; Callaway, Myrasol; Olszewski, Waldemar; Rotzschke, Olaf; Santambrogio, Laura

    2012-01-01

    In this study a proteomic approach was used to define the protein content of matched samples of afferent prenodal lymph and plasma derived from healthy volunteers. The analysis was performed using two analytical methodologies coupled with nanoliquid chromatography-tandem mass spectrometry: one-dimensional gel electrophoresis (1DEF nanoLC Orbitrap–ESI–MS/MS), and two-dimensional fluorescence difference-in-gel electrophoresis (2D-DIGE nanoLC–ESI–MS/MS). The 253 significantly identified proteins...

  9. Two-dimensional capillary origami

    Energy Technology Data Exchange (ETDEWEB)

    Brubaker, N.D., E-mail: nbrubaker@math.arizona.edu; Lega, J., E-mail: lega@math.arizona.edu

    2016-01-08

    We describe a global approach to the problem of capillary origami that captures all unfolded equilibrium configurations in the two-dimensional setting where the drop is not required to fully wet the flexible plate. We provide bifurcation diagrams showing the level of encapsulation of each equilibrium configuration as a function of the volume of liquid that it contains, as well as plots representing the energy of each equilibrium branch. These diagrams indicate at what volume level the liquid drop ceases to be attached to the endpoints of the plate, which depends on the value of the contact angle. As in the case of pinned contact points, three different parameter regimes are identified, one of which predicts instantaneous encapsulation for small initial volumes of liquid. - Highlights: • Full solution set of the two-dimensional capillary origami problem. • Fluid does not necessarily wet the entire plate. • Global energy approach provides exact differential equations satisfied by minimizers. • Bifurcation diagrams highlight three different regimes. • Conditions for spontaneous encapsulation are identified.

  10. Ultrafast two dimensional infrared chemical exchange spectroscopy

    Science.gov (United States)

    Fayer, Michael

    2011-03-01

    The method of ultrafast two dimensional infrared (2D IR) vibrational echo spectroscopy is described. Three ultrashort IR pulses tuned to the frequencies of the vibrational transitions of interest are directed into the sample. The interaction of these pulses with the molecular vibrational oscillators produces a polarization that gives rise to a fourth pulse, the vibrational echo. The vibrational echo pulse is combined with another pulse, the local oscillator, for heterodyne detection of the signal. For fixed time between the second and third pulses, the waiting time, the first pulse is scanned. Two Fourier transforms of the data yield a 2D IR spectrum. The waiting time is increased, and another spectrum is obtained. The change in the 2D IR spectra with increased waiting time provides information on the time evolution of the structure of the molecular system under observation. In a 2D IR chemical exchange experiment, two species A and B, are undergoing chemical exchange. A's are turning into B's, and B's are turning into A's, but the overall concentrations of the species are not changing. The kinetics of the chemical exchange on the ground electronic state under thermal equilibrium conditions can be obtained 2D IR spectroscopy. A vibration that has a different frequency for the two species is monitored. At very short time, there will be two peaks on the diagonal of the 2D IR spectrum, one for A and one for B. As the waiting time is increased, chemical exchange causes off-diagonal peaks to grow in. The time dependence of the growth of these off-diagonal peaks gives the chemical exchange rate. The method is applied to organic solute-solvent complex formation, orientational isomerization about a carbon-carbon single bond, migration of a hydrogen bond from one position on a molecule to another, protein structural substate interconversion, and water hydrogen bond switching between ions and water molecules. This work was supported by the Air Force Office of Scientific

  11. Two-dimensional liquid separations-mass mapping of proteins from human cancer cell lysates.

    Science.gov (United States)

    Lubman, David M; Kachman, Maureen T; Wang, Haixing; Gong, Siyuan; Yan, Fang; Hamler, Rick L; O'Neil, Kimberly A; Zhu, Kan; Buchanan, Nathan S; Barder, Timothy J

    2002-12-25

    A review of two-dimensional (2D) liquid separation methods used in our laboratory to map the protein content of human cancer cells is presented herein. The methods discussed include various means of fractionating proteins according to isoelectric point (pI) in the first dimension. The proteins in each pI fraction are subsequently separated using nonporous (NPS) reversed-phase high-performance liquid chromatography (RP-HPLC). The liquid eluent of the RP-HPLC separation is directed on-line into an electrospray ionization time-of-flight (ESI-TOF) mass spectrometer where an accurate value of the protein intact M(r) can be obtained. The result is a 2D map of pI versus M(r) analogous to 2D gel electrophoresis; however the highly accurate and reproducible M(r) serves as the basis for interlysate comparisons. In addition, the use of liquid separations allows for the collection of hundreds of purified proteins in the liquid phase for further analysis via peptide mass mapping using matrix assisted laser desorption ionization TOF MS. A description of the methodology used and its applications to analysis of several types of human cancer cell lines is described. The potential of the method for differential proteomic analysis for the identification of biomarkers of disease is discussed.

  12. Perspective: Two-dimensional resonance Raman spectroscopy

    Science.gov (United States)

    Molesky, Brian P.; Guo, Zhenkun; Cheshire, Thomas P.; Moran, Andrew M.

    2016-11-01

    Two-dimensional resonance Raman (2DRR) spectroscopy has been developed for studies of photochemical reaction mechanisms and structural heterogeneity in complex systems. The 2DRR method can leverage electronic resonance enhancement to selectively probe chromophores embedded in complex environments (e.g., a cofactor in a protein). In addition, correlations between the two dimensions of the 2DRR spectrum reveal information that is not available in traditional Raman techniques. For example, distributions of reactant and product geometries can be correlated in systems that undergo chemical reactions on the femtosecond time scale. Structural heterogeneity in an ensemble may also be reflected in the 2D spectroscopic line shapes of both reactive and non-reactive systems. In this perspective article, these capabilities of 2DRR spectroscopy are discussed in the context of recent applications to the photodissociation reactions of triiodide and myoglobin. We also address key differences between the signal generation mechanisms for 2DRR and off-resonant 2D Raman spectroscopies. Most notably, it has been shown that these two techniques are subject to a tradeoff between sensitivity to anharmonicity and susceptibility to artifacts. Overall, recent experimental developments and applications of the 2DRR method suggest great potential for the future of the technique.

  13. Elastic models of defects in two-dimensional crystals

    Science.gov (United States)

    Kolesnikova, A. L.; Orlova, T. S.; Hussainova, I.; Romanov, A. E.

    2014-12-01

    Elastic models of defects in two-dimensional (2D) crystals are presented in terms of continuum mechanics. The models are based on the classification of defects, which is founded on the dimensionality of the specification region of their self-distortions, i.e., lattice distortions associated with the formation of defects. The elastic field of an infinitesimal dislocation loop in a film is calculated for the first time. The fields of the center of dilatation, dislocation, disclination, and circular inclusion in planar 2D elastic media, namely, nanofilms and graphenes, are considered. Elastic fields of defects in 2D and 3D crystals are compared.

  14. Two-dimensional quantum repeaters

    Science.gov (United States)

    Wallnöfer, J.; Zwerger, M.; Muschik, C.; Sangouard, N.; Dür, W.

    2016-11-01

    The endeavor to develop quantum networks gave rise to a rapidly developing field with far-reaching applications such as secure communication and the realization of distributed computing tasks. This ultimately calls for the creation of flexible multiuser structures that allow for quantum communication between arbitrary pairs of parties in the network and facilitate also multiuser applications. To address this challenge, we propose a two-dimensional quantum repeater architecture to establish long-distance entanglement shared between multiple communication partners in the presence of channel noise and imperfect local control operations. The scheme is based on the creation of self-similar multiqubit entanglement structures at growing scale, where variants of entanglement swapping and multiparty entanglement purification are combined to create high-fidelity entangled states. We show how such networks can be implemented using trapped ions in cavities.

  15. Two-dimensional capillary origami

    Science.gov (United States)

    Brubaker, N. D.; Lega, J.

    2016-01-01

    We describe a global approach to the problem of capillary origami that captures all unfolded equilibrium configurations in the two-dimensional setting where the drop is not required to fully wet the flexible plate. We provide bifurcation diagrams showing the level of encapsulation of each equilibrium configuration as a function of the volume of liquid that it contains, as well as plots representing the energy of each equilibrium branch. These diagrams indicate at what volume level the liquid drop ceases to be attached to the endpoints of the plate, which depends on the value of the contact angle. As in the case of pinned contact points, three different parameter regimes are identified, one of which predicts instantaneous encapsulation for small initial volumes of liquid.

  16. 水稻蛋白质组双向电泳优化流程及方法%Optimization Process and Method of 2-D Electrophoresis for Rice Proteomics

    Institute of Scientific and Technical Information of China (English)

    丁承强; 马丹; 王绍华; 丁艳锋

    2011-01-01

    双向电泳是分析蛋白质混合物的一种有力手段,已在蛋白质组研究中得到广泛应用.水稻(Oryza sativa)作为重要的粮食作物,对其蛋白质组学研究开展较早.但由于技术复杂,对实验操作要求高,初学的研究者很难在较短的时间内掌握该实验技术.该文介绍了水稻研究中适合多个组织的双向电泳实验方法和优化流程.该优化流程能使新的研究者逐步优化实验条件,更快更好地完成双向电泳实验.同时详细介绍了实验关键环节的操作方法.%2-D electrophoresis is a powerful tool for analyzing protein mixtures. It has been widely used in proteome research. Rice is an important food crop, and proteomic research into rice has been extensive. Because of the technical complexity and time constraints, performing the procedure accurately has been difficult. This paper describes an optimization process for 2-D electrophoresis of various organs of rice. This method can help researchers optimize experimental conditions with better accuracy.

  17. Establishment and Optimization Analysis of Two-Dimensional Electrophoresis System for the Secreted Proteins of Xanthomonas campestris pv.campestris%十字花科黑腐病菌分泌蛋白质双向电泳条件的构建及优化

    Institute of Scientific and Technical Information of China (English)

    岑卫健; 成春燕; 杨丽超; 王凛; 姜伯乐

    2015-01-01

    本研究旨在建立一套适合于十字花科黑腐病菌(Xanthomonas campestris pv.campestris 8004,Xcc 8004)分泌蛋白质的双向电泳技术(two-dimensional electrophoresis,2-DE),以便更好的利用蛋白质组学技术鉴定Xcc 8004的分泌蛋白质.我们就MME和XCM2两种培养基对分泌蛋白质的诱导能力、蛋白质提取方法以及样品上样量等方面对2-DE的影响进行了比较,结果表明,XCM2培养基对Xcc 8004分泌蛋白质的诱导能力比MME强.用TCA/丙酮法沉淀蛋白质得到的双向电泳图谱背景清晰,分辨率高.分别采用400 μg、300μg、250 μg和150 μg四个不同的上样量进行双向电泳,结果显示在上样量为250~300 μg时(IPG pH 3-10,24 cm),电泳图谱分辨率最好.综上可知,XCM2培养基比较适合用于Xcc 8004分泌蛋白质的诱导,TCA/丙酮法提取分泌蛋白质为较优方法,250~300 μg是较为合适的上样量.

  18. 双向电泳技术在副干酪乳杆菌盐胁迫应激反应研究中的应用%Proteomic Analysis of Protein Induction in Lactobacillus paracasei by Salt Stress Using Two-Dimensional Electrophoresis

    Institute of Scientific and Technical Information of China (English)

    乌日娜; 岳喜庆; 武俊瑞

    2015-01-01

    对耐盐副干酪乳杆菌在盐胁迫下的应激反应进行研究,比较其在含有6 g/dL NaCl和未含有NaCl的培养基中生长至对数生长中期的蛋白质组双向电泳图谱差异。结果表明:有20个蛋白质点表达发生明显变化,经过基质辅助激光解吸/电离飞行时间质谱鉴定,其中热休克蛋白质GroEL和DnaK在盐胁迫下表达上调,参与脂肪酸合成的3-氧酰基-(酰载体蛋白)合酶Fab G表达下调,可能与该菌应对盐胁迫密切相关。%Lactobacillus paracasei LN-1 with salt tolerance property was isolated from traditional fermented food,suancai,which was made in the northeast of China. In order to understand the mechanism involved,proteomics analysis was undertaken to reveal the response of the strain during growth in medium with or without NaCl using two-dimensional electrophoresis (2-DE). Out of 20 protein spots that showed differential changes in expression,seven spots were identified by matrix assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF/MS). Further analysis showed that chaperone protein (GroEL and DnaK) and fatty acid biosynthesis enemy(Fab G) possibly play important role in Lactobacillus paracasei LN-1 to resist to salt stress.

  19. 2D-immunoblotting analysis of Sporothrix schenckii cell wall

    Directory of Open Access Journals (Sweden)

    Estela Ruiz-Baca

    2011-03-01

    Full Text Available We utilized two-dimensional gel electrophoresis and immunoblotting (2D-immunoblotting with anti-Sporothrix schenckii antibodies to identify antigenic proteins in cell wall preparations obtained from the mycelial and yeast-like morphologies of the fungus. Results showed that a 70-kDa glycoprotein (Gp70 was the major antigen detected in the cell wall of both morphologies and that a 60-kDa glycoprotein was present only in yeast-like cells. In addition to the Gp70, the wall from filament cells showed four proteins with molecular weights of 48, 55, 66 and 67 kDa, some of which exhibited several isoforms. To our knowledge, this is the first 2D-immunoblotting analysis of the S. schenckii cell wall.

  20. A novel antibody overlay technique for two-dimensional immunoelectrophoresis.

    Science.gov (United States)

    Lebecq, J C; Salhi, S L; Bastide, J M

    1984-02-10

    A new antibody overlay technique for 2-dimensional immunoelectrophoresis (2-D-IEP) is described. After the first dimension electrophoresis of the antigen, the desired amount of antiserum is applied to the initial agarose layer and then evenly distributed over a defined surface of the gel with a PVC film. This modification of the conventional 2-D-IEP procedure makes it possible to perform tandem 2-D-IEPs comparing 2 antisera on the same gel plate, rocket IEPs where several antisera are compared by electrophoresis on the same gel plate, and 2-D-IEPs with an intermediate antiserum, avoiding the need to pour an intermediate gel. With this technique, 77 antigens have been demonstrated in a Candida albicans serotype A somatic antigen preparation. This is the first description of such a large number of immunoprecipitates on the same immunoplate.

  1. 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

    proteins in alphabetical order), "basal cell markers", "differentiation markers", "proteins highly up-regulated in psoriatic skin", "microsequenced proteins" and "human autoantigens". For reference, we have also included 2-D gel (isoelectric focusing) patterns of cultured normal and psoriatic keratinocytes......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...

  2. Vibrational Properties of a Two-Dimensional Silica Kagome Lattice.

    Science.gov (United States)

    Björkman, Torbjörn; Skakalova, Viera; Kurasch, Simon; Kaiser, Ute; Meyer, Jannik C; Smet, Jurgen H; Krasheninnikov, Arkady V

    2016-12-27

    Kagome lattices are structures possessing fascinating magnetic and vibrational properties, but in spite of a large body of theoretical work, experimental realizations and investigations of their dynamics are scarce. Using a combination of Raman spectroscopy and density functional theory calculations, we study the vibrational properties of two-dimensional silica (2D-SiO2), which has a kagome lattice structure. We identify the signatures of crystalline and amorphous 2D-SiO2 structures in Raman spectra and show that, at finite temperatures, the stability of 2D-SiO2 lattice is strongly influenced by phonon-phonon interaction. Our results not only provide insights into the vibrational properties of 2D-SiO2 and kagome lattices in general but also suggest a quick nondestructive method to detect 2D-SiO2.

  3. Emergent elemental two-dimensional materials beyond graphene

    Science.gov (United States)

    Zhang, Yuanbo; Rubio, Angel; Le Lay, Guy

    2017-02-01

    Two-dimensional (2D) materials may offer the ultimate scaling beyond the 5 nm gate length. The difficulty of reliably opening a band gap in graphene has led to the search for alternative, semiconducting 2D materials. Emerging classes of elemental 2D materials stand out for their compatibility with existing technologies and/or for their diverse, tunable electronic structures. Among this group, black phosphorene has recently shown superior semiconductor performances. Silicene and germanene feature Dirac-type band dispersions, much like graphene. Calculations show that most group IV and group V elements have one or more stable 2D allotropes, with properties potentially suitable for electronic and optoelectronic applications. Here, we review the advances in these fascinating elemental 2D materials and discuss progress and challenges in their applications in future opto- and nano-electronic devices.

  4. Computationally Driven Two-Dimensional Materials Design: What Is Next?

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Jie [Materials Science; Lany, Stephan [Materials Science; Qi, Yue [Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan 48824, United States

    2017-07-17

    Two-dimensional (2D) materials offer many key advantages to innovative applications, such as spintronics and quantum information processing. Theoretical computations have accelerated 2D materials design. In this issue of ACS Nano, Kumar et al. report that ferromagnetism can be achieved in functionalized nitride MXene based on first-principles calculations. Their computational results shed light on a potentially vast group of materials for the realization of 2D magnets. In this Perspective, we briefly summarize the promising properties of 2D materials and the role theory has played in predicting these properties. In addition, we discuss challenges and opportunities to boost the power of computation for the prediction of the 'structure-property-process (synthesizability)' relationship of 2D materials.

  5. Classifying Two-dimensional Hyporeductive Triple Algebras

    CERN Document Server

    Issa, A Nourou

    2010-01-01

    Two-dimensional real hyporeductive triple algebras (h.t.a.) are investigated. A classification of such algebras is presented. As a consequence, a classification of two-dimensional real Lie triple algebras (i.e. generalized Lie triple systems) and two-dimensional real Bol algebras is given.

  6. Two-Dimensional Electronic Spectroscopy Using Incoherent Light: Theoretical Analysis

    CERN Document Server

    Turner, Daniel B; Sutor, Erika J; Hendrickson, Rebecca A; Gealy, M W; Ulness, Darin J

    2012-01-01

    Electronic energy transfer in photosynthesis occurs over a range of time scales and under a variety of intermolecular coupling conditions. Recent work has shown that electronic coupling between chromophores can lead to coherent oscillations in two-dimensional electronic spectroscopy measurements of pigment-protein complexes measured with femtosecond laser pulses. A persistent issue in the field is to reconcile the results of measurements performed using femtosecond laser pulses with physiological illumination conditions. Noisy-light spectroscopy can begin to address this question. In this work we present the theoretical analysis of incoherent two-dimensional electronic spectroscopy, I(4) 2D ES. Simulations reveal diagonal peaks, cross peaks, and coherent oscillations similar to those observed in femtosecond two-dimensional electronic spectroscopy experiments. The results also expose fundamental differences between the femtosecond-pulse and noisy-light techniques; the differences lead to new challenges and opp...

  7. Moment-based method for computing the two-dimensional discrete Hartley transform

    Science.gov (United States)

    Dong, Zhifang; Wu, Jiasong; Shu, Huazhong

    2009-10-01

    In this paper, we present a fast algorithm for computing the two-dimensional (2-D) discrete Hartley transform (DHT). By using kernel transform and Taylor expansion, the 2-D DHT is approximated by a linear sum of 2-D geometric moments. This enables us to use the fast algorithms developed for computing the 2-D moments to efficiently calculate the 2-D DHT. The proposed method achieves a simple computational structure and is suitable to deal with any sequence lengths.

  8. Two-dimensional function photonic crystals

    CERN Document Server

    Wu, Xiang-Yao; Liu, Xiao-Jing; Liang, Yu

    2016-01-01

    In this paper, we have firstly proposed two-dimensional function photonic crystals, which the dielectric constants of medium columns are the functions of space coordinates $\\vec{r}$, it is different from the two-dimensional conventional photonic crystals constituting by the medium columns of dielectric constants are constants. We find the band gaps of two-dimensional function photonic crystals are different from the two-dimensional conventional photonic crystals, and when the functions form of dielectric constants are different, the band gaps structure should be changed, which can be designed into the appropriate band gaps structures by the two-dimensional function photonic crystals.

  9. Phase-sensitive two-dimensional neutron shearing interferometer and Hartmann sensor

    Energy Technology Data Exchange (ETDEWEB)

    Baker, Kevin

    2015-12-08

    A neutron imaging system detects both the phase shift and absorption of neutrons passing through an object. The neutron imaging system is based on either of two different neutron wavefront sensor techniques: 2-D shearing interferometry and Hartmann wavefront sensing. Both approaches measure an entire two-dimensional neutron complex field, including its amplitude and phase. Each measures the full-field, two-dimensional phase gradients and, concomitantly, the two-dimensional amplitude mapping, requiring only a single measurement.

  10. Development of Novel Two-dimensional Layers, Alloys and Heterostructures

    Science.gov (United States)

    Liu, Zheng

    2015-03-01

    The one-atom-think graphene has fantastic properties and attracted tremendous interests in these years, which opens a window towards various two-dimensional (2D) atomic layers. However, making large-size and high-quality 2D layers is still a great challenge. Using chemical vapor deposition (CVD) method, we have successfully synthesized a wide varieties of highly crystalline and large scale 2D atomic layers, including h-BN, metal dichalcogenides e.g. MoS2, WS2, CdS, GaSe and MoSe2 which belong to the family of binary 2D materials. Ternary 2D alloys including BCN and MoS2xSe2 (1 - x) are also prepared and characterized. In addition, synthesis of 2D heterostructures such as vertical and lateral graphene/h-BN, vertical and lateral TMDs are also demonstrated. Complementary to CVD grown 2D layers, 2D single-crystal (bulk) such as Phosphorene (P), WTe2, SnSe2, PtS2, PtSe2, PdSe2, WSe2xTe2 (1 - x), Ta2NiS5andTa2NiSe5 are also prepared by solid reactions. There work provide a better understanding of the atomic layered materials in terms of the synthesis, atomic structure, alloying and their physical properties. Potential applications of these 2D layers e.g. optoelectronic devices, energy device and smart coating have been explored.

  11. Identification and In Silico Analysis of Major Redox Modulated Proteins from Brassica juncea Seedlings Using 2D Redox SDS PAGE (2-Dimensional Diagonal Redox Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis).

    Science.gov (United States)

    Chaurasia, Satya Prakash; Deswal, Renu

    2017-02-01

    The thiol-disulphide exchange regulates the activity of proteins by redox modulation. Many studies to analyze reactive oxygen species (ROS), particularly, hydrogen peroxide (H2O2) induced changes in the gene expression have been reported, but efforts to detect H2O2 modified proteins are comparatively few. Two-dimensional diagonal redox sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE) was used to detect polypeptides which undergo thiol-disulphide exchange in Brassica juncea seedlings following H2O2 (10 mM) treatment for 30 min. Eleven redox responsive polypeptides were identified which included cruciferin, NLI [Nuclear LIM (Lin11, Isl-1 & Mec-3 domains)] interacting protein phosphatase, RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) large subunit, and myrosinase. Redox modulation of RuBisCO large subunit was further confirmed by western blotting. However, the small subunit of RuBisCO was not affected by these redox changes. All redox modulated targets except NLI interacting protein (although it contains two cysteines) showed oxidation sensitive cysteines by in silico analysis. Interestingly, interactome of cruciferin and myrosinase indicated that they may have additional function(s) beside their well-known roles in the seedling development and abiotic stress respectively. Cruciferin showed interactions with stress associated proteins like defensing-like protein 192 and 2-cys peroxiredoxin. Similarly, myrosinase showed interactions with nitrilase and cytochrome p450 which are involved in nitrogen metabolism and/or hormone biosynthesis. This simple procedure can be used to detect major stress mediated redox changes in other plants.

  12. А heuristic algorithm for two-dimensional strip packing problem

    OpenAIRE

    Dayong, Cao; Kotov, V.M.

    2011-01-01

    In this paper, we construct an improved best-fit heuristic algorithm for two-dimensional rectangular strip packing problem (2D-RSPP), and compare it with some heuristic and metaheuristic algorithms from literatures. The experimental results show that BFBCC could produce satisfied packing layouts than these methods, especially for the large problem of 50 items or more, BFBCC could get better results in shorter time.

  13. Colloidal interactions in two-dimensional nematic emulsions

    Indian Academy of Sciences (India)

    N M Silvestre; P Patrício; M M Telo Da Gama

    2005-06-01

    We review theoretical and experimental work on colloidal interactions in two-dimensional (2D) nematic emulsions. We pay particular attention to the effects of (i) the nematic elastic constants, (ii) the size of the colloids, and (iii) the boundary conditions at the particles and the container. We consider the interactions between colloids and fluid (deformable) interfaces and the shape of fluid colloids in smectic-C films.

  14. A comparative study of two-dimensional multifractal detrended fluctuation analysis and two-dimensional multifractal detrended moving average algorithm to estimate the multifractal spectrum

    Science.gov (United States)

    Xi, Caiping; Zhang, Shunning; Xiong, Gang; Zhao, Huichang

    2016-07-01

    Multifractal detrended fluctuation analysis (MFDFA) and multifractal detrended moving average (MFDMA) algorithm have been established as two important methods to estimate the multifractal spectrum of the one-dimensional random fractal signal. They have been generalized to deal with two-dimensional and higher-dimensional fractal signals. This paper gives a brief introduction of the two-dimensional multifractal detrended fluctuation analysis (2D-MFDFA) and two-dimensional multifractal detrended moving average (2D-MFDMA) algorithm, and a detailed description of the application of the two-dimensional fractal signal processing by using the two methods. By applying the 2D-MFDFA and 2D-MFDMA to the series generated from the two-dimensional multiplicative cascading process, we systematically do the comparative analysis to get the advantages, disadvantages and the applicabilities of the two algorithms for the first time from six aspects such as the similarities and differences of the algorithm models, the statistical accuracy, the sensitivities of the sample size, the selection of scaling range, the choice of the q-orders and the calculation amount. The results provide a valuable reference on how to choose the algorithm from 2D-MFDFA and 2D-MFDMA, and how to make the schemes of the parameter settings of the two algorithms when dealing with specific signals in practical applications.

  15. Two-dimensional numerical assessment of the hydrodynamics of the Nile swamps in southern Sudan

    National Research Council Canada - National Science Library

    Petersen, G; Fohrer, N

    2010-01-01

    A two-dimensional (2D) hydrodynamic assessment of the Nile swamps in southern Sudan has been carried out using DHI MIKE 21 software based on a ground referenced and corrected Shuttle Radar Topography Mission (SRTM...

  16. Logarithmic divergent thermal conductivity in two-dimensional nonlinear lattices.

    Science.gov (United States)

    Wang, Lei; Hu, Bambi; Li, Baowen

    2012-10-01

    Heat conduction in three two-dimensional (2D) momentum-conserving nonlinear lattices are numerically calculated via both nonequilibrium heat-bath and equilibrium Green-Kubo algorithms. It is expected by mainstream theories that heat conduction in such 2D lattices is divergent and the thermal conductivity κ increases with lattice length N logarithmically. Our simulations for the purely quartic lattice firmly confirm it. However, very robust finite-size effects are observed in the calculations for the other two lattices, which well explain some existing studies and imply the extreme difficulties in observing their true asymptotic behaviors with affordable computation resources.

  17. Absolute band gaps in two-dimensional graphite photonic crystal

    Institute of Scientific and Technical Information of China (English)

    Gaoxin Qiu(仇高新); Fanglei Lin(林芳蕾); Hua Wang(王华); Yongping Li(李永平)

    2003-01-01

    The off-plane propagation of electromagnetic (EM) waves in a two-dimensional (2D) graphite photoniccrystal structure was studied using transfer matrix method. Transmission spectra calculations indicatethat such a 2D structure has a common band gap from 0.202 to 0.2035 c/a for both H and E polarizationsand for all off-plane angles form 0° up to 90°. The presence of such an absolute band gap implies that 2Dgraphite photonic crystal, which is much easier and more feasible to fabricate, can exhibit some propertiesof a three-dimensional (3D) photonic crystal.

  18. Two-dimensional carbon fundamental properties, synthesis, characterization, and applications

    CERN Document Server

    Yihong, Wu; Ting, Yu

    2013-01-01

    After a brief introduction to the fundamental properties of graphene, this book focuses on synthesis, characterization and application of various types of two-dimensional (2D) nanocarbons ranging from single/few layer graphene to carbon nanowalls and graphene oxides. Three major synthesis techniques are covered: epitaxial growth of graphene on SiC, chemical synthesis of graphene on metal, and chemical vapor deposition of vertically aligned carbon nanosheets or nanowalls. One chapter is dedicated to characterization of 2D nanocarbon using Raman spectroscopy. It provides extensive coverage for a

  19. Band alignment of two-dimensional lateral heterostructures

    CERN Document Server

    Zhang, Junfeng; Xie, Weiyu; Zhang, S B

    2016-01-01

    Band alignment in two-dimensional (2D) lateral heterostructures is fundamentally different from three-dimensional (3D), as Schottky barrier height is at the Schottky-Mott limit and band offset is at the Anderson limit, regardless interfacial conditions. This robustness arises because, in the asymptotic limit, effect of interfacial dipole vanishes. First-principles calculations of graphene/h-BN and MoS2/WS2 show that 2D junction width W is typically an order of magnitude longer than 3D. Therefore, heterostructures with dimension less than W can also be made, leading to tunable band alignment.

  20. A Direct Two-Dimensional Pressure Formulation in Molecular Dynamics

    CERN Document Server

    YD, Sumith

    2016-01-01

    Two-dimensional (2D) pressure field estimation in molecular dynamics (MD) simulations has been done using three-dimensional (3D) pressure field calculations followed by averaging, which is computationally expensive due to 3D convolutions. In this work, we develop a direct 2D pressure field estimation method which is much faster than 3D methods without losing accuracy. The method is validated with MD simulations on two systems: a liquid film and a cylindrical drop of argon suspended in surrounding vapor.

  1. A Two-dimensional Magnetohydrodynamics Scheme for General Unstructured Grids

    Science.gov (United States)

    Livne, Eli; Dessart, Luc; Burrows, Adam; Meakin, Casey A.

    2007-05-01

    We report a new finite-difference scheme for two-dimensional magnetohydrodynamics (MHD) simulations, with and without rotation, in unstructured grids with quadrilateral cells. The new scheme is implemented within the code VULCAN/2D, which already includes radiation hydrodynamics in various approximations and can be used with arbitrarily moving meshes (ALEs). The MHD scheme, which consists of cell-centered magnetic field variables, preserves the nodal finite difference representation of divB by construction, and therefore any initially divergence-free field remains divergence-free through the simulation. In this paper, we describe the new scheme in detail and present comparisons of VULCAN/2D results with those of the code ZEUS/2D for several one-dimensional and two-dimensional test problems. The code now enables two-dimensional simulations of the collapse and explosion of the rotating, magnetic cores of massive stars. Moreover, it can be used to simulate the very wide variety of astrophysical problems for which multidimensional radiation magnetohydrodynamics (RMHD) is relevant.

  2. 应用双向电泳和免疫印迹技术分析软叶针葵花粉变应原%Analysis on the total allergens of phoenix roebelenii pollen with two dimensional electrophoresis followed by immunoblotting

    Institute of Scientific and Technical Information of China (English)

    刘硕; 孟光; 郑琳麟; 李春林; 谢伟伟; 龙绮

    2016-01-01

    Objective:To investigate allergen extract and to seek the main allergens of phoenix roebelenii pollen by the technology of two dimensional electrophoresis(2-DE)in protein analysis and immunoblotting.Method:Phoenix roebelenii pollen allergen extract was prepared with routine method,2-DE combined with immunoblotting assay(Western Blotting),laser imagescanning,2-DE gel analysis software were used to analyzing its protein components.Result:About 601 soluble proteins spots were revealed in coomassie-stained gels.Most of the proteins had a molecular weight (Mr) of 20 to 130 kD,and an isoelectric point(pI) value of 4.0 to 8.0.Immunoblotting of 2-DE were showed and there were 19 specific antigen spots,compared with the controls.Conclusion:2-DE is a good method in protein analysis of ephemeroptera allergen extract,and it is useful in seeking main allergens and further research for allergic components.%目的:采用双向电泳和免疫印迹技术对软叶针葵花粉提取液蛋白质组分进行分析,寻找软叶针葵花粉的主要变应原.方法:提取软叶针葵花粉变应原,应用双向电泳(2-DE)结合免疫印迹技术,获得相应的电泳图谱和免疫印迹图谱.结果:软叶针葵花粉蛋白提取液经双向电泳后,用考马斯亮蓝染色,得到的电泳图显示约有601个主要蛋白斑点.分子量(Mr)分布约20~130 kD;等电点(pI)主要集中在4.0~8.0.免疫印迹分析结果显示,阳性组与对照组的差异蛋白点数约为19个.结论:双向电泳联合免疫印迹技术对软叶针葵花粉提取液蛋白质组分分析,可寻找到其主要变应原,并可进一步用于变应原致敏组分的研究.

  3. 益生菌Lactobacillus casei Zhang在酸胁迫下的蛋白质组学研究%Proteomics Researches on Acid Response of Lactobacillus casei Zhang Grown at Different pH Values Using Two-Dimensional Gel Electrophoresis

    Institute of Scientific and Technical Information of China (English)

    乌日娜; 岳喜庆; 张和平

    2012-01-01

    Lactobacilluscasei Zhang是1株筛选自发酵酸马奶,并具有耐酸等益生特性的益生乳杆菌。该研究利用蛋白质组双向电泳,比较了其在pH值为7.0和5.5的培养液中分别生长至对数生长期中期的蛋白质组表达差异。结果表明,有11个蛋白质点表达发生明显变化,经过基质辅助激光解吸/电离飞行时间质谱鉴定,其中有3个表达增强的蛋白质点分别鉴定为翻译因子(EF-Tu),N-乙酰氨基葡萄糖-6-磷酸脱醛酶(NagA)和小热休克蛋白(sHsp)。酸胁迫可诱导乳酸菌产生复杂的酸应激反应,涉及不同的代谢调控途径。%Lactobacillus casei Zhang, isolated from traditional home-made koumiss in Inner Mongolia of China, has been considered as a new probiotic bacterium for its characteristics, especially acid tolerance. Proteomics resear- ches were carried out to identify proteins expression of Lactobacillus casei Zhang grown at different pH values of pH 7.0 and 5.5. Cytosolic proteins of mid-exponential phase were resolved and further analyzed by two-dimensional gel electrophoresis. As results shown, eleven protein spots were found showing statistically significant differences. Three of total protein spots were identified as EF-Tu, NagA and sHsp using matrix-assisted laser desorption/ionization time- of-flight mass spectrometry (MALDI-TOF/MS) , indicating the complex response of lactic acid bacteria to acid stress.

  4. Separation of colloidal two dimensional materials by density gradient ultracentrifugation

    Energy Technology Data Exchange (ETDEWEB)

    Kuang, Yun; Song, Sha [State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029 (China); Huang, Jinyang, E-mail: huangjy@mail.buct.edu.cn [Department of Mathematics, College of Science, Beijing University of Chemical Technology, Beijing 100029 (China); Sun, Xiaoming, E-mail: sunxm@mail.buct.edu.cn [State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029 (China)

    2015-04-15

    Two-dimensional (2D) materials have been made through various approaches but obtaining monodispersed simply by synthesis optimization gained little success, which highlighted the need for introducing nanoseparation methods. Density gradient ultracentrifugation method has emerged as a versatile and scalable method for sorting colloidal 2D nanomaterials. Isopycnic separation was applied on thickness-dependent separation of graphene nanosheets. And rate-zonal separation, as a more versatile separation method, demonstrated its capability in sorting nanosheets of chemically modified single layered graphene, layered double hydroxide, and even metallic Ag. Establishing such density gradient ultracentrifugation method not only achieves monodispersed nanosheets and provides new opportunities for investigation on size dependent properties of 2D materials, but also makes the surface modification possible by introducing “reaction zones” during sedimentation of the colloids. - Graphical abstract: Two-dimensional (2D) materials have been made through various approaches but obtaining monodispersed simply by synthesis optimization gained little success, which highlighted the need for introducing nanoseparation methods. Density gradient ultracentrifugation method has emerged as a versatile and scalable method for sorting colloidal 2D nanomaterials according to their size of thickness difference. Establishing such density gradient ultracentrifugation method not only achieves monodispersed nanosheets and provides new opportunities for investigation on size dependent properties of 2D materials, but also makes the surface modification possible by introducing “reaction zones” during sedimentation of the colloids. - Highlights: • Density gradient ultracentrifugation was applied on size separation of 2D material. • Isopycnic separation was applied on separation of low density materials. • Rate-zonal separation was applied on separation of large density materials. • Size

  5. Hadamard States and Two-dimensional Gravity

    CERN Document Server

    Salehi, H

    2001-01-01

    We have used a two-dimensional analog of the Hadamard state-condition to study the local constraints on the two-point function of a linear quantum field conformally coupled to a two-dimensional gravitational background. We develop a dynamical model in which the determination of the state of the quantum field is essentially related to the determination of a conformal frame. A particular conformal frame is then introduced in which a two-dimensional gravitational equation is established.

  6. Tunable states of interlayer cations in two-dimensional materials

    Energy Technology Data Exchange (ETDEWEB)

    Sato, K.; Numata, K. [Department of Environmental Sciences, Tokyo Gakugei University, Koganei, Tokyo 184-8501 (Japan); Dai, W. [Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), College of Chemistry, Nankai University, Tianjin 300071 (China); Hunger, M. [Institute of Chemical Technology, University of Stuttgart, 70550 Stuttgart (Germany)

    2014-03-31

    The local state of cations inside the Ångstrom-scale interlayer spaces is one of the controlling factors for designing sophisticated two-dimensional (2D) materials consisting of 2D nanosheets. In the present work, the molecular mechanism on how the interlayer cation states are induced by the local structures of the 2D nanosheets is highlighted. For this purpose, the local states of Na cations in inorganic 2D materials, in which the compositional fluctuations of a few percent are introduced in the tetrahedral and octahedral units of the 2D nanosheets, were systematically studied by means of {sup 23}Na magic-angle-spinning (MAS) nuclear magnetic resonance (NMR) and {sup 23}Na multiple-quantum MAS (MQMAS) NMR spectroscopy. In contrast with an uniform distribution of Na cations expected so far, various well-defined cation states sensitive to the local structures of the 2D nanosheets were identified. The tunability of the interlayer cation states along with the local structure of the 2D nanosheets, as the smallest structural unit of the 2D material, is discussed.

  7. Two-dimensional gallium nitride realized via graphene encapsulation

    Science.gov (United States)

    Al Balushi, Zakaria Y.; Wang, Ke; Ghosh, Ram Krishna; Vilá, Rafael A.; Eichfeld, Sarah M.; Caldwell, Joshua D.; Qin, Xiaoye; Lin, Yu-Chuan; Desario, Paul A.; Stone, Greg; Subramanian, Shruti; Paul, Dennis F.; Wallace, Robert M.; Datta, Suman; Redwing, Joan M.; Robinson, Joshua A.

    2016-11-01

    The spectrum of two-dimensional (2D) and layered materials `beyond graphene’ offers a remarkable platform to study new phenomena in condensed matter physics. Among these materials, layered hexagonal boron nitride (hBN), with its wide bandgap energy (~5.0-6.0 eV), has clearly established that 2D nitrides are key to advancing 2D devices. A gap, however, remains between the theoretical prediction of 2D nitrides `beyond hBN’ and experimental realization of such structures. Here we demonstrate the synthesis of 2D gallium nitride (GaN) via a migration-enhanced encapsulated growth (MEEG) technique utilizing epitaxial graphene. We theoretically predict and experimentally validate that the atomic structure of 2D GaN grown via MEEG is notably different from reported theory. Moreover, we establish that graphene plays a critical role in stabilizing the direct-bandgap (nearly 5.0 eV), 2D buckled structure. Our results provide a foundation for discovery and stabilization of 2D nitrides that are difficult to prepare via traditional synthesis.

  8. van der Waals epitaxy and photoresponse of two-dimensional CdSe plates

    Science.gov (United States)

    Zhu, Dan-Dan; Xia, Jing; Wang, Lei; Li, Xuan-Ze; Tian, Li-Feng; Meng, Xiang-Min

    2016-06-01

    Here we demonstrate the first growth of two-dimensional (2D) single-crystalline CdSe plates on mica substrates via van der Waals epitaxy. The as-synthesized 2D plates exhibit hexagonal, truncated triangular and triangular shapes with the lateral size around several microns. Photodetectors based on 2D CdSe plates present a fast response time of 24 ms, revealing that 2D CdSe is a promising building block for ultrathin optoelectronic devices.

  9. Two-Dimensional DOA Estimation for Uniform Rectangular Array Using Reduced-Dimension Propagator Method

    Directory of Open Access Journals (Sweden)

    Ming Zhou

    2015-01-01

    Full Text Available A novel algorithm is proposed for two-dimensional direction of arrival (2D-DOA estimation with uniform rectangular array using reduced-dimension propagator method (RD-PM. The proposed algorithm requires no eigenvalue decomposition of the covariance matrix of the receive data and simplifies two-dimensional global searching in two-dimensional PM (2D-PM to one-dimensional local searching. The complexity of the proposed algorithm is much lower than that of 2D-PM. The angle estimation performance of the proposed algorithm is better than that of estimation of signal parameters via rotational invariance techniques (ESPRIT algorithm and conventional PM algorithms, also very close to 2D-PM. The angle estimation error and Cramér-Rao bound (CRB are derived in this paper. Furthermore, the proposed algorithm can achieve automatically paired 2D-DOA estimation. The simulation results verify the effectiveness of the algorithm.

  10. Strongly interacting two-dimensional Dirac fermions

    NARCIS (Netherlands)

    Lim, L.K.; Lazarides, A.; Hemmerich, Andreas; de Morais Smith, C.

    2009-01-01

    We show how strongly interacting two-dimensional Dirac fermions can be realized with ultracold atoms in a two-dimensional optical square lattice with an experimentally realistic, inherent gauge field, which breaks time reversal and inversion symmetries. We find remarkable phenomena in a temperature

  11. Topology optimization of two-dimensional waveguides

    DEFF Research Database (Denmark)

    Jensen, Jakob Søndergaard; Sigmund, Ole

    2003-01-01

    In this work we use the method of topology optimization to design two-dimensional waveguides with low transmission loss.......In this work we use the method of topology optimization to design two-dimensional waveguides with low transmission loss....

  12. Interaction of two-dimensional magnetoexcitons

    Science.gov (United States)

    Dumanov, E. V.; Podlesny, I. V.; Moskalenko, S. A.; Liberman, M. A.

    2017-04-01

    We study interaction of the two-dimensional magnetoexcitons with in-plane wave vector k→∥ = 0 , taking into account the influence of the excited Landau levels (ELLs) and of the external electric field perpendicular to the surface of the quantum well and parallel to the external magnetic field. It is shown that the account of the ELLs gives rise to the repulsion between the spinless magnetoexcitons with k→∥ = 0 in the Fock approximation, with the interaction constant g decreasing inverse proportional to the magnetic field strength B (g (0) ∼ 1 / B) . In the presence of the perpendicular electric field the Rashba spin-orbit coupling (RSOC), Zeeman splitting (ZS) and nonparabolicity of the heavy-hole dispersion law affect the Landau quantization of the electrons and holes. They move along the new cyclotron orbits, change their Coulomb interactions and cause the interaction between 2D magnetoexcitons with k→∥ = 0 . The changes of the Coulomb interactions caused by the electrons and by the holes moving with new cyclotron orbits are characterized by some coefficients, which in the absence of the electric field turn to be unity. The differences between these coefficients of the electron-hole pairs forming the magnetoexcitons determine their affinities to the interactions. The interactions between the homogeneous, semihomogeneous and heterogeneous magnetoexcitons forming the symmetric states with the same signs of their affinities are attractive whereas in the case of different sign affinities are repulsive. In the heterogeneous asymmetric states the interactions have opposite signs in comparison with the symmetric states. In all these cases the interaction constant g have the dependence g (0) 1 /√{ B} .

  13. 2-D Animation's Not Just for Mickey Mouse.

    Science.gov (United States)

    Weinman, Lynda

    1995-01-01

    Discusses characteristics of two-dimensional (2-D) animation; highlights include character animation, painting issues, and motion graphics. Sidebars present Silicon Graphics animations tools and 2-D animation programs for the desktop computer. (DGM)

  14. The human keratinocyte two-dimensional protein database (update 1994): towards an integrated approach to the study of cell proliferation, differentiation and skin diseases

    DEFF Research Database (Denmark)

    Celis, J E; Rasmussen, H H; Olsen, E

    1994-01-01

    The master two-dimensional (2-D) gel database of human keratinocytes currently lists 3087 cellular proteins (2168 isoelectric focusing, IEF; and 919 none-quilibrium pH gradient electrophoresis, NEPHGE), many of which correspond to posttranslational modifications, 890 polypeptides have been...... identified (protein name, organelle components, etc.) using one or a combination of procedures that include (i) comigration with known human proteins, (ii) 2-D gel immunoblotting using specific antibodies (iii) microsequencing of Coomassie Brilliant Blue stained proteins, (iv) mass spectrometry and (v...... in the database. We also report a database of proteins recovered from the medium of noncultured, unfractionated keratinocytes. This database lists 398 polypeptides (309 IEF; 89 NEPHGE) of which 76 have been identified. The aim of the comprehensive databases is to gather, through a systematic study...

  15. A spectroelectrochemical cell for ultrafast two-dimensional infrared spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    El Khoury, Youssef; Van Wilderen, Luuk J. G. W.; Vogt, Tim; Winter, Ernst; Bredenbeck, Jens, E-mail: bredenbeck@biophysik.uni-frankfurt.org, E-mail: bredenbeck@biophysik.uni-frankfurt.de [Institut für Biophysik, Johann Wolfgang Goethe-Universität, Max-von-Laue-Strasse 1, 60438 Frankfurt (Germany)

    2015-08-15

    A spectroelectrochemical cell has been designed to combine electrochemistry and ultrafast two-dimensional infrared (2D-IR) spectroscopy, which is a powerful tool to extract structure and dynamics information on the femtosecond to picosecond time scale. Our design is based on a gold mirror with the dual role of performing electrochemistry and reflecting IR light. To provide the high optical surface quality required for laser spectroscopy, the gold surface is made by electron beam evaporation on a glass substrate. Electrochemical cycling facilitates in situ collection of ultrafast dynamics of redox-active molecules by means of 2D-IR. The IR beams are operated in reflection mode so that they travel twice through the sample, i.e., the signal size is doubled. This methodology is optimal for small sample volumes and successfully tested with the ferricyanide/ferrocyanide redox system of which the corresponding electrochemically induced 2D-IR difference spectrum is reported.

  16. Superfluid phase transition in two-dimensional excitonic systems

    Energy Technology Data Exchange (ETDEWEB)

    Apinyan, V.; Kopeć, T.K., E-mail: kopec@int.pan.wroc.pl

    2014-03-01

    We study the superfluid phase transition in the two-dimensional (2D) excitonic system. Employing the extended Falicov–Kimball model (EFKM) and considering the local quantum correlations in the system composed of conduction band electrons and valence band holes we demonstrate the existence of the excitonic insulator (EI) state in the system. We show that at very low temperatures, the particle phase stiffness in the pure-2D excitonic system, governed by the non-local cross correlations, is responsible for the vortex–antivortex binding phase-field state, known as the Berezinskii–Kosterlitz–Thouless (BKT) superfluid state. We demonstrate that the existence of excitonic insulator phase is a necessary prerequisite, leading to quasi-long-range order in the 2D excitonic system.

  17. Two-dimensional electronic spectroscopy with birefringent wedges

    Energy Technology Data Exchange (ETDEWEB)

    Réhault, Julien; Maiuri, Margherita; Oriana, Aurelio; Cerullo, Giulio [IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano (Italy)

    2014-12-15

    We present a simple experimental setup for performing two-dimensional (2D) electronic spectroscopy in the partially collinear pump-probe geometry. The setup uses a sequence of birefringent wedges to create and delay a pair of phase-locked, collinear pump pulses, with extremely high phase stability and reproducibility. Continuous delay scanning is possible without any active stabilization or position tracking, and allows to record rapidly and easily 2D spectra. The setup works over a broad spectral range from the ultraviolet to the near-IR, it is compatible with few-optical-cycle pulses and can be easily reconfigured to two-colour operation. A simple method for scattering suppression is also introduced. As a proof of principle, we present degenerate and two-color 2D spectra of the light-harvesting complex 1 of purple bacteria.

  18. Nonlinear optical response of a two-dimensional atomic crystal.

    Science.gov (United States)

    Merano, Michele

    2016-01-01

    The theory of Bloembergen and Pershan for the light waves at the boundary of nonlinear media is extended to a nonlinear two-dimensional (2D) atomic crystal, i.e., a single planar atomic lattice, placed between linear bulk media. The crystal is treated as a zero-thickness interface, a real 2D system. Harmonic waves emanate from it. Generalization of the laws of reflection and refraction give the direction and the intensity of the harmonic waves. As a particular case that contains all the essential physical features, second-order harmonic generation is considered. The theory, due to its simplicity that stems from the special character of a single planar atomic lattice, is able to elucidate and explain the rich experimental details of harmonic generation from a 2D atomic crystal.

  19. A spectroelectrochemical cell for ultrafast two-dimensional infrared spectroscopy

    Science.gov (United States)

    El Khoury, Youssef; Van Wilderen, Luuk J. G. W.; Vogt, Tim; Winter, Ernst; Bredenbeck, Jens

    2015-08-01

    A spectroelectrochemical cell has been designed to combine electrochemistry and ultrafast two-dimensional infrared (2D-IR) spectroscopy, which is a powerful tool to extract structure and dynamics information on the femtosecond to picosecond time scale. Our design is based on a gold mirror with the dual role of performing electrochemistry and reflecting IR light. To provide the high optical surface quality required for laser spectroscopy, the gold surface is made by electron beam evaporation on a glass substrate. Electrochemical cycling facilitates in situ collection of ultrafast dynamics of redox-active molecules by means of 2D-IR. The IR beams are operated in reflection mode so that they travel twice through the sample, i.e., the signal size is doubled. This methodology is optimal for small sample volumes and successfully tested with the ferricyanide/ferrocyanide redox system of which the corresponding electrochemically induced 2D-IR difference spectrum is reported.

  20. Synthesis of borophenes: Anisotropic, two-dimensional boron polymorphs

    Science.gov (United States)

    Mannix, Andrew J.; Zhou, Xiang-Feng; Kiraly, Brian; Wood, Joshua D.; Alducin, Diego; Myers, Benjamin D.; Liu, Xiaolong; Fisher, Brandon L.; Santiago, Ulises; Guest, Jeffrey R.; Yacaman, Miguel Jose; Ponce, Arturo; Oganov, Artem R.; Hersam, Mark C.; Guisinger, Nathan P.

    2016-01-01

    At the atomic-cluster scale, pure boron is markedly similar to carbon, forming simple planar molecules and cage-like fullerenes.Theoretical studies predict that two-dimensional (2D) boron sheets will adopt an atomic configuration similar to that of boron atomic clusters. We synthesized atomically thin, crystalline 2D boron sheets (i.e., borophene) on silver surfaces under ultrahigh-vacuum conditions. Atomic-scale characterization, supported by theoretical calculations, revealed structures reminiscent of fused boron clusters with multiple scales of anisotropic, out-of-plane buckling. Unlike bulk boron allotropes, borophene shows metallic characteristics that are consistent with predictions of a highly anisotropic, 2D metal. PMID:26680195

  1. Proximity Induced Superconducting Properties in One and Two Dimensional Semiconductors

    DEFF Research Database (Denmark)

    Kjærgaard, Morten

    a voltage is passed through the Josephson junction, we observe multiple Andreev reflections and preliminary results point to a highly transmissive interface between the 2D electron gas and the superconductor. In the theoretical section we demonstrate analytically and numerically, that in a 1D nanowire......This report is concerned with the properties of one and two dimensional semiconducting materials when brought into contact with a superconductor. Experimentally we study the 2D electron gas in an InGaAs/InAs heterostructure with aluminum grown in situ on the surface, and theoretically we show...... that a superconducting 1D nanowire can harbor Majorana bound states in the absence of spin–orbit coupling. We fabricate and measure micrometer–sized mesoscopic devices demonstrating the inheritance of superconducting properties in the 2D electron gas. By placing a quantum point contact proximal to the interface between...

  2. A renormalization group analysis of two-dimensional magnetohydrodynamic turbulence

    Science.gov (United States)

    Liang, Wenli Z.; Diamond, P. H.

    1993-01-01

    The renormalization group (RNG) method is used to study the physics of two-dimensional (2D) magnetohydrodynamic (MHD) turbulence. It is shown that, for a turbulent magnetofluid in two dimensions, no RNG transformation fixed point exists on account of the coexistence of energy transfer to small scales and mean-square magnetic flux transfer to large scales. The absence of a fixed point renders the RNG method incapable of describing the 2D MHD system. A similar conclusion is reached for 2D hydrodynamics, where enstrophy flows to small scales and energy to large scales. These analyses suggest that the applicability of the RNG method to turbulent systems is intrinsically limited, especially in the case of systems with dual-direction transfer.

  3. Quasi-Two-Dimensional Magnetism in Co-Based Shandites

    Science.gov (United States)

    Kassem, Mohamed A.; Tabata, Yoshikazu; Waki, Takeshi; Nakamura, Hiroyuki

    2016-06-01

    We report quasi-two-dimensional (Q2D) itinerant electron magnetism in the layered Co-based shandites. Comprehensive magnetization measurements were performed using single crystals of Co3Sn2-xInxS2 (0 ≤ x ≤ 2) and Co3-yFeySn2S2 (0 ≤ y ≤ 0.5). The magnetic parameters of both systems; the Curie temperature TC, effective moment peff and spontaneous moment ps; exhibit almost identical variations against the In- and Fe-concentrations, indicating significance of the electron count on the magnetism in the Co-based shandite. The ferromagnetic-nonmagnetic quantum phase transition is found around xc ˜ 0.8. Analysis based on the extended Q2D spin fluctuation theory clearly reveals the highly Q2D itinerant electron character of the ferromagnetism in the Co-based shandites.

  4. Two-dimensional Imaging Velocity Interferometry: Technique and Data Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Erskine, D J; Smith, R F; Bolme, C; Celliers, P; Collins, G

    2011-03-23

    We describe the data analysis procedures for an emerging interferometric technique for measuring motion across a two-dimensional image at a moment in time, i.e. a snapshot 2d-VISAR. Velocity interferometers (VISAR) measuring target motion to high precision have been an important diagnostic in shockwave physics for many years Until recently, this diagnostic has been limited to measuring motion at points or lines across a target. We introduce an emerging interferometric technique for measuring motion across a two-dimensional image, which could be called a snapshot 2d-VISAR. If a sufficiently fast movie camera technology existed, it could be placed behind a traditional VISAR optical system and record a 2d image vs time. But since that technology is not yet available, we use a CCD detector to record a single 2d image, with the pulsed nature of the illumination providing the time resolution. Consequently, since we are using pulsed illumination having a coherence length shorter than the VISAR interferometer delay ({approx}0.1 ns), we must use the white light velocimetry configuration to produce fringes with significant visibility. In this scheme, two interferometers (illuminating, detecting) having nearly identical delays are used in series, with one before the target and one after. This produces fringes with at most 50% visibility, but otherwise has the same fringe shift per target motion of a traditional VISAR. The 2d-VISAR observes a new world of information about shock behavior not readily accessible by traditional point or 1d-VISARS, simultaneously providing both a velocity map and an 'ordinary' snapshot photograph of the target. The 2d-VISAR has been used to observe nonuniformities in NIF related targets (polycrystalline diamond, Be), and in Si and Al.

  5. The analysis of protein differences in cerebrospinal fluid of tuberculous meningitis and cryptococcus meningitis by two-dimensional electrophoresis%应用双向电泳分析结核性脑膜炎与隐球菌性脑膜炎脑脊液的蛋白差异

    Institute of Scientific and Technical Information of China (English)

    黄绍梅; 杨瑜; 邱薇; 吴睿彦; 谢贝; 刘志辉; 陈志成

    2016-01-01

    Objective To screen the diagnostic markers between tuberculous meningitis and cryptococcus meningitis by analyzing the protein differences in cerebrospinal fluid (CSF).Methods The proteins in CSF of 4 cases of tuberculous meningitis and 4 cases of cryptococcal meningitis were separated by two-dimensional gel electrophoresis (2-DE).The differential proteins expression was descriptively analyzed according to the protein isoelectric point PI,molecular weight,matching rate,gray value by PDQuest8.0 software.Results 111 and 114 protein spots were captured from CSF of tuberculose meningitis and cryptococcus meningitis.The molecular weight of proteins ranged from 10 to 130 kDa.The isoelectric point (PI) was from 4.4 to 6.7.The matching rate of two groups was 95%.There were 24 differential proteins between two groups,of which 3 proteins were expressed only in tuberculous meningitis and 2 proteins expressed only in cryptococcal meningitis.19 matching protein point were two-fold differential expression.Conclusion 2-DE profiles with high resolution and reproducibility of CSF for tuberculous meningitis and cryptococcus meningitis are established,and some differences in protein expression exist between the two.%目的 比较分析结核性脑膜炎(TBM)与隐球菌性脑膜炎脑脊液的差异蛋白质,筛选二者的鉴别诊断标志物.方法 采用双向凝胶电泳技术对4例TBM和4例隐球菌性脑膜炎脑脊液蛋白进行电泳分离,以PDQuest8.0软件根据蛋白的等电点PI、分子量、匹配率、灰度值等进行差异蛋白描述性分析.结果 结核性、隐球菌性两组脑脊液分别检测到蛋白点数为111和114,蛋白点分子量均分布为10~130 kDa,等电点PI为4.4~6.7间.两组脑脊液蛋白图谱匹配率为95%,产生24个差异蛋白点,其中3个蛋白点只在TBM中表达,2个蛋白点只在隐球菌性脑膜炎中表达,19个匹配蛋白点存在2倍差异表达.结论 双向电泳技术可得到分辨率和重复率较高

  6. Analysis of the IEA 2D test. 2D, 3D, steady or unsteady airflow?

    DEFF Research Database (Denmark)

    Cortes, Ines Olmedo; Nielsen, Peter V.

    The “IEA Annex 20 two-dimensional test case” was defined by proffesor Peter V. Nielsen (1990) and was originally considered two-dimensional and steady flow. However, some recent works considering the case as three dimensional have shown different solutions from the 2D case as well as different so...

  7. Extension of modified power method to two-dimensional problems

    Science.gov (United States)

    Zhang, Peng; Lee, Hyunsuk; Lee, Deokjung

    2016-09-01

    In this study, the generalized modified power method was extended to two-dimensional problems. A direct application of the method to two-dimensional problems was shown to be unstable when the number of requested eigenmodes is larger than a certain problem dependent number. The root cause of this instability has been identified as the degeneracy of the transfer matrix. In order to resolve this instability, the number of sub-regions for the transfer matrix was increased to be larger than the number of requested eigenmodes; and a new transfer matrix was introduced accordingly which can be calculated by the least square method. The stability of the new method has been successfully demonstrated with a neutron diffusion eigenvalue problem and the 2D C5G7 benchmark problem.

  8. 染矽尘大鼠早期肺组织蛋白质双向电泳图谱差异分析%Differential analysis of two-dimensional gel electrophoresis profiles in lung tissue of rats exposed to silica early

    Institute of Scientific and Technical Information of China (English)

    陈娟娟; 蒋洪彦; 刘萍; 刘伟; 魏茂提; 王世鑫; 翁亚光

    2009-01-01

    Objective To analyze the differences of lung tissue proteins in rats exposed to silica early by using comparative proteomics method and investigate the related mechanism with the occurrence and development of silicosis. Methods Adult male Wistar rats were randomly divided into control group and silica-treated group. The animal model was established by intratracheal (IT) instillation with silica suspension. On the 14th day after establishment of animal model, rats were sacrificed and lung tissues were collected. The total proteins were separated by means of two-dimensional gel electrophoresis (2-DE) and the differentially expressed proteins were identified by using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). In addition, Western blotting was performed to verify the expression of certain candidate protein. Results Eleven differential expression protein spots were tested by MALDI-TOF-MS,and six proteins were identified. The levels of cathepsin D precursor, peroxiredoxin-1 (Prx-1),heat shock cognate 71 000 protein (HSP7C), heterogeneous nuclear ribonucleoprotein A3 (hnRNPA3) and fatty acid-binding protein (epidermal, E-FABP) were up-regulated in silica-treated group with the optical density (A) values. These values were 116.50±12.56,148.75±22.40;40.00±1.63,66.00± 13.93;51.25±7.37,92.75±8.69;83.00±6.48,122.75±24.62;50.75±6.50,93.50±23.10 and 100.25±19.99,142.50±21.21 respectively. The statistical difference was observed as compared with control group(t=-2.51,-3.71,-7.28,-3.12,-3.56 and-2.90,P<0.05). However, SEC14-like protein 3 with the A values 153.00±11.28,109.75±18.32 was down-regulated (t=4.02, P<0.01) Western blotting showed that in the expression of Prx-1 was higher in silica-treated group (0.61±0.05) than that in the control (0.35+0.05) (t=-7.24, P<0.01) when calculating the semi-quantification of this protein using ratio of optical density. Conclusion 2-DE pattern of lung tissue from rats exposed

  9. Two dimensional density and its fluctuation measurements by using phase imaging method in GAMMA 10

    Energy Technology Data Exchange (ETDEWEB)

    Yoshikawa, M.; Negishi, S.; Shima, Y.; Hojo, H.; Imai, T. [Plasma Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577 (Japan); Mase, A. [Kyushu University, 6-1 Kasuga-koen, Kasuga, Fukuoka 816-8580 (Japan); Kogi, Y. [Fukuoka Institute of Technology, 3-30-1 Wajiro-higashi, Higashiku, Fukuoka 811-0295 (Japan)

    2010-10-15

    Two dimensional (2D) plasma image analysis is useful to study the improvement of plasma confinement in magnetically confined fusion plasmas. We have constructed a 2D interferometer system with phase imaging method for studying 2D plasma density distribution and its fluctuation measurement in the tandem mirror GAMMA 10. 2D profiles of electron density and its fluctuation have been successfully obtained by using this 2D phase imaging system. We show that 2D plasma density and fluctuation profiles clearly depends on the axial confining potential formation with application of plug electron cyclotron heating in GAMMA 10.

  10. Two-dimensional coupled electron-hole layers in high magnetic fields

    NARCIS (Netherlands)

    Parlangeli, Andrea

    2000-01-01

    In solids, it is nowadays possible to create structures in which electrons are confined into a two-dimensional (2D) plane. The physics of a 2D electron gas (2DEG) has proved to be very rich, in particular in the presence of a transverse magnetic field. The Quantum Hall Effect, i.e. the quantization

  11. Dipeptide Structural Analysis Using Two-Dimensional NMR for the Undergraduate Advanced Laboratory

    Science.gov (United States)

    Gonzalez, Elizabeth; Dolino, Drew; Schwartzenburg, Danielle; Steiger, Michelle A.

    2015-01-01

    A laboratory experiment was developed to introduce students in either an organic chemistry or biochemistry lab course to two-dimensional nuclear magnetic resonance (2D NMR) spectroscopy using simple biomolecules. The goal of this experiment is for students to understand and interpret the information provided by a 2D NMR spectrum. Students are…

  12. Dipeptide Structural Analysis Using Two-Dimensional NMR for the Undergraduate Advanced Laboratory

    Science.gov (United States)

    Gonzalez, Elizabeth; Dolino, Drew; Schwartzenburg, Danielle; Steiger, Michelle A.

    2015-01-01

    A laboratory experiment was developed to introduce students in either an organic chemistry or biochemistry lab course to two-dimensional nuclear magnetic resonance (2D NMR) spectroscopy using simple biomolecules. The goal of this experiment is for students to understand and interpret the information provided by a 2D NMR spectrum. Students are…

  13. Two-Dimensional Hydrous Silica : Nanosheets and Nanotubes Predicted from First-Principles Simulations

    NARCIS (Netherlands)

    Fang, Changming; Van Blaaderen, Alfons; Van Huis, Marijn A.

    2015-01-01

    Two-dimensional (2D) hydrous silica sheets (HSSs) and hydrous silica nanotubes (HSNTs) have many unique properties and potential applications. Although preparation of 2D HSSs was patented already about half a century ago, very little is known about their structure and physical properties. He we pred

  14. Two-dimensional multiferroics in monolayer group IV monochalcogenides

    Science.gov (United States)

    Wang, Hua; Qian, Xiaofeng

    2017-03-01

    Low-dimensional multiferroic materials hold great promises in miniaturized device applications such as nanoscale transducers, actuators, sensors, photovoltaics, and nonvolatile memories. Here, using first-principles theory we predict that two-dimensional (2D) monolayer group IV monochalcogenides including GeS, GeSe, SnS, and SnSe are a class of 2D semiconducting multiferroics with giant strongly-coupled in-plane spontaneous ferroelectric polarization and spontaneous ferroelastic lattice strain that are thermodynamically stable at room temperature and beyond, and can be effectively modulated by elastic strain engineering. Their optical absorption spectra exhibit strong in-plane anisotropy with visible-spectrum excitonic gaps and sizable exciton binding energies, rendering the unique characteristics of low-dimensional semiconductors. More importantly, the predicted low domain wall energy and small migration barrier together with the coupled multiferroic order and anisotropic electronic structures suggest their great potentials for tunable multiferroic functional devices by manipulating external electrical, mechanical, and optical field to control the internal responses, and enable the development of four device concepts including 2D ferroelectric memory, 2D ferroelastic memory, and 2D ferroelastoelectric nonvolatile photonic memory as well as 2D ferroelectric excitonic photovoltaics.

  15. On the critical behaviour of two-dimensional liquid crystals

    Directory of Open Access Journals (Sweden)

    A.l. Fariñas-Sánchez

    2010-01-01

    Full Text Available The Lebwohl-Lasher (LL model is the traditional model used to describe the nematic-isotropic transition of real liquid crystals. In this paper, we develop a numerical study of the temperature behaviour and of finite-size scaling of the two-dimensional (2D LL-model. We discuss two possible scenarios. In the first one, the 2D LL-model presents a phase transition similar to the topological transition appearing in the 2D XY-model. In the second one, the 2D LL-model does not exhibit any critical transition, but its low temperature behaviour is rather characterized by a crossover from a disordered phase to an ordered phase at zero temperature. We realize and discuss various comparisons with the 2D XY-model and the 2D Heisenberg model. Having added finite-size scaling behaviour of the order parameter and conformal mapping of order parameter profile to previous studies, we analyze the critical scaling of the probability distribution function, hyperscaling relations and stiffness order parameter and conclude that the second scenario (no critical transition is the most plausible.

  16. Ab Initio Prediction of Piezoelectricity in Two-Dimensional Materials.

    Science.gov (United States)

    Blonsky, Michael N; Zhuang, Houlong L; Singh, Arunima K; Hennig, Richard G

    2015-10-27

    Two-dimensional (2D) materials present many unique materials concepts, including material properties that sometimes differ dramatically from those of their bulk counterparts. One of these properties, piezoelectricity, is important for micro- and nanoelectromechanical systems applications. Using symmetry analysis, we determine the independent piezoelectric coefficients for four groups of predicted and synthesized 2D materials. We calculate with density-functional perturbation theory the stiffness and piezoelectric tensors of these materials. We determine the in-plane piezoelectric coefficient d11 for 37 materials within the families of 2D metal dichalcogenides, metal oxides, and III-V semiconductor materials. A majority of the structures, including CrSe2, CrTe2, CaO, CdO, ZnO, and InN, have d11 coefficients greater than 5 pm/V, a typical value for bulk piezoelectric materials. Our symmetry analysis shows that buckled 2D materials exhibit an out-of-plane coefficient d31. We find that d31 for 8 III-V semiconductors ranges from 0.02 to 0.6 pm/V. From statistical analysis, we identify correlations between the piezoelectric coefficients and the electronic and structural properties of the 2D materials that elucidate the origin of the piezoelectricity. Among the 37 2D materials, CdO, ZnO, and CrTe2 stand out for their combination of large piezoelectric coefficient and low formation energy and are recommended for experimental exploration.

  17. Soluble, Exfoliated Two-Dimensional Nanosheets as Excellent Aqueous Lubricants.

    Science.gov (United States)

    Zhang, Wenling; Cao, Yanlin; Tian, Pengyi; Guo, Fei; Tian, Yu; Zheng, Wen; Ji, Xuqiang; Liu, Jingquan

    2016-11-30

    Dispersion in water of two-dimensional (2D) nanosheets is conducive to their practical applications in fundamental science communities due to their abundance, low cost, and ecofriendliness. However, it is difficult to achieve stable aqueous 2D material suspensions because of the intrinsic hydrophobic properties of the layered materials. Here, we report an effective and economic way of producing various 2D nanosheets (h-BN, MoS2, MoSe2, WS2, and graphene) as aqueous dispersions using carbon quantum dots (CQDs) as exfoliation agents and stabilizers. The dispersion was prepared through a liquid phase exfoliation. The as-synthesized stable 2D nanosheets based dispersions were characterized by UV-vis, HRTEM, AFM, Raman, XPS, and XRD. The solutions based on CQD decorated 2D nanosheets were utilized as aqueous lubricants, which realized a friction coefficient as low as 0.02 and even achieved a superlubricity under certain working conditions. The excellent lubricating properties were attributed to the synergetic effects of the 2D nanosheets and CQDs, such as good dispersion stability and easy-sliding interlayer structure. This work thus proposes a novel strategy for the design and preparation of high-performance water based green lubricants.

  18. Comparative analysis of prostate-specific antigen by two-dimensional gel electrophoresis and capillary electrophoresis.

    Science.gov (United States)

    Barrabés, Sílvia; Farina-Gomez, Noemi; Llop, Esther; Puerta, Angel; Diez-Masa, Jose Carlos; Perry, Antoinette; de Llorens, Rafael; de Frutos, Mercedes; Peracaula, Rosa

    2017-02-01

    Serum levels of Prostate-Specific Antigen (PSA) are not fully specific for prostate cancer (PCa) diagnosis and several efforts are focused on searching to improve PCa markers through the study of PSA subforms that could be cancer associated. We have previously reported by 2DE a decrease in the sialic acid content of PSA from PCa compared to benign prostatic hyperplasia patients based on the different proportion of the PSA spots. However, faster and more quantitative techniques, easier to automate than 2DE, are desirable. In this study, we examined the potential of CE for resolving PSA subforms in different samples and compared the results with those obtained by 2DE. We first fractionated by OFFGEL the subforms of PSA from seminal plasma according to their pIs and analyzed each separated fraction by 2DE and CE. We also analyzed PSA and high pI PSA, both from seminal plasma, and PSA from urine of a PCa patient. These samples with different PSA spots proportions by 2DE, due to different posttranslational modifications, also presented different CE profiles. This study shows that CE is a useful and complementary technique to 2DE for analyzing samples with different PSA subforms, which is of high clinical interest. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Two Dimensional Plasmonic Cavities on Moire Surfaces

    Science.gov (United States)

    Balci, Sinan; Kocabas, Askin; Karabiyik, Mustafa; Kocabas, Coskun; Aydinli, Atilla

    2010-03-01

    We investigate surface plasmon polariton (SPP) cavitiy modes on two dimensional Moire surfaces in the visible spectrum. Two dimensional hexagonal Moire surface can be recorded on a photoresist layer using Interference lithography (IL). Two sequential exposures at slightly different angles in IL generate one dimensional Moire surfaces. Further sequential exposure for the same sample at slightly different angles after turning the sample 60 degrees around its own axis generates two dimensional hexagonal Moire cavity. Spectroscopic reflection measurements have shown plasmonic band gaps and cavity states at all the azimuthal angles (omnidirectional cavity and band gap formation) investigated. The plasmonic band gap edge and the cavity states energies show six fold symmetry on the two dimensional Moire surface as measured in reflection measurements.

  20. Two-dimensional function photonic crystals

    Science.gov (United States)

    Liu, Xiao-Jing; Liang, Yu; Ma, Ji; Zhang, Si-Qi; Li, Hong; Wu, Xiang-Yao; Wu, Yi-Heng

    2017-01-01

    In this paper, we have studied two-dimensional function photonic crystals, in which the dielectric constants of medium columns are the functions of space coordinates , that can become true easily by electro-optical effect and optical kerr effect. We calculated the band gap structures of TE and TM waves, and found the TE (TM) wave band gaps of function photonic crystals are wider (narrower) than the conventional photonic crystals. For the two-dimensional function photonic crystals, when the dielectric constant functions change, the band gaps numbers, width and position should be changed, and the band gap structures of two-dimensional function photonic crystals can be adjusted flexibly, the needed band gap structures can be designed by the two-dimensional function photonic crystals, and it can be of help to design optical devices.

  1. 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; ...

  2. A two-dimensional protein map of Pleurotus ostreatus microsomes-proteome dynamics.

    Science.gov (United States)

    Petráčková, Denisa; Halada, Petr; Bezoušková, Silvia; Křesinová, Zdena; Svobodová, Kateřina

    2016-01-01

    Recent studies documented that several processes in filamentous fungi are connected with microsomal enzyme activities. In this work, microsomal subproteomes of Pleurotus ostreatus were analyzed by two-dimensional (2-D) polyacrylamide gel electrophoresis and matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry analysis. To assess proteome dynamics, microsomal proteins were isolated from fungal cultures after 7 and 12 days of cultivation. Additionally, 10 mg/L of 17α-ethinylestradiol (EE2) was treated with the cultures during 2 days. Despite the EE2 degradation by the fungus reached 97 and 76.3 % in 7- and 12-day-old cultures, respectively, only a minor effect on the composition of microsomal proteins was observed. The changes in protein maps related to ageing prevailed over those induced by EE2. Epoxide hydrolase, known to metabolize EE2, was detected in 12-day-old cultures only which suggests differences in EE2 degradation pathways utilized by fungal cultures of different age. The majority (32 %) of identified microsomal proteins were parts of mitochondrial energy metabolism.

  3. Three-dimensional versus two-dimensional vision in laparoscopy

    DEFF Research Database (Denmark)

    Sørensen, Stine Maya Dreier; Savran, Mona M; Konge, Lars;

    2016-01-01

    BACKGROUND: Laparoscopic surgery is widely used, and results in accelerated patient recovery time and hospital stay were compared with laparotomy. However, laparoscopic surgery is more challenging compared with open surgery, in part because surgeons must operate in a three-dimensional (3D) space...... through a two-dimensional (2D) projection on a monitor, which results in loss of depth perception. To counter this problem, 3D imaging for laparoscopy was developed. A systematic review of the literature was performed to assess the effect of 3D laparoscopy. METHODS: A systematic search of the literature...

  4. Complex Saddles in Two-dimensional Gauge Theory

    CERN Document Server

    Buividovich, P V; Valgushev, S N

    2015-01-01

    We study numerically the saddle point structure of two-dimensional (2D) lattice gauge theory, represented by the Gross-Witten-Wadia unitary matrix model. The saddle points are in general complex-valued, even though the original integration variables and action are real. We confirm the trans-series/instanton gas structure in the weak-coupling phase, and identify a new complex-saddle interpretation of non-perturbative effects in the strong-coupling phase. In both phases, eigenvalue tunneling refers to eigenvalues moving off the real interval, into the complex plane, and the weak-to-strong coupling phase transition is driven by saddle condensation.

  5. Two Dimensional Spatial Independent Component Analysis and Its Application in fMRI Data Process

    Institute of Scientific and Technical Information of China (English)

    CHEN Hua-fu; YAO De-zhong

    2005-01-01

    One important application of independent component analysis (ICA) is in image processing. A two dimensional (2-D) composite ICA algorithm framework for 2-D image independent component analysis (2-D ICA) is proposed. The 2-D nature of the algorithm provides it an advantage of circumventing the roundabout transforming procedures between two dimensional (2-D) image data and one-dimensional (1-D) signal. Moreover the combination of the Newton (fixed-point algorithm) and natural gradient algorithms in this composite algorithm increases its efficiency and robustness. The convincing results of a successful example in functional magnetic resonance imaging (fMRI) show the potential application of composite 2-D ICA in the brain activity detection.

  6. Electron Cryomicroscopy of Membrane Proteins: Specimen Preparation for Two-Dimensional Crystals and Single Particles

    OpenAIRE

    Schmidt-Krey, Ingeborg; Rubinstein, John L.

    2010-01-01

    Membrane protein structure and function can be studied by two powerful and highly complementary electron cryomicroscopy (cryo-EM) methods: electron crystallography of two-dimensional (2D) crystals and single particle analysis of detergent-solubilized protein complexes. To obtain the highest-possible resolution data from membrane proteins, whether prepared as 2D crystals or single particles, cryo-EM samples must be vitrified with great care. Grid preparation for cryo-EM of 2D crystals is possi...

  7. 25th anniversary article: hybrid nanostructures based on two-dimensional nanomaterials.

    Science.gov (United States)

    Huang, Xiao; Tan, Chaoliang; Yin, Zongyou; Zhang, Hua

    2014-04-09

    Two-dimensional (2D) nanomaterials, such as graphene and transition metal dichalcogenides (TMDs), receive a lot of attention, because of their intriguing properties and wide applications in catalysis, energy-storage devices, electronics, optoelectronics, and so on. To further enhance the performance of their application, these 2D nanomaterials are hybridized with other functional nanostructures. In this review, the latest studies of 2D nanomaterial-based hybrid nanostructures are discussed, focusing on their preparation methods, properties, and applications.

  8. Perspectives for spintronics in 2D materials

    Directory of Open Access Journals (Sweden)

    Wei Han

    2016-03-01

    Full Text Available The past decade has been especially creative for spintronics since the (rediscovery of various two dimensional (2D materials. Due to the unusual physical characteristics, 2D materials have provided new platforms to probe the spin interaction with other degrees of freedom for electrons, as well as to be used for novel spintronics applications. This review briefly presents the most important recent and ongoing research for spintronics in 2D materials.

  9. Two Dimensional Organometal Halide Perovskite Nanorods with Tunable Optical Properties.

    Science.gov (United States)

    Aharon, Sigalit; Etgar, Lioz

    2016-05-11

    Organo-metal halide perovskite is an efficient light harvester in photovoltaic solar cells. Organometal halide perovskite is used mainly in its "bulk" form in the solar cell. Confined perovskite nanostructures could be a promising candidate for efficient optoelectronic devices, taking advantage of the superior bulk properties of organo-metal halide perovskite, as well as the nanoscale properties. In this paper, we present facile low-temperature synthesis of two-dimensional (2D) lead halide perovskite nanorods (NRs). These NRs show a shift to higher energies in the absorbance and in the photoluminescence compared to the bulk material, which supports their 2D structure. X-ray diffraction (XRD) analysis of the NRs demonstrates their 2D nature combined with the tetragonal 3D perovskite structure. In addition, by alternating the halide composition, we were able to tune the optical properties of the NRs. Fast Fourier transform, and electron diffraction show the tetragonal structure of these NRs. By varying the ligands ratio (e.g., octylammonium to oleic acid) in the synthesis, we were able to provide the formation mechanism of these novel 2D perovskite NRs. The 2D perovskite NRs are promising candidates for a variety of optoelectronic applications, such as light-emitting diodes, lasing, solar cells, and sensors.

  10. Generalized non-separable two-dimensional Dammann encoding method

    Science.gov (United States)

    Yu, Junjie; Zhou, Changhe; Zhu, Linwei; Lu, Yancong; Wu, Jun; Jia, Wei

    2017-01-01

    We generalize for the first time, to the best of our knowledge, the Dammann encoding method into non-separable two-dimensional (2D) structures for designing various pure-phase Dammann encoding gratings (DEGs). For examples, three types of non-separable 2D DEGs, including non-separable binary Dammann vortex gratings, non-separable binary distorted Dammann gratings, and non-separable continuous-phase cubic gratings, are designed theoretically and demonstrated experimentally. Correspondingly, it is shown that 2D square arrays of optical vortices with topological charges proportional to the diffraction orders, focus spots shifting along both transversal and axial directions with equal spacings, and Airy-like beams with controllable orientation for each beam, are generated in symmetry or asymmetry by these three DEGs, respectively. Also, it is shown that a more complex-shaped array of modulated beams could be achieved by this non-separable 2D Dammann encoding method, which will be a big challenge for those conventional separable 2D Dammann encoding gratings. Furthermore, the diffractive efficiency of the gratings can be improved around ∼10% when the non-separable structure is applied, compared with their conventional separable counterparts. Such improvement in the efficiency should be of high significance for some specific applications.

  11. Gate-induced superconductivity in two-dimensional atomic crystals

    Science.gov (United States)

    Saito, Yu; Nojima, Tsutomu; Iwasa, Yoshihiro

    2016-09-01

    Two-dimensional (2D) crystals are attracting growing interest in condensed matter physics, since these systems exhibit not only rich electronic and photonic properties but also exotic electronic phase transitions including superconductivity and charge density wave. Moreover, owing to the recent development of transfer methods after exfoliation and electric-double-layer transistors, superconducting 2D atomic crystals, the thicknesses of which are below 1-2 nm, have been successfully obtained. Here, we present a topical review on the recent discoveries of 2D crystalline superconductors by ionic-liquid gating and a series of their novel properties. In particular, we highlight two topics; quantum metallic states (or possible metallic ground states) and superconductivity robust against in-plane magnetic fields. These phenomena can be discussed with the effects of weakened disorder and/or broken spacial inversion symmetry leading to valley-dependent spin-momentum locking (spin-valley locking). These examples suggest the superconducting 2D crystals are new platforms for investigating the intrinsic quantum phases as well as exotic nature in 2D superconductors.

  12. Band alignment of two-dimensional lateral heterostructures

    Science.gov (United States)

    Zhang, Junfeng; Xie, Weiyu; Zhao, Jijun; Zhang, Shengbai

    2017-03-01

    Recent experimental synthesis of two-dimensional (2D) heterostructures opens a door to new opportunities in tailoring the electronic properties for novel 2D devices. Here, we show that a wide range of lateral 2D heterostructures could have a prominent advantage over the traditional three-dimensional (3D) heterostructures, because their band alignments are insensitive to the interfacial conditions. They should be at the Schottky-Mott limits for semiconductor-metal junctions and at the Anderson limits for semiconductor junctions, respectively. This fundamental difference from the 3D heterostructures is rooted in the fact that, in the asymptotic limit of large distance, the effect of the interfacial dipole vanishes for 2D systems. Due to the slow decay of the dipole field and the dependence on the vacuum thickness, however, studies based on first-principles calculations often failed to reach such a conclusion. Taking graphene/hexagonal-BN and MoS2/WS2 lateral heterostructures as the respective prototypes, we show that the converged junction width can be order of magnitude longer than that for 3D junctions. The present results provide vital guidance to high-quality transport devices wherever a lateral 2D heterostructure is involved.

  13. Two-Dimensional Tail-Biting Convolutional Codes

    CERN Document Server

    Alfandary, Liam

    2011-01-01

    The multidimensional convolutional codes are an extension of the notion of convolutional codes (CCs) to several dimensions of time. This paper explores the class of two-dimensional convolutional codes (2D CCs) and 2D tail-biting convolutional codes (2D TBCCs), in particular, from several aspects. First, we derive several basic algebraic properties of these codes, applying algebraic methods in order to find bijective encoders, create parity check matrices and to inverse encoders. Next, we discuss the minimum distance and weight distribution properties of these codes. Extending an existing tree-search algorithm to two dimensions, we apply it to find codes with high minimum distance. Word-error probability asymptotes for sample codes are given and compared with other codes. The results of this approach suggest that 2D TBCCs can perform better than comparable 1D TBCCs or other codes. We then present several novel iterative suboptimal algorithms for soft decoding 2D CCs, which are based on belief propagation. Two ...

  14. Two-dimensional gel proteome reference map of human small intestine

    Directory of Open Access Journals (Sweden)

    Canzonieri Vincenzo

    2009-03-01

    Full Text Available Abstract Background The small intestine is an important human organ that plays a central role in many physiological functions including digestion, absorption, secretion and defense. Duodenal pathologies include, for instance, the ulcer associated to Helicobacter Pylori infection, adenoma and, in genetically predisposed individuals, celiac disease. Alterations in the bowel reduce its capability to absorb nutrients, minerals and fat-soluble vitamins. Anemia and osteopenia or osteoporosis may develop as a consequence of vitamins malabsorption. Adenoma is a benign tumor that has the potential to become cancerous. Adult celiac disease patients present an overall risk of cancer that is almost twice than that found in the general population. These disease processes are not completely known. To date, a two dimensional (2D reference map of proteins expressed in human duodenal tissue is not yet available: the aim of our study was to characterize the 2D protein map, and to identify proteins of duodenal mucosa of adult individuals without duodenal illness, to create a protein database. This approach, may be useful for comparing similar protein samples in different laboratories and for the molecular characterization of intestinal pathologies without recurring to the use of surgical material. Results The enrolled population comprised five selected samples (3 males and 2 females, aged 19 to 42, taken from 20 adult subjects, on their first visit at the gastroenterology unit for a suspected celiac disease, who did not turn to be affected by any duodenal pathology after gastrointestinal and histological evaluations. Proteins extracted from the five duodenal mucosal specimens were singly separated by 2D gel electrophoresis. After image analysis of each 2D gel, 179 protein spots, representing 145 unique proteins, from 218 spots tested, were successfully identified by MALDI-TOF ms analysis. Normalized volumes, for each protein, have been reported for every gel

  15. Assessment of the Left Ventricular Systolic Function in Dilated Cardiomyopathy Patients by Two -dimensional Speckle Tracking Imaging( 2D - STI)%二维斑点追踪成像技术评价扩张型心肌病患者左心室心肌纵向收缩功能

    Institute of Scientific and Technical Information of China (English)

    黄俊; 胡元平; 宋樟伟; 杨炜宇; 徐瑞; 倪显达

    2012-01-01

    Objective To assess the left ventricular systolic function in patients with dilated cardiomyopathy ( DCM ) . Methods 35 healthy subjects and 39 dilated cardiomyopathy patients underwent conventional echocardiography examination. Left atrial ( LA) diameter were measured by M - mode echocardiography, left ventricular( LV) end - systolic volume, end - diastolic volume and left ventricular ejection fraction (LVEF) were calculated by bi -plane Simpson's method. The peak velocity during early diastole(Ve) and late diastole (Va) of anterior mitral valve were measured by pulse -waved doppler, and the ratio Ve/Va was calculated. We acquired the apical four - chamber, two - chamber and the long - axis views of the left ventricular images in these patients with GE - Vivid7 - dimension. Then the peak longitudinal velocity, strain and strain rate in systolic period were measured and recorded. Results The values of LAD, LVESV and LVEDV in DCM patients were significantly higher than those of healthy subjects (P 0. 05 ) . The peak velocity in systolic period of the base and middle LV segments in DCM patients were lower than those of the healthy subjects (P < 0. 05). The peak longitudinal strain and strain rate were significantly lower than healthy subjects (P < 0. 01). The peak velocity of the healthy subjects and the DCM patients were descent from the base to the apex. Conclusion The peak velocity, stain and strain rate of regional myocardial function in long - axis of left ventricular can be analyzed by 2D - STI, and it is a feasible technique for the assessment of cardiac longitudinal systolic function in DCM patients, and it can be widely used in the cardiac examination.%目的 评价二维斑点追踪成像技术(2D - STI)在扩张型心肌病(dilated cardiomyopathy,DCM)患者的左心室心肌纵向收缩功能应用价值.方法 对39例DCM患者和35例正常对照组行常规超声心动图检查得到左心房内径(LAD)、左心室射血分数(LVEF)、过二尖瓣口

  16. Interpolation by two-dimensional cubic convolution

    Science.gov (United States)

    Shi, Jiazheng; Reichenbach, Stephen E.

    2003-08-01

    This paper presents results of image interpolation with an improved method for two-dimensional cubic convolution. Convolution with a piecewise cubic is one of the most popular methods for image reconstruction, but the traditional approach uses a separable two-dimensional convolution kernel that is based on a one-dimensional derivation. The traditional, separable method is sub-optimal for the usual case of non-separable images. The improved method in this paper implements the most general non-separable, two-dimensional, piecewise-cubic interpolator with constraints for symmetry, continuity, and smoothness. The improved method of two-dimensional cubic convolution has three parameters that can be tuned to yield maximal fidelity for specific scene ensembles characterized by autocorrelation or power-spectrum. This paper illustrates examples for several scene models (a circular disk of parametric size, a square pulse with parametric rotation, and a Markov random field with parametric spatial detail) and actual images -- presenting the optimal parameters and the resulting fidelity for each model. In these examples, improved two-dimensional cubic convolution is superior to several other popular small-kernel interpolation methods.

  17. Epi-two-dimensional flow and generalized enstrophy

    CERN Document Server

    Yoshida, Zensho

    2016-01-01

    The conservation of the enstrophy ($L^2$ norm of the vorticity $\\omega$) plays an essential role in the physics and mathematics of two-dimensional (2D) Euler fluids. Generalizing to compressible ideal (inviscid and barotropic) fluids, the generalized enstrophy $\\int_{\\Sigma(t)} f(\\omega/\\rho)\\rho\\, d^2 x$, ($f$ an arbitrary smooth function, $\\rho$ the density, and $\\Sigma(t)$ an arbitrary 2D domain co-moving with the fluid) is a constant of motion, and plays the same role. On the other hand, for the three-dimensional (3D) ideal fluid, the helicity $\\int_{M} {V}\\cdot\\omega\\,d^3x$, ($V$ the flow velocity, $\\omega=\

  18. Two-dimensional atom localization induced by a squeezed vacuum

    Science.gov (United States)

    Wang, Fei; Xu, Jun

    2016-10-01

    A scheme of two-dimensional (2D) atom localization induced by a squeezed vacuum is proposed, in which the three-level V-type atoms interact with two classical standing-wave fields. It is found that when the environment is changed from an ordinary vacuum to a squeezed vacuum, the 2D atom localization is realized by detecting the position-dependent resonance fluorescence spectrum. For comparison, we demonstrate that the atom localization originating from the quantum interference effect is distinct from that induced by a squeezed vacuum. Furthermore, the combined effects of the squeezed vacuum and quantum interference are also discussed under appropriate conditions. The internal physical mechanism is analyzed in terms of dressed-state representation. Project supported by the National Natural Science Foundation of China (Grant Nos. 11574179 and 11204099) and the Natural Science Foundation of Hubei Province, China (Grant No. 2014CFC1148).

  19. Oriented Two-Dimensional Porous Organic Cage Crystals.

    Science.gov (United States)

    Jiang, Shan; Song, Qilei; Massey, Alan; Chong, Samantha Y; Chen, Linjiang; Sun, Shijing; Hasell, Tom; Raval, Rasmita; Sivaniah, Easan; Cheetham, Anthony K; Cooper, Andrew I

    2017-08-01

    The formation of two-dimensional (2D) oriented porous organic cage crystals (consisting of imine-based tetrahedral molecules) on various substrates (such as silicon wafers and glass) by solution-processing is reported. Insight into the crystallinity, preferred orientation, and cage crystal growth was obtained by experimental and computational techniques. For the first time, structural defects in porous molecular materials were observed directly and the defect concentration could be correlated with crystal growth rate. These oriented crystals suggest potential for future applications, such as solution-processable molecular crystalline 2D membranes for molecular separations. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  20. Thermal conductivity of disordered two-dimensional binary alloys.

    Science.gov (United States)

    Zhou, Yang; Guo, Zhi-Xin; Cao, Hai-Yuan; Chen, Shi-You; Xiang, Hong-Jun; Gong, Xin-Gao

    2016-10-20

    Using non-equilibrium molecular dynamics simulations, we have studied the effect of disorder on the thermal conductivity of two-dimensional (2D) C1-xNx alloys. We find that the thermal conductivity not only depends on the substitution concentration of nitrogen, but also strongly depends on the disorder distribution. A general linear relationship is revealed between the thermal conductivity and the participation ratio of phonons in 2D alloys. Localization mode analysis further indicates that the thermal conductivity variation in the ordered alloys can be attributed to the number of inequivalent atoms. As for the disordered alloys, we find that the thermal conductivity variation can be described by a simple linear formula with the disorder degree and the substitution concentration. The present study suggests some general guidance for phonon manipulation and thermal engineering in low dimensional alloys.

  1. Two-dimensional random arrays for real time volumetric imaging

    DEFF Research Database (Denmark)

    Davidsen, Richard E.; Jensen, Jørgen Arendt; Smith, Stephen W.

    1994-01-01

    Two-dimensional arrays are necessary for a variety of ultrasonic imaging techniques, including elevation focusing, 2-D phase aberration correction, and real time volumetric imaging. In order to reduce system cost and complexity, sparse 2-D arrays have been considered with element geometries...... real time volumetric imaging system, which employs a wide transmit beam and receive mode parallel processing to increase image frame rate. Depth-of-field comparisons were made from simulated on-axis and off-axis beamplots at ranges from 30 to 160 mm for both coaxial and offset transmit and receive...... selected ad hoc, by algorithm, or by random process. Two random sparse array geometries and a sparse array with a Mills cross receive pattern were simulated and compared to a fully sampled aperture with the same overall dimensions. The sparse arrays were designed to the constraints of the Duke University...

  2. Soliton nanoantennas in two-dimensional arrays of quantum dots

    CERN Document Server

    Gligorić, G; Hadžievski, Lj; Slepyan, G Ya; Malomed, B A

    2015-01-01

    We consider two-dimensional (2D) arrays of self-organized semiconductor quantum dots (QDs) strongly interacting with electromagnetic field in the regime of Rabi oscillations. The QD array built of two-level states is modelled by two coupled systems of discrete nonlinear Schr\\"{o}dinger equations. Localized modes in the form of single-peaked fundamental and vortical stationary Rabi solitons and self-trapped breathers have been found. The results for the stability, mobility and radiative properties of the Rabi modes suggest a concept of a self-assembled 2D \\textit{% soliton-based nano-antenna}, which should be stable against imperfections In particular, we discuss the implementation of such a nano-antenna in the form of surface plasmon solitons in graphene, and illustrate possibilities to control their operation by means of optical tools.

  3. Design of two-dimensional digital filters using neural networks

    Institute of Scientific and Technical Information of China (English)

    Wang Xiaohua; He Yigang

    2005-01-01

    A new approach for the design of two-dimensional (2-D) linear phase FIR digital filters based on a new neural networks algorithm (NNA) is provided. A compact expression for the transfer function of a 2-D linear phase FIR filter is derived based on its frequency response characteristic, and the NNA, based on minimizing the square-error in the frequency-domain, is established according to the compact expression. To illustrate the stability of the NNA, the convergence theorem is presented and proved. Design examples are also given, and the results show that the ripple is considerably small in passband and stopband, and the NNA-based method is of powerful stability and requires quite little amount of computations.

  4. Two-dimensional spatial patterning in developmental systems.

    Science.gov (United States)

    Torii, Keiko U

    2012-08-01

    Multicellular organisms produce complex tissues with specialized cell types. During animal development, numerous cell-cell interactions shape tissue patterning through mechanisms involving contact-dependent cell migration and ligand-receptor-mediated lateral inhibition. Owing to the presence of cell walls, plant cells neither migrate nor undergo apoptosis as a means to correct for mis-specified cells. How can plants generate functional tissue patterns? This review aims to deduce fundamental principles of pattern formation through examining two-dimensional (2-D) spatial tissue patterning in plants and animals. Turing's mathematical framework will be introduced and applied to classic examples of de novo 2-D patterning in both animal and plant systems. By comparing their regulatory circuits, new insights into the similarities and differences of the basic principles governing tissue patterning will be discussed. Copyright © 2012 Elsevier Ltd. All rights reserved.

  5. Ultrabroadband two-quantum two-dimensional electronic spectroscopy

    Science.gov (United States)

    Gellen, Tobias A.; Bizimana, Laurie A.; Carbery, William P.; Breen, Ilana; Turner, Daniel B.

    2016-08-01

    A recent theoretical study proposed that two-quantum (2Q) two-dimensional (2D) electronic spectroscopy should be a background-free probe of post-Hartree-Fock electronic correlations. Testing this theoretical prediction requires an instrument capable of not only detecting multiple transitions among molecular excited states but also distinguishing molecular 2Q signals from nonresonant response. Herein we describe a 2Q 2D spectrometer with a spectral range of 300 nm that is passively phase stable and uses only beamsplitters and mirrors. We developed and implemented a dual-chopping balanced-detection method to resolve the weak molecular 2Q signals. Experiments performed on cresyl violet perchlorate and rhodamine 6G revealed distinct 2Q signals convolved with nonresonant response. Density functional theory computations helped reveal the molecular origin of these signals. The experimental and computational results demonstrate that 2Q electronic spectra can provide a singular probe of highly excited electronic states.

  6. Two-Dimensional Hexagonal Transition-Metal Oxide for Spintronics.

    Science.gov (United States)

    Kan, Erjun; Li, Ming; Hu, Shuanglin; Xiao, Chuanyun; Xiang, Hongjun; Deng, Kaiming

    2013-04-04

    Two-dimensional materials have been the hot subject of studies due to their great potential in applications. However, their applications in spintronics have been blocked by the difficulty in producing ordered spin structures in 2D structures. Here we demonstrated that the ultrathin films of recently experimentally realized wurtzite MnO can automatically transform into a stable graphitic structure with ordered spin arrangement via density functional calculation, and the stability of graphitic structure can be enhanced by external strain. Moreover, the antiferromagnetic ordering of graphitic MnO single layer can be switched into half-metallic ferromagnetism by small hole-doping, and the estimated Curie temperature is higher than 300 K. Thus, our results highlight a promising way toward 2D magnetic materials.

  7. Review—Two-Dimensional Layered Materials for Energy Storage Applications

    KAUST Repository

    Kumar, Pushpendra

    2016-07-02

    Rechargeable batteries are most important energy storage devices in modern society with the rapid development and increasing demand for handy electronic devices and electric vehicles. The higher surface-to-volume ratio two-dimensional (2D) materials, especially transition metal dichalcogenides (TMDCs) and transition metal carbide/nitrite generally referred as MXene, have attracted intensive research activities due to their fascinating physical/chemical properties with extensive applications. One of the growing applications is to use these 2D materials as potential electrodes for rechargeable batteries and electrochemical capacitors. This review is an attempt to summarize the research and development of TMDCs, MXenes and their hybrid structures in energy storage systems. (C) The Author(s) 2016. Published by ECS. All rights reserved.

  8. 应用优化的双向电泳技术建立纤维堆囊菌S00157-2蛋白质组数据库%Establishment of Sorangium cellulosum So0157-2 Proteome Database Using Optimized Two-dimensional Electrophoresis Protocol

    Institute of Scientific and Technical Information of China (English)

    张鹏翼; 李越中; 吴志红; 刘红; 徐培培; 熊娟

    2012-01-01

    堆囊菌丰富的次级代谢产物是新药的重要来源,而蛋白质组学分析是研究代谢调控的有效方法.然而堆囊菌含有大量的胞外多糖以及黏液,干扰了蛋白质组学分析中蛋白质的溶解度、分辨率及重现性.为了高通量地筛选Sorangium cellulosum So0157-2表达的特异性蛋白,实验优化了S.cellulosum So0157-2双向电泳方法.首先,S.cellulosum So0157-2蛋白在裂解液中有更好的溶解度.pH 3~10非线性胶条和1 mg的蛋白上样量适用于第一向等电聚焦,分别提高了蛋白质点的分辨率和低丰度蛋白质的表达.15% SDS-PAGE改善了S.cellulosum So0157-2蛋白分离的分辨率和重现性.最终,通过优化的双向电泳方法获得了S.cellulosum So0157-2在M26培养基中培养3天的全蛋白质表达谱,并检测到552个蛋白质点.进而对表达蛋白通过MALDI-TOF-MS进行质谱鉴定,其中474个蛋白质得到鉴定,鉴定率85.9%.得到鉴定的蛋白质包括细胞结构和功能组分,以及细胞代谢合成酶类,其中8个蛋白质与糖类的转化和代谢相关,这有助于糖基化埃博霉素A的深入研究.该优化方法为进一步建立纤维堆囊菌So0157-2在各种培养条件下的蛋白质组表达数据库打下基础.%The rich classes of secondary metabolites from the genus Sorangium have been an important source of new drugs.The proteome analysis is an effective method to study the regulation of metabolism.However,the genus Sorangium contains a large amount of exopolysaccharides or slime that interferes with protein solubility,resolution,and repeatability in proteome analysis.To perform high-throughput screening of the specific proteins expressed by Sorangium cellulosum So0157-2,we optimized the two-dimensional electrophoresis(2-DE)protocol.Firstly,the proteins have better solubility in lysis buffer.The pH 3 ~ 10 NL strip is appropriate for the first-dimensional isoelectric focusing,improving the resolution of protein spots.1 mg

  9. TWO-DIMENSIONAL TOPOLOGY OF COSMOLOGICAL REIONIZATION

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yougang; Xu, Yidong; Chen, Xuelei [Key Laboratory of Computational Astrophysics, National Astronomical Observatories, Chinese Academy of Sciences, Beijing, 100012 China (China); Park, Changbom [School of Physics, Korea Institute for Advanced Study, 85 Hoegiro, Dongdaemun-gu, Seoul 130-722 (Korea, Republic of); Kim, Juhan, E-mail: wangyg@bao.ac.cn, E-mail: cbp@kias.re.kr [Center for Advanced Computation, Korea Institute for Advanced Study, 85 Hoegiro, Dongdaemun-gu, Seoul 130-722 (Korea, Republic of)

    2015-11-20

    We study the two-dimensional topology of the 21-cm differential brightness temperature for two hydrodynamic radiative transfer simulations and two semi-numerical models. In each model, we calculate the two-dimensional genus curve for the early, middle, and late epochs of reionization. It is found that the genus curve depends strongly on the ionized fraction of hydrogen in each model. The genus curves are significantly different for different reionization scenarios even when the ionized faction is the same. We find that the two-dimensional topology analysis method is a useful tool to constrain the reionization models. Our method can be applied to the future observations such as those of the Square Kilometre Array.

  10. Two dimensional topology of cosmological reionization

    CERN Document Server

    Wang, Yougang; Xu, Yidong; Chen, Xuelei; Kim, Juhan

    2015-01-01

    We study the two-dimensional topology of the 21-cm differential brightness temperature for two hydrodynamic radiative transfer simulations and two semi-numerical models. In each model, we calculate the two dimensional genus curve for the early, middle and late epochs of reionization. It is found that the genus curve depends strongly on the ionized fraction of hydrogen in each model. The genus curves are significantly different for different reionization scenarios even when the ionized faction is the same. We find that the two-dimensional topology analysis method is a useful tool to constrain the reionization models. Our method can be applied to the future observations such as those of the Square Kilometer Array.

  11. On final states of two-dimensional decaying turbulence

    Science.gov (United States)

    Yin, Z.

    2004-12-01

    Numerical and analytical studies of final states of two-dimensional (2D) decaying turbulence are carried out. The first part of this work is trying to give a definition for final states of 2D decaying turbulence. The functional relation of ω-ψ, which is frequently adopted as the characterization of those final states, is merely a sufficient but not necessary condition; moreover, it is not proper to use it as the definition. It is found that the method through the value of the effective area S covered by the scatter ω-ψ plot, initially suggested by Read, Rhines, and White ["Geostrophic scatter diagrams and potential vorticity dynamics," J. Atmos. Sci. 43, 3226 (1986)] is more general and suitable for the definition. Based on this concept, a definition is presented, which covers all existing results in late states of decaying 2D flows (including some previous unexplainable weird double-valued ω-ψ scatter plots). The remaining part of the paper is trying to further study 2D decaying turbulence with the assistance of this definition. Some numerical results, leading to "bar" final states and further verifying the predictive ability of statistical mechanics [Yin, Montgomery, and Clercx, "Alternative statistical-mechanical descriptions of decaying two-dimensional turbulence in terms of patches and points," Phys. Fluids 15, 1937 (2003)], are reported. It is realized that some simulations with narrow-band energy spectral initial conditions result in some final states that cannot be very well interpreted by the statistical theory (meanwhile, those final states are still in the scope of the definition).

  12. Materials synthesis: Two-dimensional gallium nitride

    Science.gov (United States)

    Koratkar, Nikhil A.

    2016-11-01

    Graphene is used as a capping sheet to synthesize 2D gallium nitride by means of migration-enhanced encapsulation growth. This technique may allow the stabilization of 2D materials that are not amenable to synthesis by traditional methods.

  13. Atom-Based Geometrical Fingerprinting of Conformal Two-Dimensional Materials

    Science.gov (United States)

    Mehboudi, Mehrshad

    The shape of two-dimensional materials plays a significant role on their chemical and physical properties. Two-dimensional materials are basic meshes that are formed by mesh points (vertices) given by atomic positions, and connecting lines (edges) between points given by chemical bonds. Therefore the study of local shape and geometry of two-dimensional materials is a fundamental prerequisite to investigate physical and chemical properties. Hereby the use of discrete geometry to discuss the shape of two-dimensional materials is initiated. The local geometry of a surface embodied in 3D space is determined using four invariant numbers from the metric and curvature tensors which indicates how much the surface is stretched and curved under a deformation as compared to a reference pre-deformed conformation. Many different disciplines advance theories on conformal two-dimensional materials by relying on continuum mechanics and fitting continuum surfaces to the shape of conformal two-dimensional materials. However two-dimensional materials are inherently discrete. The continuum models are only applicable when the size of two-dimensional materials is significantly large and the deformation is less than a few percent. In this research, the knowledge of discrete differential geometry was used to tell the local shape of conformal two-dimensional materials. Three kind of two-dimensional materials are discussed: 1) one atom thickness structures such as graphene and hexagonal boron nitride; 2) high and low buckled 2D meshes like stanene, leadene, aluminum phosphate; and, 3) multi layer 2D materials such as Bi2Se3 and WSe2. The lattice structures of these materials were created by designing a mechanical model - the mechanical model was devised in the form of a Gaussian bump and density-functional theory was used to inform the local height; and, the local geometries are also discussed.

  14. Image interpolation by two-dimensional parametric cubic convolution.

    Science.gov (United States)

    Shi, Jiazheng; Reichenbach, Stephen E

    2006-07-01

    Cubic convolution is a popular method for image interpolation. Traditionally, the piecewise-cubic kernel has been derived in one dimension with one parameter and applied to two-dimensional (2-D) images in a separable fashion. However, images typically are statistically nonseparable, which motivates this investigation of nonseparable cubic convolution. This paper derives two new nonseparable, 2-D cubic-convolution kernels. The first kernel, with three parameters (designated 2D-3PCC), is the most general 2-D, piecewise-cubic interpolator defined on [-2, 2] x [-2, 2] with constraints for biaxial symmetry, diagonal (or 90 degrees rotational) symmetry, continuity, and smoothness. The second kernel, with five parameters (designated 2D-5PCC), relaxes the constraint of diagonal symmetry, based on the observation that many images have rotationally asymmetric statistical properties. This paper also develops a closed-form solution for determining the optimal parameter values for parametric cubic-convolution kernels with respect to ensembles of scenes characterized by autocorrelation (or power spectrum). This solution establishes a practical foundation for adaptive interpolation based on local autocorrelation estimates. Quantitative fidelity analyses and visual experiments indicate that these new methods can outperform several popular interpolation methods. An analysis of the error budgets for reconstruction error associated with blurring and aliasing illustrates that the methods improve interpolation fidelity for images with aliased components. For images with little or no aliasing, the methods yield results similar to other popular methods. Both 2D-3PCC and 2D-5PCC are low-order polynomials with small spatial support and so are easy to implement and efficient to apply.

  15. Mobility anisotropy of two-dimensional semiconductors

    Science.gov (United States)

    Lang, Haifeng; Zhang, Shuqing; Liu, Zhirong

    2016-12-01

    The carrier mobility of anisotropic two-dimensional semiconductors under longitudinal acoustic phonon scattering was theoretically studied using deformation potential theory. Based on the Boltzmann equation with the relaxation time approximation, an analytic formula of intrinsic anisotropic mobility was derived, showing that the influence of effective mass on mobility anisotropy is larger than those of deformation potential constant or elastic modulus. Parameters were collected for various anisotropic two-dimensional materials (black phosphorus, Hittorf's phosphorus, BC2N , MXene, TiS3, and GeCH3) to calculate their mobility anisotropy. It was revealed that the anisotropic ratio is overestimated by the previously described method.

  16. Towards two-dimensional search engines

    OpenAIRE

    Ermann, Leonardo; Chepelianskii, Alexei D.; Shepelyansky, Dima L.

    2011-01-01

    We study the statistical properties of various directed networks using ranking of their nodes based on the dominant vectors of the Google matrix known as PageRank and CheiRank. On average PageRank orders nodes proportionally to a number of ingoing links, while CheiRank orders nodes proportionally to a number of outgoing links. In this way the ranking of nodes becomes two-dimensional that paves the way for development of two-dimensional search engines of new type. Statistical properties of inf...

  17. The two dimensional fold test in paleomagnetism using ipython notebook

    Science.gov (United States)

    Setiabudidaya, Dedi; Piper, John D. A.

    2016-01-01

    One aspect of paleomagnetic analysis prone to controversy is the result of the fold test used to evaluate the age of a magnetisation component relative to the age of a structural event. Initially, the fold test was conducted by comparing the Fisherian precision parameter (k) to results from different limbs of a fold structure before and after tilt adjustment. To accommodate synfolding magnetisation, the tilt correction can be performed in stepwise fashion to both limbs simultaneously, here called one dimensional (1D) fold test. The two dimensional (2D) fold test described in this paper is carried out by applying stepwise tilt adjustment to each limb of the fold separately. The rationale for this is that tilts observed on contrasting limbs of deformed structure may not be synchronous or even belong to the same episode of deformation. A program for the procedure is presented here which generates two dimensional values of the k-parameter visually presented in contoured form. The use of ipython notebook enables this 2D fold test to be performed interactively and yield a more precise evaluation than the primitive 1D fold test.

  18. Comprehensive two-dimensional liquid chromatographic analysis of poloxamers.

    Science.gov (United States)

    Malik, Muhammad Imran; Lee, Sanghoon; Chang, Taihyun

    2016-04-15

    Poloxamers are low molar mass triblock copolymers of poly(ethylene oxide) (PEO) and poly(propylene oxide) (PPO), having number of applications as non-ionic surfactants. Comprehensive one and two-dimensional liquid chromatographic (LC) analysis of these materials is proposed in this study. The separation of oligomers of both types (PEO and PPO) is demonstrated for several commercial poloxamers. This is accomplished at the critical conditions for one of the block while interaction for the other block. Reversed phase LC at CAP of PEO allowed for oligomeric separation of triblock copolymers with regard to PPO block whereas normal phase LC at CAP of PPO renders oligomeric separation with respect to PEO block. The oligomeric separation with regard to PEO and PPO are coupled online (comprehensive 2D-LC) to reveal two-dimensional contour plots by unconventional 2D IC×IC (interaction chromatography) coupling. The study provides chemical composition mapping of both PEO and PPO, equivalent to combined molar mass and chemical composition mapping for several commercial poloxamers.

  19. Kronecker Product of Two-dimensional Arrays

    Institute of Scientific and Technical Information of China (English)

    Lei Hu

    2006-01-01

    Kronecker sequences constructed from short sequences are good sequences for spread spectrum communication systems. In this paper we study a similar problem for two-dimensional arrays, and we determine the linear complexity of the Kronecker product of two arrays. Our result shows that similar good property on linear complexity holds for Kronecker product of arrays.

  20. Two-Dimensional Toda-Heisenberg Lattice

    Directory of Open Access Journals (Sweden)

    Vadim E. Vekslerchik

    2013-06-01

    Full Text Available We consider a nonlinear model that is a combination of the anisotropic two-dimensional classical Heisenberg and Toda-like lattices. In the framework of the Hirota direct approach, we present the field equations of this model as a bilinear system, which is closely related to the Ablowitz-Ladik hierarchy, and derive its N-soliton solutions.

  1. A novel two dimensional particle velocity sensor

    NARCIS (Netherlands)

    Pjetri, Olti; Wiegerink, Remco J.; Lammerink, Theo S.; Krijnen, Gijs J.

    2013-01-01

    In this paper we present a two wire, two-dimensional particle velocity sensor. The miniature sensor of size 1.0x2.5x0.525 mm, consisting of only two crossed wires, shows excellent directional sensitivity in both directions, thus requiring no directivity calibration, and is relatively easy to fabrica

  2. Two-dimensional microstrip detector for neutrons

    Energy Technology Data Exchange (ETDEWEB)

    Oed, A. [Institut Max von Laue - Paul Langevin (ILL), 38 - Grenoble (France)

    1997-04-01

    Because of their robust design, gas microstrip detectors, which were developed at ILL, can be assembled relatively quickly, provided the prefabricated components are available. At the beginning of 1996, orders were received for the construction of three two-dimensional neutron detectors. These detectors have been completed. The detectors are outlined below. (author). 2 refs.

  3. Two-dimensional magma-repository interactions

    NARCIS (Netherlands)

    Bokhove, O.

    2001-01-01

    Two-dimensional simulations of magma-repository interactions reveal that the three phases --a shock tube, shock reflection and amplification, and shock attenuation and decay phase-- in a one-dimensional flow tube model have a precursor. This newly identified phase ``zero'' consists of the impact of

  4. Performance Estimation for Two-Dimensional Brownian Rotary Ratchet Systems

    Science.gov (United States)

    Tutu, Hiroki; Horita, Takehiko; Ouchi, Katsuya

    2015-04-01

    Within the context of the Brownian ratchet model, a molecular rotary system that can perform unidirectional rotations induced by linearly polarized ac fields and produce positive work under loads was studied. The model is based on the Langevin equation for a particle in a two-dimensional (2D) three-tooth ratchet potential of threefold symmetry. The performance of the system is characterized by the coercive torque, i.e., the strength of the load competing with the torque induced by the ac driving field, and the energy efficiency in force conversion from the driving field to the torque. We propose a master equation for coarse-grained states, which takes into account the boundary motion between states, and develop a kinetic description to estimate the mean angular momentum (MAM) and powers relevant to the energy balance equation. The framework of analysis incorporates several 2D characteristics and is applicable to a wide class of models of smooth 2D ratchet potential. We confirm that the obtained expressions for MAM, power, and efficiency of the model can enable us to predict qualitative behaviors. We also discuss the usefulness of the torque/power relationship for experimental analyses, and propose a characteristic for 2D ratchet systems.

  5. Filtering and control for classes of two-dimensional systems

    CERN Document Server

    Wu, Ligang

    2015-01-01

    This book focuses on filtering, control and model-reduction problems for two-dimensional (2-D) systems with imperfect information. The time-delayed 2-D systems covered have system parameters subject to uncertain, stochastic and parameter-varying changes. After an initial introduction of 2-D systems and the ideas of linear repetitive processes, the text is divided into two parts detailing: ·         general theory and methods of analysis and optimal synthesis for 2-D systems; and ·         application of the general theory to the particular case of differential/discrete linear repetitive processes. The methods developed provide a framework for stability and performance analysis, optimal and robust controller and filter design and model approximation for the systems considered. Solutions to the design problems are couched in terms of linear matrix inequalities. For readers interested in the state of the art in linear filtering, control and model reduction, Filtering and Control for Classes of ...

  6. Two-dimensional state in driven magnetohydrodynamic turbulence.

    Science.gov (United States)

    Bigot, Barbara; Galtier, Sébastien

    2011-02-01

    The dynamics of the two-dimensional (2D) state in driven three-dimensional (3D) incompressible magnetohydrodynamic turbulence is investigated through high-resolution direct numerical simulations and in the presence of an external magnetic field at various intensities. For such a flow the 2D state (or slow mode) and the 3D modes correspond, respectively, to spectral fluctuations in the plane k(∥)=0 and in the area k(∥)>0. It is shown that if initially the 2D state is set to zero it becomes nonnegligible in few turnover times, particularly when the external magnetic field is strong. The maintenance of a large-scale driving leads to a break for the energy spectra of 3D modes; when the driving is stopped, the previous break is removed and a decay phase emerges with Alfvénic fluctuations. For a strong external magnetic field the energy at large perpendicular scales lies mainly in the 2D state, and in all situations a pinning effect is observed at small scales.

  7. Two dimensional electron spin resonance: Structure and dynamics of biomolecules

    Science.gov (United States)

    Saxena, Sunil; Freed, Jack H.

    1998-03-01

    The potential of two dimensional (2D) electron spin resonance (ESR) for measuring the structural properties and slow dynamics of labeled biomolecules will be presented. Specifically, it will be shown how the recently developed method of double quantum (DQ) 2D ESR (S. Saxena and J. H. Freed, J. Chem. Phys. 107), 1317, (1997) can be used to measure large interelectron distances in bilabeled peptides. The need for DQ ESR spectroscopy, as well as the challenges and advantages of this method will be discussed. The elucidation of the slow reorientational dynamics of this peptide (S. Saxena and J. H. Freed, J. Phys. Chem. A, 101) 7998 (1997) in a glassy medium using COSY and 2D ELDOR ESR spectroscopy will be demonstrated. The contributions to the homogeneous relaxation time, T_2, from the overall and/or internal rotations of the nitroxide can be distinguished from the COSY spectrum. The growth of spectral diffusion cross-peaks^2 with mixing time in the 2D ELDOR spectra can be used to directly determine a correlation time from the experiment which can be related to the rotational correlation time.

  8. Two-Dimensional Halide Perovskites: Tuning Electronic Activities of Defects.

    Science.gov (United States)

    Liu, Yuanyue; Xiao, Hai; Goddard, William A

    2016-05-11

    Two-dimensional (2D) halide perovskites are emerging as promising candidates for nanoelectronics and optoelectronics. To realize their full potential, it is important to understand the role of those defects that can strongly impact material properties. In contrast to other popular 2D semiconductors (e.g., transition metal dichalcogenides MX2) for which defects typically induce harmful traps, we show that the electronic activities of defects in 2D perovskites are significantly tunable. For example, even with a fixed lattice orientation one can change the synthesis conditions to convert a line defect (edge or grain boundary) from electron acceptor to inactive site without deep gap states. We show that this difference originates from the enhanced ionic bonding in these perovskites compared with MX2. The donors tend to have high formation energies and the harmful defects are difficult to form at a low halide chemical potential. Thus, we unveil unique properties of defects in 2D perovskites and suggest practical routes to improve them.

  9. Broken Ergodicity in Two-Dimensional Homogeneous Magnetohydrodynamic Turbulence

    Science.gov (United States)

    Shebalin, John V.

    2010-01-01

    Two-dimensional (2-D) homogeneous magnetohydrodynamic (MHD) turbulence has many of the same qualitative features as three-dimensional (3-D) homogeneous MHD turbulence.The se features include several ideal invariants, along with the phenomenon of broken ergodicity. Broken ergodicity appears when certain modes act like random variables with mean values that are large compared to their standard deviations, indicating a coherent structure or dynamo.Recently, the origin of broken ergodicity in 3-D MHD turbulence that is manifest in the lowest wavenumbers was explained. Here, a detailed description of the origins of broken ergodicity in 2-D MHD turbulence is presented. It will be seen that broken ergodicity in ideal 2-D MHD turbulence can be manifest in the lowest wavenumbers of a finite numerical model for certain initial conditions or in the highest wavenumbers for another set of initial conditions.T he origins of broken ergodicity in ideal 2-D homogeneous MHD turbulence are found through an eigen analysis of the covariance matrices of the modal probability density functions.It will also be shown that when the lowest wavenumber magnetic field becomes quasi-stationary, the higher wavenumber modes can propagate as Alfven waves on these almost static large-scale magnetic structures

  10. Photonics and optoelectronics of two-dimensional materials beyond graphene

    Science.gov (United States)

    Ponraj, Joice Sophia; Xu, Zai-Quan; Chander Dhanabalan, Sathish; Mu, Haoran; Wang, Yusheng; Yuan, Jian; Li, Pengfei; Thakur, Siddharatha; Ashrafi, Mursal; Mccoubrey, Kenneth; Zhang, Yupeng; Li, Shaojuan; Zhang, Han; Bao, Qiaoliang

    2016-11-01

    Apart from conventional materials, the study of two-dimensional (2D) materials has emerged as a significant field of study for a variety of applications. Graphene-like 2D materials are important elements of potential optoelectronics applications due to their exceptional electronic and optical properties. The processing of these materials towards the realization of devices has been one of the main motivations for the recent development of photonics and optoelectronics. The recent progress in photonic devices based on graphene-like 2D materials, especially topological insulators (TIs) and transition metal dichalcogenides (TMDs) with the methodology level discussions from the viewpoint of state-of-the-art designs in device geometry and materials are detailed in this review. We have started the article with an overview of the electronic properties and continued by highlighting their linear and nonlinear optical properties. The production of TIs and TMDs by different methods is detailed. The following main applications focused towards device fabrication are elaborated: (1) photodetectors, (2) photovoltaic devices, (3) light-emitting devices, (4) flexible devices and (5) laser applications. The possibility of employing these 2D materials in different fields is also suggested based on their properties in the prospective part. This review will not only greatly complement the detailed knowledge of the device physics of these materials, but also provide contemporary perception for the researchers who wish to consider these materials for various applications by following the path of graphene.

  11. Anisotropic dielectric properties of two-dimensional matrix in pseudo-spin ferroelectric system

    Science.gov (United States)

    Kim, Se-Hun

    2016-10-01

    The anisotropic dielectric properties of a two-dimensional (2D) ferroelectric system were studied using the statistical calculation of the pseudo-spin Ising Hamiltonian model. It is necessary to delay the time for measurements of the observable and the independence of the new spin configuration under Monte Carlo sampling, in which the thermal equilibrium state depends on the temperature and size of the system. The autocorrelation time constants of the normalized relaxation function were determined by taking temperature and 2D lattice size into account. We discuss the dielectric constants of a two-dimensional ferroelectric system by using the Metropolis method in view of the Slater-Takagi defect energies.

  12. Non-Linear Non Stationary Analysis of Two-Dimensional Time-Series Applied to GRACE Data Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The proposed innovative two-dimensional (2D) adaptive analysis will be tested NASA's Gravity Recovery and Climate Experiment (GRACE) mission database in phase I in...

  13. Non-Linear Non Stationary Analysis of Two-Dimensional Time-Series Applied to GRACE Data Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The proposed innovative two-dimensional (2D) empirical mode decomposition (EMD) analysis was applied to NASA's Gravity Recovery and Climate Experiment (GRACE)...

  14. Two-dimensional zymography differentiates gelatinase isoforms in stimulated microglial cells and in brain tissues of acute brain injuries.

    Science.gov (United States)

    Chen, Shanyan; Meng, Fanjun; Chen, Zhenzhou; Tomlinson, Brittany N; Wesley, Jennifer M; Sun, Grace Y; Whaley-Connell, Adam T; Sowers, James R; Cui, Jiankun; Gu, Zezong

    2015-01-01

    Excessive activation of gelatinases (MMP-2/-9) is a key cause of detrimental outcomes in neurodegenerative diseases. A single-dimension zymography has been widely used to determine gelatinase expression and activity, but this method is inadequate in resolving complex enzyme isoforms, because gelatinase expression and activity could be modified at transcriptional and posttranslational levels. In this study, we investigated gelatinase isoforms under in vitro and in vivo conditions using two-dimensional (2D) gelatin zymography electrophoresis, a protocol allowing separation of proteins based on isoelectric points (pI) and molecular weights. We observed organomercuric chemical 4-aminophenylmercuric acetate-induced activation of MMP-2 isoforms with variant pI values in the conditioned medium of human fibrosarcoma HT1080 cells. Studies with murine BV-2 microglial cells indicated a series of proform MMP-9 spots separated by variant pI values due to stimulation with lipopolysaccharide (LPS). The MMP-9 pI values were shifted after treatment with alkaline phosphatase, suggesting presence of phosphorylated isoforms due to the proinflammatory stimulation. Similar MMP-9 isoforms with variant pI values in the same molecular weight were also found in mouse brains after ischemic and traumatic brain injuries. In contrast, there was no detectable pI differentiation of MMP-9 in the brains of chronic Zucker obese rats. These results demonstrated effective use of 2D zymography to separate modified MMP isoforms with variant pI values and to detect posttranslational modifications under different pathological conditions.

  15. Two-dimensional graphene analogues for biomedical applications.

    Science.gov (United States)

    Chen, Yu; Tan, Chaoliang; Zhang, Hua; Wang, Lianzhou

    2015-05-07

    The increasing demand of clinical biomedicine and fast development of nanobiotechnology has substantially promoted the generation of a variety of organic/inorganic nanosystems for biomedical applications. Biocompatible two-dimensional (2D) graphene analogues (e.g., nanosheets of transition metal dichalcogenides, transition metal oxides, g-C3N4, Bi2Se3, BN, etc.), which are referred to as 2D-GAs, have emerged as a new unique family of nanomaterials that show unprecedented advantages and superior performances in biomedicine due to their unique compositional, structural and physicochemical features. In this review, we summarize the state-of-the-art progress of this dynamically developed material family with a particular focus on biomedical applications. After the introduction, the second section of the article summarizes a range of synthetic methods for new types of 2D-GAs as well as their surface functionalization. The subsequent section provides a snapshot on the use of these biocompatible 2D-GAs for a broad spectrum of biomedical applications, including therapeutic (photothermal/photodynamic therapy, chemotherapy and synergistic therapy), diagnostic (fluorescent/magnetic resonance/computed tomography/photoacoustic imaging) and theranostic (concurrent diagnostic imaging and therapy) applications, especially on oncology. In addition, we briefly present the biosensing applications of these 2D-GAs for the detection of biomacromolecules and their in vitro/in vivo biosafety evaluations. The last section summarizes some critical unresolved issues, possible challenges/obstacles and also proposes future perspectives related to the rational design and construction of 2D-GAs for biomedical engineering, which are believed to promote their clinical translations for benefiting the personalized medicine and human health.

  16. Two-dimensional materials for novel liquid separation membranes

    Science.gov (United States)

    Ying, Yulong; Yang, Yefeng; Ying, Wen; Peng, Xinsheng

    2016-08-01

    Demand for a perfect molecular-level separation membrane with ultrafast permeation and a robust mechanical property for any kind of species to be blocked in water purification and desalination is urgent. In recent years, due to their intrinsic characteristics, such as a unique mono-atom thick structure, outstanding mechanical strength and excellent flexibility, as well as facile and large-scale production, graphene and its large family of two-dimensional (2D) materials are regarded as ideal membrane materials for ultrafast molecular separation. A perfect separation membrane should be as thin as possible to maximize its flux, mechanically robust and without failure even if under high loading pressure, and have a narrow nanochannel size distribution to guarantee its selectivity. The latest breakthrough in 2D material-based membranes will be reviewed both in theories and experiments, including their current state-of-the-art fabrication, structure design, simulation and applications. Special attention will be focused on the designs and strategies employed to control microstructures to enhance permeation and selectivity for liquid separation. In addition, critical views on the separation mechanism within two-dimensional material-based membranes will be provided based on a discussion of the effects of intrinsic defects during growth, predefined nanopores and nanochannels during subsequent fabrication processes, the interlayer spacing of stacking 2D material flakes and the surface charge or functional groups. Furthermore, we will summarize the significant progress of these 2D material-based membranes for liquid separation in nanofiltration/ultrafiltration and pervaporation. Lastly, we will recall issues requiring attention, and discuss existing questionable conclusions in some articles and emerging challenges. This review will serve as a valuable platform to provide a compact source of relevant and timely information about the development of 2D material-based membranes as

  17. Defect Characterization Using Two-Dimensional Arrays

    Science.gov (United States)

    Velichko, A.; Wilcox, P. D.

    2011-06-01

    2D arrays are able to `view' a given defect from a range of angles leading to the possibility of obtaining richer characterization detail than possible with 1D arrays. In this paper a quantitative comparison of 2D arrays with different element layouts is performed. A technique for extracting the scattering matrix of a defect from the raw 2D array data is also presented. The method is tested on experimental data for characterization of various volumetric defects.

  18. Synthesis of two-dimensional materials by selective extraction.

    Science.gov (United States)

    Naguib, Michael; Gogotsi, Yury

    2015-01-20

    CONSPECTUS: Two-dimensional (2D) materials have attracted much attention in the past decade. They offer high specific surface area, as well as electronic structure and properties that differ from their bulk counterparts due to the low dimensionality. Graphene is the best known and the most studied 2D material, but metal oxides and hydroxides (including clays), dichalcogenides, boron nitride (BN), and other materials that are one or several atoms thick are receiving increasing attention. They may deliver a combination of properties that cannot be provided by other materials. The most common synthesis approach in general is by reacting different elements or compounds to form a new compound. However, this approach does not necessarily work well for low-dimensional structures, since it favors formation of energetically preferred 3D (bulk) solids. Many 2D materials are produced by exfoliation of van der Waals solids, such as graphite or MoS2, breaking large particles into 2D layers. However, these approaches are not universal; for example, 2D transition metal carbides cannot be produced by any of them. An alternative but less studied way of material synthesis is the selective extraction process, which is based on the difference in reactivity and stability between the different components (elements or structural units) of the original material. It can be achieved using thermal, chemical, or electrochemical processes. Many 2D materials have been synthesized using selective extraction, such as graphene from SiC, transition metal oxides (TMO) from layered 3D salts, and transition metal carbides or carbonitrides (MXenes) from MAX phases. Selective extraction synthesis is critically important when the bonds between the building blocks of the material are too strong (e.g., in carbides) to be broken mechanically in order to form nanostructures. Unlike extractive metallurgy, where the extracted metal is the goal of the process, selective extraction of one or more elements from

  19. Two-Dimensional Plasmonics in Massive and Massless Electron Gases

    Science.gov (United States)

    Yoon, Hosang

    Plasmonic waves in solid-state are caused by collective oscillation of mobile charges inside or at the surface of conductors. In particular, surface plasmonic waves propagating at the skin of metals have recently attracted interest, as they reduce the wavelength of electromagnetic waves coupled to them by up to ˜10 times, allowing one to create miniaturized wave devices at optical frequencies. In contrast, plasmonic waves on two-dimensional (2D) conductors appear at much lower infrared and THz-GHz frequencies, near or in the electronics regime, and can achieve far stronger wavelength reduction factor reaching well above 100. In this thesis, we study the unique machinery of 2D plasmonic waves behind this ultra-subwavelength confinement and explore how it can be used to create various interesting devices. To this end, we first develop a physically intuitive theoretical formulation of 2D plasmonic waves, whose two main components---the Coulomb restoration force and inertia of the collectively oscillating charges---are combined into a transmission-line-like model. We then use this formulation to create various ultra-subwavelength 2D plasmonic devices. For the 2D conductor, we first choose GaAs/AlGaAs heterostructure---a 2D electron gas consisting of massive (m* > 0) electrons---demonstrating plasmonic bandgap crystals, interferometers, and negatively refracting metamaterials. We then examine a 2D plasmonic device based on graphene, a 2D electron gas consisting of effectively massless (m* = 0) electrons. We theoretically show and experimentally demonstrate that the massless electrons in graphene can surprisingly exhibit a collective mass when subjected to a collective excitation, providing the inertia that is essential for the propagation of 2D plasmonic waves. Lastly, we theoretically investigate the thermal current fluctuation behaviors in massive and massless electron gases. While seemingly unrelated on first sight, we show that the thermal current fluctuation is

  20. Comparison of Free Spectral Range and Quality Factor for Two-Dimensional Square and Circular Microcavities

    Institute of Scientific and Technical Information of China (English)

    国伟华; 黄永箴; 陆巧银; 于丽娟

    2004-01-01

    Free spectral range of whispering-gallery (WG)-like modes in a two-dimensional (2D) square microcavity is found to be twice that in a 2D circular microcavity. The quality factor of the WG-like mode with the low mode number in a 2D square microcavity, calculated by the finite-difference time-domain (FDTD) technique and the Pade approximation method, is found to exceed that of the WG mode in 2D circular microcavity with the same cavity dimension and close mode wavelength.

  1. Electronics based on two-dimensional materials.

    Science.gov (United States)

    Fiori, Gianluca; Bonaccorso, Francesco; Iannaccone, Giuseppe; Palacios, Tomás; Neumaier, Daniel; Seabaugh, Alan; Banerjee, Sanjay K; Colombo, Luigi

    2014-10-01

    The compelling demand for higher performance and lower power consumption in electronic systems is the main driving force of the electronics industry's quest for devices and/or architectures based on new materials. Here, we provide a review of electronic devices based on two-dimensional materials, outlining their potential as a technological option beyond scaled complementary metal-oxide-semiconductor switches. We focus on the performance limits and advantages of these materials and associated technologies, when exploited for both digital and analog applications, focusing on the main figures of merit needed to meet industry requirements. We also discuss the use of two-dimensional materials as an enabling factor for flexible electronics and provide our perspectives on future developments.

  2. Two-dimensional ranking of Wikipedia articles

    Science.gov (United States)

    Zhirov, A. O.; Zhirov, O. V.; Shepelyansky, D. L.

    2010-10-01

    The Library of Babel, described by Jorge Luis Borges, stores an enormous amount of information. The Library exists ab aeterno. Wikipedia, a free online encyclopaedia, becomes a modern analogue of such a Library. Information retrieval and ranking of Wikipedia articles become the challenge of modern society. While PageRank highlights very well known nodes with many ingoing links, CheiRank highlights very communicative nodes with many outgoing links. In this way the ranking becomes two-dimensional. Using CheiRank and PageRank we analyze the properties of two-dimensional ranking of all Wikipedia English articles and show that it gives their reliable classification with rich and nontrivial features. Detailed studies are done for countries, universities, personalities, physicists, chess players, Dow-Jones companies and other categories.

  3. Two-Dimensional NMR Lineshape Analysis

    Science.gov (United States)

    Waudby, Christopher A.; Ramos, Andres; Cabrita, Lisa D.; Christodoulou, John

    2016-04-01

    NMR titration experiments are a rich source of structural, mechanistic, thermodynamic and kinetic information on biomolecular interactions, which can be extracted through the quantitative analysis of resonance lineshapes. However, applications of such analyses are frequently limited by peak overlap inherent to complex biomolecular systems. Moreover, systematic errors may arise due to the analysis of two-dimensional data using theoretical frameworks developed for one-dimensional experiments. Here we introduce a more accurate and convenient method for the analysis of such data, based on the direct quantum mechanical simulation and fitting of entire two-dimensional experiments, which we implement in a new software tool, TITAN (TITration ANalysis). We expect the approach, which we demonstrate for a variety of protein-protein and protein-ligand interactions, to be particularly useful in providing information on multi-step or multi-component interactions.

  4. Towards two-dimensional search engines

    CERN Document Server

    Ermann, Leonardo; Shepelyansky, Dima L

    2011-01-01

    We study the statistical properties of various directed networks using ranking of their nodes based on the dominant vectors of the Google matrix known as PageRank and CheiRank. On average PageRank orders nodes proportionally to a number of ingoing links, while CheiRank orders nodes proportionally to a number of outgoing links. In this way the ranking of nodes becomes two-dimensional that paves the way for development of two-dimensional search engines of new type. Information flow properties on PageRank-CheiRank plane are analyzed for networks of British, French and Italian Universities, Wikipedia, Linux Kernel, gene regulation and other networks. Methods of spam links control are also analyzed.

  5. Toward two-dimensional search engines

    Science.gov (United States)

    Ermann, L.; Chepelianskii, A. D.; Shepelyansky, D. L.

    2012-07-01

    We study the statistical properties of various directed networks using ranking of their nodes based on the dominant vectors of the Google matrix known as PageRank and CheiRank. On average PageRank orders nodes proportionally to a number of ingoing links, while CheiRank orders nodes proportionally to a number of outgoing links. In this way, the ranking of nodes becomes two dimensional which paves the way for the development of two-dimensional search engines of a new type. Statistical properties of information flow on the PageRank-CheiRank plane are analyzed for networks of British, French and Italian universities, Wikipedia, Linux Kernel, gene regulation and other networks. A special emphasis is done for British universities networks using the large database publicly available in the UK. Methods of spam links control are also analyzed.

  6. Identification of cellular proteins that interact with Newcastle Disease Virus and human Respiratory Syncytial Virus by a two-dimensional virus overlay protein binding assay (VOPBA).

    Science.gov (United States)

    Holguera, Javier; Villar, Enrique; Muñoz-Barroso, Isabel

    2014-10-13

    Although it is well documented that the initial attachment receptors for Newcastle Disease Virus (NDV) and Respiratory Syncytial Virus (RSV) are sialic acid-containing molecules and glycosaminoglycans respectively, the exact nature of the receptors for both viruses remains to be deciphered. Moreover, additional molecules at the host cell surface might be involved in the entry mechanism. With the aim of identifying the cellular proteins that interact with NDV and RSV at the cell surface, we performed a virus overlay protein binding assay (VOPBA). Cell membrane lysates were separated by two dimensional (2D) gel electrophoresis and electrotransferred to PVDF membranes, after which they were probed with high viral concentrations. NDV interacted with a Protein Disulfide Isomerase from chicken fibroblasts. In the case of RSV, we detected 15 reactive spots, which were identified as six different proteins, of which nucleolin was outstanding. We discuss the possible role of PDI and nucleolin in NDV and RSV entry, respectively.

  7. Two-Dimensional Scheduling: A Review

    Directory of Open Access Journals (Sweden)

    Zhuolei Xiao

    2013-07-01

    Full Text Available In this study, we present a literature review, classification schemes and analysis of methodology for scheduling problems on Batch Processing machine (BP with both processing time and job size constraints which is also regarded as Two-Dimensional (TD scheduling. Special attention is given to scheduling problems with non-identical job sizes and processing times, with details of the basic algorithms and other significant results.

  8. Two dimensional fermions in four dimensional YM

    CERN Document Server

    Narayanan, R

    2009-01-01

    Dirac fermions in the fundamental representation of SU(N) live on a two dimensional torus flatly embedded in $R^4$. They interact with a four dimensional SU(N) Yang Mills vector potential preserving a global chiral symmetry at finite $N$. As the size of the torus in units of $\\frac{1}{\\Lambda_{SU(N)}}$ is varied from small to large, the chiral symmetry gets spontaneously broken in the infinite $N$ limit.

  9. String breaking in two-dimensional QCD

    CERN Document Server

    Hornbostel, K J

    1999-01-01

    I present results of a numerical calculation of the effects of light quark-antiquark pairs on the linear heavy-quark potential in light-cone quantized two-dimensional QCD. I extract the potential from the Q-Qbar component of the ground-state wavefunction, and observe string breaking at the heavy-light meson pair threshold. I briefly comment on the states responsible for the breaking.

  10. Two-dimensional supramolecular electron spin arrays.

    Science.gov (United States)

    Wäckerlin, Christian; Nowakowski, Jan; Liu, Shi-Xia; Jaggi, Michael; Siewert, Dorota; Girovsky, Jan; Shchyrba, Aneliia; Hählen, Tatjana; Kleibert, Armin; Oppeneer, Peter M; Nolting, Frithjof; Decurtins, Silvio; Jung, Thomas A; Ballav, Nirmalya

    2013-05-07

    A bottom-up approach is introduced to fabricate two-dimensional self-assembled layers of molecular spin-systems containing Mn and Fe ions arranged in a chessboard lattice. We demonstrate that the Mn and Fe spin states can be reversibly operated by their selective response to coordination/decoordination of volatile ligands like ammonia (NH3). Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Two dimensional echocardiographic detection of intraatrial masses.

    Science.gov (United States)

    DePace, N L; Soulen, R L; Kotler, M N; Mintz, G S

    1981-11-01

    With two dimensional echocardiography, a left atrial mass was detected in 19 patients. Of these, 10 patients with rheumatic mitral stenosis had a left atrial thrombus. The distinctive two dimensional echocardiographic features of left atrial thrombus included a mass of irregular nonmobile laminated echos within an enlarged atrial cavity, usually with a broad base of attachment to the posterior left atrial wall. Seven patients had a left atrial myxoma. Usually, the myxoma appeared as a mottled ovoid, sharply demarcated mobile mass attached to the interatrial septum. One patient had a right atrial angiosarcoma that appeared as a nonmobile mass extending from the inferior vena caval-right atrial junction into the right atrial cavity. One patient had a left atrial leiomyosarcoma producing a highly mobile mass attached to the lateral wall of the left atrium. M mode echocardiography detected six of the seven myxomas, one thrombus and neither of the other tumors. Thus, two dimensional echocardiography appears to be the technique of choice in the detection, localization and differentiation of intraatrial masses.

  12. Exploring early and late Toxoplasma gondii strain RH infection by two-dimensional immunoblots of chicken immunoglobulin G and M profiles.

    Directory of Open Access Journals (Sweden)

    Saeed El-Ashram

    Full Text Available Toxoplasma gondii is an intracellular apicomplexan parasite infecting warm-blooded vertebrate hosts, with only early infection stage being contained with drugs. But diagnosis differencing early and late infection was not available. In the present investigation, 2-dimensional immunobloting was used to explore early and late infections in chickens. The protein expression of T. gondii was determined by image analysis of the tachyzoites proteome separated by standard-one and conventional two-dimentional gel polyacrylamide electrophoresis (2D- PAGE. Pooled gels were prepared from tachyzoites of T. gondii. A representative gel spanning a pH range of 3-10 of the tachyzoite proteome consisted of 1306 distinct polypeptide spots. Two-dimensional electrophoresis (2-DE combined with 2-DE immunoblotting was used to resolve and compare immunoglobulins (Igs M & G patterns against Toxoplasma gondii strain RH (mouse virulent strain. Total tachyzoite proteins of T. gondii were separated by two-dimensional gel electrophoresis and analyzed by Western blotting for their reactivity with the 7 and 56 days post-infection (dpi SPF chicken antisera. Different antigenic determinant patterns were detected during analysis with M and G immunoglobulins. Of the total number of polypeptide spots analyzed (1306 differentially expressed protein spots, 6.97% were identified as having shared antigenic polypeptide spots on immunoblot profiles with IgG and IgM antibodies regardless the time after infection. Furthermore, some of the immunoreactive polypeptide spots seemed to be related to the stage of infection. Interestingly, we found natural antibodies to toxoplasmic antigens, in addition to the highly conserved antigenic determinants that reacted with non-specific secondary antibody; goat anti-chicken IgG antibodies conjugated with horseradish peroxidase. In conclusion, unique reactive polypeptide spots are promising candidates for designation of molecular markers to discriminate

  13. Differentiating Fragmentation Pathways of Cholesterol by Two-Dimensional Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

    Science.gov (United States)

    van Agthoven, Maria A.; Barrow, Mark P.; Chiron, Lionel; Coutouly, Marie-Aude; Kilgour, David; Wootton, Christopher A.; Wei, Juan; Soulby, Andrew; Delsuc, Marc-André; Rolando, Christian; O'Connor, Peter B.

    2015-12-01

    Two-dimensional Fourier transform ion cyclotron resonance mass spectrometry is a data-independent analytical method that records the fragmentation patterns of all the compounds in a sample. This study shows the implementation of atmospheric pressure photoionization with two-dimensional (2D) Fourier transform ion cyclotron resonance mass spectrometry. In the resulting 2D mass spectrum, the fragmentation patterns of the radical and protonated species from cholesterol are differentiated. This study shows the use of fragment ion lines, precursor ion lines, and neutral loss lines in the 2D mass spectrum to determine fragmentation mechanisms of known compounds and to gain information on unknown ion species in the spectrum. In concert with high resolution mass spectrometry, 2D Fourier transform ion cyclotron resonance mass spectrometry can be a useful tool for the structural analysis of small molecules.

  14. Volumetric display containing multiple two-dimensional color motion pictures

    Science.gov (United States)

    Hirayama, R.; Shiraki, A.; Nakayama, H.; Kakue, T.; Shimobaba, T.; Ito, T.

    2014-06-01

    We have developed an algorithm which can record multiple two-dimensional (2-D) gradated projection patterns in a single three-dimensional (3-D) object. Each recorded pattern has the individual projected direction and can only be seen from the direction. The proposed algorithm has two important features: the number of recorded patterns is theoretically infinite and no meaningful pattern can be seen outside of the projected directions. In this paper, we expanded the algorithm to record multiple 2-D projection patterns in color. There are two popular ways of color mixing: additive one and subtractive one. Additive color mixing used to mix light is based on RGB colors and subtractive color mixing used to mix inks is based on CMY colors. We made two coloring methods based on the additive mixing and subtractive mixing. We performed numerical simulations of the coloring methods, and confirmed their effectiveness. We also fabricated two types of volumetric display and applied the proposed algorithm to them. One is a cubic displays constructed by light-emitting diodes (LEDs) in 8×8×8 array. Lighting patterns of LEDs are controlled by a microcomputer board. The other one is made of 7×7 array of threads. Each thread is illuminated by a projector connected with PC. As a result of the implementation, we succeeded in recording multiple 2-D color motion pictures in the volumetric displays. Our algorithm can be applied to digital signage, media art and so forth.

  15. Theory of two-dimensional ESR with nuclear modulation

    Science.gov (United States)

    Gamliel, Dan; Freed, Jack H.

    A formalism for computing 2D ESR lineshapes with nuclear modulation is developed in a form which is useful for planning phase cycles for particular purposes. A simple method of processing spectra, utilizing quadrature detection, is shown to enhance the selectivity of the phase cycling techniques. Computed ESR-COSY, ESR-SECSY, and 2D ELDOR lineshapes are presented for several kinds of polycrystalline and single-crystal samples which exhibit nuclear modulation, due to one or several nuclei. The two-dimensional methods are found to give more detailed structural information than the corresponding ESEEM spectra. New phase cycles are found to eliminate completely all transverse and axial peaks in 2D ELDOR and in ESR-COSY, and at the same time eliminate all artifacts arising from incomplete image rejection. Other phase cycles are presented for selecting in those experiments only axial peaks, for measuring T1. It is also shown how selective phase cycles may help to distinguish between coherent and exchange cross peaks. In the special case of nitroxides in typical Zeeman fields, there are no significant nuclear modulation effects from the 14N nuclear spin interaction, but those from the protons (or deuterons) will, in general, be significant.

  16. Interactions between lasers and two-dimensional transition metal dichalcogenides.

    Science.gov (United States)

    Lu, Junpeng; Liu, Hongwei; Tok, Eng Soon; Sow, Chorng-Haur

    2016-05-03

    The recent increasing research interest in two-dimensional (2D) layered materials has led to an explosion of in the discovery of novel physical and chemical phenomena in these materials. Among the 2D family, group-VI transition metal dichalcogenides (TMDs), such as represented by MoS2 and WSe2, are remarkable semiconductors with sizable energy band gaps, which make the TMDs promising building blocks for new generation optoelectronics. On the other hand, the specificity and tunability of the band gaps can generate particularly strong light-matter interactions between TMD crystals and specific photons, which can trigger complex and interesting phenomena such as photo-scattering, photo-excitation, photo-destruction, photo-physical modification, photochemical reaction and photo-oxidation. Herein, we provide an overview of the phenomena explained by various interactions between lasers and the 2D TMDs. Characterizations of the optical fundamentals of the TMDs via laser spectroscopies are reviewed. Subsequently, photoelectric conversion devices enabled by laser excitation and the functionality extension and performance improvement of the TMDs materials via laser modification are comprehensively summarized. Finally, we conclude the review by discussing the prospects for further development in this research area.

  17. Transparent Conductive Two-Dimensional Titanium Carbide Epitaxial Thin Films.

    Science.gov (United States)

    Halim, Joseph; Lukatskaya, Maria R; Cook, Kevin M; Lu, Jun; Smith, Cole R; Näslund, Lars-Åke; May, Steven J; Hultman, Lars; Gogotsi, Yury; Eklund, Per; Barsoum, Michel W

    2014-04-08

    Since the discovery of graphene, the quest for two-dimensional (2D) materials has intensified greatly. Recently, a new family of 2D transition metal carbides and carbonitrides (MXenes) was discovered that is both conducting and hydrophilic, an uncommon combination. To date MXenes have been produced as powders, flakes, and colloidal solutions. Herein, we report on the fabrication of ∼1 × 1 cm(2) Ti3C2 films by selective etching of Al, from sputter-deposited epitaxial Ti3AlC2 films, in aqueous HF or NH4HF2. Films that were about 19 nm thick, etched with NH4HF2, transmit ∼90% of the light in the visible-to-infrared range and exhibit metallic conductivity down to ∼100 K. Below 100 K, the films' resistivity increases with decreasing temperature and they exhibit negative magnetoresistance-both observations consistent with a weak localization phenomenon characteristic of many 2D defective solids. This advance opens the door for the use of MXenes in electronic, photonic, and sensing applications.

  18. Two-dimensional magnetic ordering in a multilayer structure

    Indian Academy of Sciences (India)

    M K Mukhopadhyay; M K Sanyal

    2006-07-01

    The effect of confinement from one, two or from all three directions on magnetic ordering has remained an active field of research for almost 100 years. The role of dipolar interactions and anisotropy are important to obtain, the otherwise forbidden, ferromagnetic ordering at finite temperature for ions arranged in two-dimensional (2D) arrays (monolayers). We have demonstrated that conventional low-temperature magnetometry and polarized neutron scattering measurements can be performed to study short-range ferromagnetic ordering of in-plane spins in 2D systems using a multilayer stack of non-interacting monolayers of gadolinium ions formed by Langmuir–Blodgett (LB) technique. The spontaneous magnetization could not be detected in the heterogeneous magnetic phase observed here and the saturation value of the net magnetization was found to depend on the sample temperature and applied magnetic field. The net magnetization rises exponentially with lowering temperature and then reaches saturation following a ln( ) dependence. The ln( ) dependence of magnetization has been predicted from spin-wave theory of 2D in-plane spin system with ferromagnetic interaction. The experimental findings reported here could be explained by extending this theory to a temperature domain of < 1.

  19. Criticality in Two-Dimensional Quantum Systems: Tensor Network Approach

    CERN Document Server

    Ran, Shi-Ju; Li, Wei; Lewenstein, Maciej; Su, Gang

    2016-01-01

    Determination and characterization of criticality in two-dimensional (2D) quantum many-body systems belong to the most important challenges and problems of quantum physics. In this paper we propose an efficient scheme to solve this problem by utilizing the infinite projected entangled pair state (iPEPS), and tensor network (TN) representations. We show that the criticality of a 2D state is faithfully reproduced by the ground state (dubbed as boundary state) of a one-dimensional effective Hamiltonian constructed from its iPEPS representation. We demonstrate that for a critical state the correlation length and the entanglement spectrum of the boundary state are essentially different from those of a gapped iPEPS. This provides a solid indicator that allows to identify the criticality of the 2D state. Our scheme is verified on the resonating valence bond (RVB) states on kagom\\'e and square lattices, where the boundary state of the honeycomb RVB is found to be described by a $c=1$ conformal field theory. We apply ...

  20. Observation of asymmetrically imploded core plasmas with a two-dimensional sampling image x-ray streak camera.

    Science.gov (United States)

    Shiraga, Hiroyuki; Lee, Myongdok; Mahigashi, Norimitsu; Fujioka, Shinsuke; Azechi, Hiroshi

    2008-10-01

    A shell target with a cone for guiding the heating beam has been proposed for the fast ignition scheme. Implosion of such target is no longer symmetric because of the cone. A fast two-dimensional x-ray imaging technique, two-dimensional (2D) sampling image x-ray streak camera was applied for the first time to observation of the dynamics of implosion and core plasma. X-ray emission image of the plasma was sampled with two-dimensionally distributed image sampling points, streaked with the tube, and the recorded signals were reconstructed as sequential 2D frame images. Shape and movement of the core plasma were clearly observed.