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Sample records for two-dimensional dna gel

  1. 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.

  2. DNA-PKcs-OBA/Ku associate in the absence of DNA, as revealed by two-dimensional capillary gel electromobility shift assay.

    Science.gov (United States)

    Ruiz, Marcia T; Nichols, Amanda; Price, Gerald B; Zannis-Hadjopoulos, Maria

    2002-08-01

    Ors-binding activity (OBA) has been previously purified by its ability to specifically interact with A3/4, a 36-bp mammalian origin consensus sequence [1]. Peptide sequence analyses identified OBA as Ku86, the largest subunit of Ku antigen, a heterodimeric protein (Ku70/Ku86) involved in several autoimmune disorders [2-5]. The affinity-purified fraction containing OBA/Ku is also enriched for DNA-dependent protein kinase DNA-PKcs, the catalytic subunit of the DNA-PK holoenzyme, of which Ku antigen is the DNA-binding subunit [6-8]. Glycerol-gradient sedimentation analyses have demonstrated the presence of OBA/Ku in a high-molecular-weight complex. In order to investigate whether OBA/Ku and DNA-PKcs are associated in this fraction, we have used a modification of the two-dimensional gel electrophoresis technique originally described [9]. Electromobility shift assays were developed in native capillary gels, which were subsequently used for sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) in the second dimension. The gels were then processed for Western blotting using the Ku70, Ku86 and DNA-PKcs antibodies. This approach has revealed the association of OBA/Ku and DNA-PKcs to give rise to the DNA-PK holoenzyme irrespective of the presence, or the absence of DNA. Altogether, we have proven the utility of this technique for the study of protein-protein and protein-DNA interactions.

  3. 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...

  4. 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.

  5. 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

  6. 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...

  7. 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...

  8. Explorative data analysis of two-dimensional electrophoresis gels

    DEFF Research Database (Denmark)

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

    2004-01-01

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

  9. 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...

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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....

  15. 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.

  16. 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.

  17. 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.

  18. Two-dimensional DNA displays for comparisons of bacterial genomes

    Directory of Open Access Journals (Sweden)

    Malloff Chad

    2003-01-01

    Full Text Available We have developed two whole genome-scanning techniques to aid in the discovery of polymorphisms as well as horizontally acquired genes in prokaryotic organisms. First, two-dimensional bacterial genomic display (2DBGD was developed using restriction enzyme fragmentation to separate genomic DNA based on size, and then employing denaturing gradient gel electrophoresis (DGGE in the second dimension to exploit differences in sequence composition. This technique was used to generate high-resolution displays that enable the direct comparison of > 800 genomic fragments simultaneously and can be adapted for the high-throughput comparison of bacterial genomes. 2DBGDs are capable of detecting acquired and altered DNA, however, only in very closely related strains. If used to compare more distantly related strains (e.g. different species within a genus numerous small changes (i.e. small deletions and point mutations unrelated to the interesting phenotype, would encumber the comparison of 2DBGDs. For this reason a second method, bacterial comparative genomic hybridization (BCGH, was developed to directly compare bacterial genomes to identify gain or loss of genomic DNA. BCGH relies on performing 2DBGD on a pooled sample of genomic DNA from 2 strains to be compared and subsequently hybridizing the resulting 2DBGD blot separately with DNA from each individual strain. Unique spots (hybridization signals represent foreign DNA. The identification of novel DNA is easily achieved by excising the DNA from a dried gel followed by subsequent cloning and sequencing. 2DBGD and BCGH thus represent novel high resolution genome scanning techniques for directly identifying altered and/or acquired DNA.

  19. 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.

  20. Self-assembly of two-dimensional DNA crystals

    Institute of Scientific and Technical Information of China (English)

    SONG Cheng; CHEN Yaqing; WEI Shuai; YOU Xiaozeng; XIAO Shoujun

    2004-01-01

    Self-assembly of synthetic oligonucleotides into two-dimensional lattices presents a 'bottom-up' approach to the fabrication of devices on nanometer scale. We report the design and observation of two-dimensional crystalline forms of DNAs that are composed of twenty-one plane oligonucleotides and one phosphate-modified oligonucleotide. These synthetic sequences are designed to self-assemble into four double-crossover (DX) DNA tiles. The 'sticky ends' of these tiles that associate according to Watson-Crick's base pairing are programmed to build up specific periodic patterns upto tens of microns. The patterned crystals are visualized by the transmission electron microscopy.

  1. 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.

  2. 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.

  3. Two-dimensional gel-based protein standardization verified by western blot analysis.

    Science.gov (United States)

    Haniu, Hisao; Watanabe, Daisuke; Kawashima, Yusuke; Matsumoto, Hiroyuki

    2015-01-01

    In data presentation of biochemical investigation the amount of a target protein is shown in the y-axis against the x-axis representing time, concentrations of various agents, or other parameters. Western blot is a versatile and convenient tool in such an analysis to quantify and display the amount of proteins. In western blot, so-called housekeeping gene product(s), or "housekeeping proteins," are widely used as internal standards. The rationale of using housekeeping proteins for standardization of western blot is based on the assumption that the expression of chosen housekeeping gene is always constant, which could be false under certain physiological or pathological conditions. We have devised a two-dimensional gel-based standardization method in which the protein content of each sample is determined by scanning the total protein density of two-dimensional gels and the expression of each protein is quantified as the density ratio of each protein divided by the density of the total proteins on the two-dimensional gel. The advantage of this standardization method is that it is not based on any presumed "housekeeping proteins" that are supposed to be being expressed constantly under all physiological conditions. We will show that the total density of a two-dimensional gel can render a reliable protein standardization parameter by running western blot analysis on one of the proteins analyzed by two-dimensional gels.

  4. 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.

  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. 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...

  7. 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...

  8. 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...

  9. 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...

  10. 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.

  11. 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.

  12. [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.

  13. 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.

  14. 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.

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

    Directory of Open Access Journals (Sweden)

    J Vejayan

    2010-01-01

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

  16. 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).

  17. 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.

  18. 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.

  19. Comprehensive two-dimensional gel protein databases offer a global approach to the analysis of human cells: the transformed amnion cells (AMA) master database and its link to genome DNA sequence data

    DEFF Research Database (Denmark)

    Celis, J E; Gesser, B; Rasmussen, H H;

    1990-01-01

    qualitative and quantitative annotations has been established. The protein numbers in this database differ from those reported in an earlier version (Celis et al. Leukemia 1988, 2,561-602) as a result of changes in the scanning hardware. The reported information includes: percentage of total radioactivity...... recovered from the gels (based on quantitations of polypeptides labeled with a mixture of 16 14C-amino acids), protein name (including credit to investigators that aided identification), antibody against protein, cellular localization, (nuclear, 40S hnRNP, 20S snRNP U5, proteasomes, endoplasmic reticulum...

  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. 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.

  3. Isothermal hybridization kinetics of DNA assembly of two-dimensional DNA origami.

    Science.gov (United States)

    Song, Jie; Zhang, Zhao; Zhang, Shuai; Liu, Lei; Li, Qiang; Xie, Erqing; Gothelf, Kurt Vesterager; Besenbacher, Flemming; Dong, Mingdong

    2013-09-09

    The Watson-Crick base-pairing with specificity and predictability makes DNA molecules suitable for building versatile nanoscale structures and devices, and the DNA origami method enables researchers to incorporate more complexities into DNA-based devices. Thermally controlled atomic force microscopy in combination with nanomechanical spectroscopy with forces controlled in the pico Newton (pN) range as a novel technique is introduced to directly investigate the kinetics of multistrand DNA hybridization events on DNA origami nanopores under defined isothermal conditions. For the synthesis of DNA nanostructures under isothermal conditions at 60 °C, a higher hybridization rate, fewer defects, and a higher stability are achieved compared to room-temperature studies. By quantifying the assembly times for filling pores in origami structures at several constant temperatures, the fill factors show a consistent exponential increase over time. Furthermore, the local hybridization rate can be accelerated by adding a higher concentration of the staples. The new insight gained on the kinetics of staple-scaffold hybridization on the synthesis of two dimensional DNA origami structures may open up new routes and ideas for designing DNA assembly systems with increased potential for their application.

  4. 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...

  5. 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...

  6. 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.

  7. 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...

  8. 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.

  9. Supercapacitors based on two dimensional VO2 nanosheet electrodes in organic gel electrolyte

    KAUST Repository

    Rakhi, R.B.

    2016-10-16

    VO2 is a low band-gap semiconductor with relatively high conductivity among transition metal oxides, which makes it an interesting material for supercapacitor electrode applications. The performance of VO2 as supercapacitor electrode in organic electrolytes has never been reported before. Herein, two-dimensional nanosheets of VO2 are prepared by the simultaneous solution reduction and exfoliation from bulk V2O5 powder by hydrothermal method. A specific capacitance of 405 Fg−1 is achieved for VO2 based supercapacitor in an organic electrolyte, in three electrode configuration. The symmetric capacitor based on VO2 nanosheet electrodes and the liquid organic electrolyte exhibits an energy density of 46 Wh kg−1 at a power density of 1.4 kW kg−1 at a constant current density of 1 Ag−1. Furthermore, flexible solid-state supercapacitors are fabricated using same electrode material and Alumina-silica based gel electrolyte. The solid-state device delivers a specific capacitance of 145 Fg−1 and a device capacitance of 36 Fg−1 at a discharge current density of 1 Ag−1. Series combination of three solid state capacitors is capable of lighting up a red LED for more than 1 minute.

  10. Mapping of 34 minisatellite loci resolved by two-dimensional DNA typing

    DEFF Research Database (Denmark)

    Børglum, Anders; Nyegaard, Mette; Kvistgaard, AB

    1997-01-01

    Two-dimensional (2-D) DNA typing is based on electrophoretic separation of genomic DNA fragments in two dimensions according to independent criteria (size and base-pair sequence), followed by hybridization analysis using multilocus probes. The technique allows simultaneous visualization of severa...

  11. 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

  12. 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

  13. 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...

  14. 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...

  15. 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...

  16. 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...

  17. 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.

  18. 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...

  19. Two Dimensional Yau-Hausdorff Distance with Applications on Comparison of DNA and Protein Sequences.

    Directory of Open Access Journals (Sweden)

    Kun Tian

    Full Text Available Comparing DNA or protein sequences plays an important role in the functional analysis of genomes. Despite many methods available for sequences comparison, few methods retain the information content of sequences. We propose a new approach, the Yau-Hausdorff method, which considers all translations and rotations when seeking the best match of graphical curves of DNA or protein sequences. The complexity of this method is lower than that of any other two dimensional minimum Hausdorff algorithm. The Yau-Hausdorff method can be used for measuring the similarity of DNA sequences based on two important tools: the Yau-Hausdorff distance and graphical representation of DNA sequences. The graphical representations of DNA sequences conserve all sequence information and the Yau-Hausdorff distance is mathematically proved as a true metric. Therefore, the proposed distance can preciously measure the similarity of DNA sequences. The phylogenetic analyses of DNA sequences by the Yau-Hausdorff distance show the accuracy and stability of our approach in similarity comparison of DNA or protein sequences. This study demonstrates that Yau-Hausdorff distance is a natural metric for DNA and protein sequences with high level of stability. The approach can be also applied to similarity analysis of protein sequences by graphic representations, as well as general two dimensional shape matching.

  20. Two Dimensional Yau-Hausdorff Distance with Applications on Comparison of DNA and Protein Sequences.

    Science.gov (United States)

    Tian, Kun; Yang, Xiaoqian; Kong, Qin; Yin, Changchuan; He, Rong L; Yau, Stephen S-T

    2015-01-01

    Comparing DNA or protein sequences plays an important role in the functional analysis of genomes. Despite many methods available for sequences comparison, few methods retain the information content of sequences. We propose a new approach, the Yau-Hausdorff method, which considers all translations and rotations when seeking the best match of graphical curves of DNA or protein sequences. The complexity of this method is lower than that of any other two dimensional minimum Hausdorff algorithm. The Yau-Hausdorff method can be used for measuring the similarity of DNA sequences based on two important tools: the Yau-Hausdorff distance and graphical representation of DNA sequences. The graphical representations of DNA sequences conserve all sequence information and the Yau-Hausdorff distance is mathematically proved as a true metric. Therefore, the proposed distance can preciously measure the similarity of DNA sequences. The phylogenetic analyses of DNA sequences by the Yau-Hausdorff distance show the accuracy and stability of our approach in similarity comparison of DNA or protein sequences. This study demonstrates that Yau-Hausdorff distance is a natural metric for DNA and protein sequences with high level of stability. The approach can be also applied to similarity analysis of protein sequences by graphic representations, as well as general two dimensional shape matching.

  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. Self-assembly of two-dimensional binary quasicrystals: a possible route to a DNA quasicrystal

    Science.gov (United States)

    Reinhardt, Aleks; Schreck, John S.; Romano, Flavio; Doye, Jonathan P. K.

    2017-01-01

    We use Monte Carlo simulations and free-energy techniques to show that binary solutions of penta- and hexavalent two-dimensional patchy particles can form thermodynamically stable quasicrystals even at very narrow patch widths, provided their patch interactions are chosen in an appropriate way. Such patchy particles can be thought of as a coarse-grained representation of DNA multi-arm ‘star’ motifs, which can be chosen to bond with one another very specifically by tuning the DNA sequences of the protruding arms. We explore several possible design strategies and conclude that DNA star tiles that are designed to interact with one another in a specific but not overly constrained way could potentially be used to construct soft quasicrystals in experiment. We verify that such star tiles can form stable dodecagonal motifs using oxDNA, a realistic coarse-grained model of DNA.

  3. Self-assembly of two-dimensional binary quasicrystals: A possible route to a DNA quasicrystal

    CERN Document Server

    Reinhardt, Aleks; Romano, Flavio; Doye, Jonathan P K

    2016-01-01

    We use Monte Carlo simulations and free-energy techniques to show that binary solutions of penta- and hexavalent two-dimensional patchy particles can form thermodynamically stable quasicrystals even at very narrow patch widths, provided their patch interactions are chosen in an appropriate way. Such patchy particles can be thought of as a coarse-grained representation of DNA multi-arm `star' motifs, which can be chosen to bond with one another very specifically by tuning the DNA sequences of the protruding arms. We explore several possible design strategies and conclude that DNA star tiles that are designed to interact with one another in a specific but not overly constrained way could potentially be used to construct soft quasicrystals in experiment. We verify that such star tiles can form stable dodecagonal motifs using oxDNA, a realistic coarse-grained model of DNA.

  4. 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...

  5. Diffusion of dextran probes in a self-assembled fibrous gel composed of two-dimensional arborols.

    Science.gov (United States)

    Sun, Jirun; Lyles, Bethany F; Yu, Keunok Han; Weddell, Jaime; Pople, John; Hetzer, Max; De Kee, Daniel; Russo, Paul S

    2008-01-10

    Two-dimensional arborols are bolaform amphiphiles in which a central, hydrophobic spacer separates twin hydrophilic ends. Under appropriate conditions, these relatively small molecules assemble into very long fibers; subsequently, the system gels if the arborol concentration is sufficiently high. The diffusion of linear or slightly branched dextran probes in 3 and 6% arborol gels, as determined by fluorescence photobleaching recovery, resembles that of dextrans in water, suggesting a highly open network structure. Melting the gels produces almost no change in diffusion of the dextran probes. Small-angle X-ray scattering (SAXS) of wet arborol gels at different concentrations and temperatures reveals the diameter of the repeating unit of the fibers to be 8.26+/-0.68 nm. This dimension, which is independent of concentration and temperature, exceeds the length of a single arborol molecule by about a factor of 3. Rheological investigation identifies the linear response regime of the gels and permits an examination of the weak correlation between dextran probe diffusion and gel viscoelasticity.

  6. Mapping of 34 minisatellite loci resolved by two-dimensional DNA typing

    DEFF Research Database (Denmark)

    Børglum, Anders; Nyegaard, Mette; Kvistgaard, AB

    1997-01-01

    Two-dimensional (2-D) DNA typing is based on electrophoretic separation of genomic DNA fragments in two dimensions according to independent criteria (size and base-pair sequence), followed by hybridization analysis using multilocus probes. The technique allows simultaneous visualization of several...... could be deduced, showing no evidence of clustering. In the analysis of spot patterns, use was made of a computerized image analysis system specifically designed for 2-D DNA typing. Since experimental variations between different separation patterns were automatically corrected for with this program......, rapid and reliable scorings could be obtained. The results presented demonstrate the availability of reliable genetic information throughout the 2-D separation pattern. Adding the use of semiautomated computerized pattern analysis, this study further substantiates the applicability of 2-D DNA typing...

  7. Stiffer double-stranded DNA in two-dimensional confinement due to bending anisotropy

    Science.gov (United States)

    Salari, H.; Eslami-Mossallam, B.; Ranjbar, H. F.; Ejtehadi, M. R.

    2016-12-01

    Using analytical approach and Monte Carlo (MC) simulations, we study the elastic behavior of the intrinsically twisted elastic ribbons with bending anisotropy, such as double-stranded DNA (dsDNA), in two-dimensional (2D) confinement. We show that, due to the bending anisotropy, the persistence length of dsDNA in 2D conformations is always greater than three-dimensional (3D) conformations. This result is in consistence with the measured values for DNA persistence length in 2D and 3D in equal biological conditions. We also show that in two dimensions, an anisotropic, intrinsically twisted polymer exhibits an implicit twist-bend coupling, which leads to the transient curvature increasing with a half helical turn periodicity along the bent polymer.

  8. Two-dimensional salt and temperature DNA denaturation analysis using a magnetoresistive sensor

    DEFF Research Database (Denmark)

    Rizzi, Giovanni; Dufva, Martin; Hansen, Mikkel Fougt

    2017-01-01

    . The results demonstrate that concentration melting provides an attractive alternative to temperature melting in on-chip DNA denaturation experiments and further show that the magnetoresistive platform is attractive due to its low cross-sensitivity to temperature and liquid composition....... temperature as well as salt concentration. The salt concentration melting curves were found to be more reliable than temperature melting curves. We performed a two-dimensional mapping of the melting profiles of a target to probes targeting its wild type (WT) and mutant type (MT) variants in the temperature...

  9. 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.

  10. 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.

  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. 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.

  13. 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

  14. 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.

  15. DNA sequencing by two-dimensional materials: As theoretical modeling meets experiments.

    Science.gov (United States)

    Liang, Lijun; Shen, Jia-Wei; Zhang, Zhisen; Wang, Qi

    2017-03-15

    Owing to their extraordinary electrical, chemical, optical, mechanical and structural properties, two-dimensional (2D) materials (mainly including graphene, boron nitride, MoS2 etc.) have stimulated exploding interests in sensor applications. 2D-material based nanoscale DNA sequencing is a single-molecule technique with revolutionary potential. In this paper, we review the methodology of DNA sequencing based on the measurements of ionic current, force peak, and transverse electrical currents etc. by 2D materials. The advantages and disadvantages of DNA sequencing by 2D materials are discussed. Besides the recent development of experiments, we will focus on the theoretical calculations of DNA sequencing, which have been played a critical role in the development of this field. Special emphasis will focus on the disagreements between experiments and theoretical calculations, and the explanations for the discrepancy will be highlighted. Finally, some new plausible sequencing methods from computational studies will be discussed, which may be applied in the realistic DNA sequencing experiments in future.

  16. 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.

  17. 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

  18. 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].

  19. 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.

  20. 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....

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

    Science.gov (United States)

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

    2013-12-19

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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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...

  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 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...

  8. 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.

  9. 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

  10. The sequence d(CGGCGGCCGC) self-assembles into a two dimensional rhombic DNA lattice

    Energy Technology Data Exchange (ETDEWEB)

    Venkadesh, S.; Mandal, P.K. [CAS in Crystallography and Biophysics, University of Madras, Chennai 600 025 (India); Gautham, N., E-mail: n_gautham@hotmail.com [CAS in Crystallography and Biophysics, University of Madras, Chennai 600 025 (India)

    2011-04-15

    Highlights: {yields} This is the first crystal structure of a four-way junction with sticky ends. {yields} Four junction structures bind to each other and form a rhombic cavity. {yields} Each rhombus binds to others to form 'infinite' 2D tiles. {yields} This is an example of bottom-up fabrication of a DNA nano-lattice. -- Abstract: We report here the crystal structure of the partially self-complementary decameric sequence d(CGGCGGCCGC), which self assembles to form a four-way junction with sticky ends. Each junction binds to four others through Watson-Crick base pairing at the sticky ends to form a rhombic structure. The rhombuses bind to each other and form two dimensional tiles. The tiles stack to form the crystal. The crystal diffracted in the space group P1 to a resolution of 2.5 A. The junction has the anti-parallel stacked-X conformation like other junction structures, though the formation of the rhombic net noticeably alters the details of the junction geometry.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

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

    Science.gov (United States)

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

  18. 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...

  19. 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...

  20. 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 ...

  1. The master two-dimensional gel database of human AMA cell proteins: towards linking protein and genome sequence and mapping information (update 1991)

    DEFF Research Database (Denmark)

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

    1991-01-01

    The master two-dimensional gel database of human AMA cells currently lists 3801 cellular and secreted proteins, of which 371 cellular polypeptides (306 IEF; 65 NEPHGE) were added to the master images during the last 10 months. These include: (i) very basic and acidic proteins that do not focus un...

  2. 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.

  3. 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.

  4. 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...

  5. Spermidine-induced two-dimensional DNA condensations on mica surfaces: A different pathway from condensations in solution

    Institute of Scientific and Technical Information of China (English)

    ZHANG XingHua; HOU XiMiao; JI Chao; LI Ming; DOU ShuoXing; WANG PengYe

    2009-01-01

    With atomic force microscopy (AFM) we systematically studied the DNA condensations on mica surfaces induced by multivalent cation spermidine. The pattern of the DNA condensates is a flat single layer, with a core in the centre and DNA wrapping around it at high density. We assume this to be a two-dimensional condensation of free coiled DNA onto negatively charged mica surfaces by the multivalent cation. The DNA molecules condense on mica surfaces via a pathway different from the formation of toroids, rods or globules in bulk solutions. We give an explanation to why toroid structures are difficult to be observed by AFM, and further discuss the relationship between DNA condensations in solutions and on mica surfaces. The present work will be helpful for understanding the behaviors of DNA on charged surfaces, which might be significantly different from that in solutions.

  6. 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.

  7. Comparative two-dimensional gel analysis and microsequencing identifies gelsolin as one of the most prominent downregulated markers of transformed human fibroblast and epithelial cells

    DEFF Research Database (Denmark)

    Vandekerckhove, J; Bauw, G; Vancompernolle, K

    1990-01-01

    A systematic comparison of the protein synthesis patterns of cultured normal and transformed human fibroblasts and epithelial cells, using two-dimensional gel protein analysis combined with computerized imaging and data acquisition, identified a 90-kD protein (SSP 5714) as one of the most striking...... downregulated markers typical of the transformed state. Using the information stored in the comprehensive human cellular protein database, we found this protein strongly expressed in several fetal tissues and one of them, epidermis, served as a source for preparative two-dimensional gel electrophoresis. Partial...... and by coelectrophoresis with purified human gelsolin. These results suggest that an important regulatory protein of the microfilament system may play a role in defining the phenotype of transformed human fibroblast and epithelial cells in culture. Udgivelsesdato: 1990-Jul...

  8. 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...

  9. Transfer of Two-Dimensional Oligonucleotide Patterns onto Stereocontrolled Plasmonic Nanostructures through DNA-Origami-Based Nanoimprinting Lithography.

    Science.gov (United States)

    Zhang, Yinan; Chao, Jie; Liu, Huajie; Wang, Fei; Su, Shao; Liu, Bing; Zhang, Lan; Shi, Jiye; Wang, Lihua; Huang, Wei; Wang, Lianhui; Fan, Chunhai

    2016-07-04

    The precise functionalization of self-assembled nanostructures with spatial and stereocontrol is a major objective of nanotechnology and holds great promise for many applications. Herein, the nanoscale addressability of DNA origami was exploited to develop a precise copy-machine-like platform that can transfer two-dimensional oligonucleotide patterns onto the surface of gold nanoparticles (AuNPs) through a deliberately designed toehold-initiated DNA displacement reaction. This strategy of DNA-origami-based nanoimprinting lithography (DONIL) demonstrates high precision in controlling the valence and valence angles of AuNPs. These DNA-decorated AuNPs act as precursors in the construction of discrete AuNP clusters with desired chirality.

  10. Proteome analysis of barley seeds: Identification of major proteins from two-dimensional gels (pl 4-7)

    DEFF Research Database (Denmark)

    Østergaard, O.; Finnie, Christine; Laugesen, S.;

    2004-01-01

    -soluble proteins in extracts of mature barley (Hordeum vulgare) seeds and to follow their fate during germination. About 1200 and 600 spots of p/ 4-7 were detected on 2-D gels by silver staining and colloidal Coomassie Brilliant Blue staining, respectively. About 300 spots were selected for in-gel digestion...

  11. 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.

  12. Determining degradation and synthesis rates of arabidopsis proteins using the kinetics of progressive 15N labeling of two-dimensional gel-separated protein spots.

    Science.gov (United States)

    Li, Lei; Nelson, Clark J; Solheim, Cory; Whelan, James; Millar, A Harvey

    2012-06-01

    The growth and development of plant tissues is associated with an ordered succession of cellular processes that are reflected in the appearance and disappearance of proteins. The control of the kinetics of protein turnover is central to how plants can rapidly and specifically alter protein abundance and thus molecular function in response to environmental or developmental cues. However, the processes of turnover are largely hidden during periods of apparent steady-state protein abundance, and even when proteins accumulate it is unclear whether enhanced synthesis or decreased degradation is responsible. We have used a (15)N labeling strategy with inorganic nitrogen sources coupled to a two-dimensional fluorescence difference gel electrophoresis and mass spectrometry analysis of two-dimensional IEF/SDS-PAGE gel spots to define the rate of protein synthesis (K(S)) and degradation (K(D)) of Arabidopsis cell culture proteins. Through analysis of MALDI-TOF/TOF mass spectra from 120 protein spots, we were able to quantify K(S) and K(D) for 84 proteins across six functional groups and observe over 65-fold variation in protein degradation rates. K(S) and K(D) correlate with functional roles of the proteins in the cell and the time in the cell culture cycle. This approach is based on progressive (15)N labeling that is innocuous for the plant cells and, because it can be used to target analysis of proteins through the use of specific gel spots, it has broad applicability.

  13. 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.

  14. 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.

  15. An optical comparator for measuring two-dimensional polyacrylamide gel electrophoresis records using an on-line microcomputer.

    Science.gov (United States)

    Spragg, S P; Jones, M I; Hill, B J

    1983-03-01

    A comparator which makes it possible to compare two wet gels or photographic negatives or autoradiograms through a flickering light system has been built. The system consists of two special-purpose projectors which combine the images on a digitizing platform. When the lights are switched On and off out of phase, the positions of the common components remain unchanged, whereas those that are spatially displaced appear to jump from side to side and those present in one image but not the other switch on and off. This produces a flickering image in which differences are readily seen. Commercial camera lenses were used to construct the projectors and the overall specifications for the system are given. The coordinates of both the displaced components, as well as the selected standards from the two images, are digitized and entered automatically into an on-line microcomputer. By using an iterative procedure for collecting records from several superimposable records of the gel, it is possible to compensate for the lack of total reproducibility over the whole gels. These coordinates are then normalized and superimposed on a master map through a television display using a curser to adjust the coordinates. The whole procedure can be repeated for many gels using a common reference gel in the comparator, and the result is a set of normalized coordinates which can be plotted on a single map to provide a final record of the experiments.

  16. Programming Self-Assembly of DNA Origami Honeycomb Two-Dimensional Lattices and Plasmonic Metamaterials.

    Science.gov (United States)

    Wang, Pengfei; Gaitanaros, Stavros; Lee, Seungwoo; Bathe, Mark; Shih, William M; Ke, Yonggang

    2016-06-22

    Scaffolded DNA origami has proven to be a versatile method for generating functional nanostructures with prescribed sub-100 nm shapes. Programming DNA-origami tiles to form large-scale 2D lattices that span hundreds of nanometers to the micrometer scale could provide an enabling platform for diverse applications ranging from metamaterials to surface-based biophysical assays. Toward this end, here we design a family of hexagonal DNA-origami tiles using computer-aided design and demonstrate successful self-assembly of micrometer-scale 2D honeycomb lattices and tubes by controlling their geometric and mechanical properties including their interconnecting strands. Our results offer insight into programmed self-assembly of low-defect supra-molecular DNA-origami 2D lattices and tubes. In addition, we demonstrate that these DNA-origami hexagon tiles and honeycomb lattices are versatile platforms for assembling optical metamaterials via programmable spatial arrangement of gold nanoparticles (AuNPs) into cluster and superlattice geometries.

  17. Growth of two-dimensional KGd(WO 4) 2 nanorods by modified sol-gel Pechini method

    Science.gov (United States)

    Thangaraju, D.; Samuel, P.; Moorthy Babu, S.

    2010-08-01

    KGd (WO 4) 2 nanocrystalline powder was obtained by modified sol-gel Pechini method. The synthesis procedure was optimized with TGA and DTA analyses. Synthesized polymeric resin was calcinated at 550 and 700 °C using resistive furnace in an open atmosphere. Crystallinity of annealed powder was confirmed using X-ray diffraction. Absorption peaks of FT-IR for gel and the annealed samples, at two different temperatures show the decomposition of citrate-ethylene glycol complex and formation of KGW particles. Raman analysis confirms that the derived particles have well constructed bridges of W-O-O-W. External morphology of the particles was analysed through SEM.

  18. Temperature and magnetic field effects on electron transport through DNA molecules in a two-dimensional four-channel system.

    Science.gov (United States)

    Joe, Yong S; Lee, Sun H; Hedin, Eric R; Kim, Young D

    2013-06-01

    We utilize a two-dimensional four-channel DNA model, with a tight-binding (TB) Hamiltonian, and investigate the temperature and the magnetic field dependence of the transport behavior of a short DNA molecule. Random variation of the hopping integrals due to the thermal structural disorder, which partially destroy phase coherence of electrons and reduce quantum interference, leads to a reduction of the localization length and causes suppressed overall transmission. We also incorporate a variation of magnetic field flux density into the hopping integrals as a phase factor and observe Aharonov-Bohm (AB) oscillations in the transmission. It is shown that for non-zero magnetic flux, the transmission zero leaves the real-energy axis and moves up into the complex-energy plane. We also point out that the hydrogen bonds between the base pair with flux variations play a role to determine the periodicity of AB oscillations in the transmission.

  19. Two dimensional gel human protein databases offer a systematic approach to the study of cell proliferation and differentiation

    DEFF Research Database (Denmark)

    Celis, J E; Gesser, B; Dejgaard, K;

    1989-01-01

    Human cellular protein databases have been established using computer-analyzed 2D gel electrophoresis. These databases, which include information on various properties of proteins, offer a global approach to the study of regulation of cell proliferation and differentiation. Furthermore, thanks...

  20. 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.

  1. The Energy Landscape for the Self-Assembly of a Two-Dimensional DNA Origami Complex.

    Science.gov (United States)

    Fern, Joshua; Lu, Jennifer; Schulman, Rebecca

    2016-02-23

    While the self-assembly of different types of DNA origami into well-defined complexes could produce nanostructures on which thousands of locations can be independently functionalized with nanometer-scale precision, current assembly processes have low yields. Biomolecular complex formation requires relatively strong interactions and reversible assembly pathways that prevent kinetic trapping. To characterize how these issues control origami complex yields, the equilibrium constants for each possible reaction for the assembly of a heterotetrameric ring, the unit cell of a rectangular lattice, were measured using fluorescence colocalization microscopy. We found that origami interface structure controlled reaction free energies. Cooperativity, measured for the first time for a DNA nanostructure assembly reaction, was weak. Simulations of assembly kinetics suggest assembly occurs via parallel pathways with the primary mechanism of assembly being hierarchical: two dimers form that then bind to one another to complete the ring.

  2. Two-dimensional self-assembly of DNA-functionalized gold nanoparticles

    Science.gov (United States)

    Wang, Wenjie; Zhang, Honghu; Hagen, Noah; Kuzmenko, Ivan; Akinc, Mufit; Travesset, Alex; Mallapragada, Surya; Vaknin, David

    2D superlattices of nanoparticles (NPs) are promising candidates for nano-devices. It is still challenging to develop a simple yet efficient protocol to assemble NPs in a controlled manner. Here, we report on formation of 2D Gibbs monolayers of single-stranded DNA-coated gold nanoparticles (ssDNA-AuNPs) at the air-water interface by manipulation of salts contents. MgCl2 and CaCl2 in solutions facilitate the accumulation of the non-complementary ssDNA-AuNPs on aqueous surfaces. Grazing-incidence small-angle X-ray scattering (GISAXS) and X-ray reflectivity show that the surface AuNPs assembly forms a mono-particle layer and undergoes a transformation from short-range to long-range (hexagonal) order above a threshold of [MgCl2] or [CaCl2]. For solutions that include two kinds of ssDNA-AuNPs with complementary base-pairing, the surface AuNPs form a thicker film and only in-plane short-range order is observed. By using other salts (NaCl or LaCl3) at concentrations of similar ionic strength to those of MgCl2 or CaCl2, we find that surface adsorbed NPs lack any orders. X-ray fluorescence measurements provide direct evidence of surface enrichment of AuNPs and divalent ions (Ca2 +) . The work was supported by the Office of Basic Energy Sciences, USDOE under Contract No. DE-AC02-07CH11358 and DE-AC02-06CH11357.

  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. 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.

  5. 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

    )vaccinia virus expression of full length cDNAs, and (vi) in vitro transcription/translation of full-length cDNAs. This year, special emphasis has been given to the identification of signal transduction components by using 2-D gel immunoblotting of crude keratinocyte lysates in combination with enhanced......--through a systematic study of ekeratinocytes--qualitative and quantitative information on proteins and their genes that may allow us to identify abnormal patterns of gene expression and to pinpoint signaling pathways and components affected in various skin diseases, cancer included. Udgivelsesdato: 1995-Dec...

  6. 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.

  7. 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.

  8. 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.

  9. DNA DAMAGE QUANTITATION BY ALKALINE GEL ELECTROPHORESIS.

    Energy Technology Data Exchange (ETDEWEB)

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

    2004-03-24

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

  10. Characterization of cyst and trophozoite proteins of environmental isolates of Acanthamoeba castellanii by two-dimensional gel electrophoresis.

    Science.gov (United States)

    Dao, Yap Ray Ming; Chooi, Lim Patricia Kim; Li, Chan Li; Fung, Wong Shew; Wah, Mak Joon

    2014-03-01

    Acanthamoeba castellanii has been known to possess pathogenic properties, such as acanthamoebic keratitis and granulomatous amoebic encephalitis. The role of proteases and proteins in the pathogenesis of these infections is still poorly understood. As Acanthamoeba sp is a ubiquitous protozoon found in the natural environment they can potentially cause human infections. This study characterized cyst and trophozoite proteins of 3 environmental A. castellanii isolates in comparison with a clinical isolate, ATCC 50492. The latter and environmental IMU1 isolate had 100% genotype identity with A. castellanii and demonstrated protein spots with higher molecular weights (> 95 kDa) at relatively higher isoelectric values (> pI 7.00) compared to the two other environmental isolates (IMU4 and IMU5) that had 99% genotype identity to A. castellanii based on 16 S rDNA sequence. Thus such trophozoite proteins may be involved with the parasite's ability to cause acanthamoebic keratitis.

  11. 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.

  12. 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...

  13. 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.

  14. Ultrathin Two-Dimensional Covalent Organic Framework Nanosheets: Preparation and Application in Highly Sensitive and Selective DNA Detection

    KAUST Repository

    Peng, Yongwu

    2017-06-03

    The ability to prepare ultrathin two-dimensional (2D) covalent organic framework (COF) nanosheets (NSs) in high yield is of great importance for the further exploration of their unique properties and potential applications. Herein, by elaborately designing and choosing two flexible molecules with C3v molecular symmetry as building units, a novel imine-linked COF, namely TPA-COF, with hexagonal layered structure and sheet-like morphology, is synthesized. Since the flexible building units are integrated into the COF skeletons, the interlayer stacking becomes weak, resulting in the easy exfoliation of TPA-COF into ultrathin 2D NSs. Impressively, for the first time, the detailed structural information, i.e. the pore channels and individual building units in the NSs, is clearly visualized by using the recently developed low-dose imaging technique of transmission electron microscopy (TEM). As a proof-of-concept application, the obtained ultrathin COF NSs are used as a novel fluorescence sensing platform for the highly sensitive and selective detection of DNA.

  15. 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

  16. 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.

  17. Re-entrant DNA gels

    Science.gov (United States)

    Bomboi, Francesca; Romano, Flavio; Leo, Manuela; Fernandez-Castanon, Javier; Cerbino, Roberto; Bellini, Tommaso; Bordi, Federico; Filetici, Patrizia; Sciortino, Francesco

    2016-10-01

    DNA is acquiring a primary role in material development, self-assembling by design into complex supramolecular aggregates, the building block of a new-materials world. Using DNA nanoconstructs to translate sophisticated theoretical intuitions into experimental realizations by closely matching idealized models of colloidal particles is a much less explored avenue. Here we experimentally show that an appropriate selection of competing interactions enciphered in multiple DNA sequences results into the successful design of a one-pot DNA hydrogel that melts both on heating and on cooling. The relaxation time, measured by light scattering, slows down dramatically in a limited window of temperatures. The phase diagram displays a peculiar re-entrant shape, the hallmark of the competition between different bonding patterns. Our study shows that it is possible to rationally design biocompatible bulk materials with unconventional phase diagrams and tuneable properties by encoding into DNA sequences both the particle shape and the physics of the collective response.

  18. Gel Electrophoresis of Gold-DNA Nanoconjugates

    Directory of Open Access Journals (Sweden)

    T. Pellegrino

    2007-01-01

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

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. Supramolecular gel electrophoresis of large DNA fragments.

    Science.gov (United States)

    Tazawa, Shohei; Kobayashi, Kazuhiro; Oyoshi, Takanori; Yamanaka, Masamichi

    2017-07-06

    Pulsed-field gel electrophoresis is a frequent technique used to separate exceptionally large DNA fragments. In a typical continuous field electrophoresis, it is challenging to separate DNA fragments larger than 20 kbp because they migrate at a comparable rate. To overcome this challenge, it is necessary to develop a novel matrix for the electrophoresis. Here, we describe the electrophoresis of large DNA fragments up to 166 kbp using a supramolecular gel matrix and a typical continuous field electrophoresis system. C3 -symmetric tris-urea self-assembled into a supramolecular hydrogel in tris-boric acid-EDTA buffer, a typical buffer for DNA electrophoresis, and the supramolecular hydrogel was used as a matrix for electrophoresis to separate large DNA fragments. Three types of DNA marker, the λ-Hind III digest (2 to 23 kbp), Lambda DNA-Mono Cut Mix (10 to 49 kbp), and Marker 7 GT (10 to 165 kbp), were analyzed in this study. Large DNA fragments of greater than 100 kbp showed distinct mobility using a typical continuous field electrophoresis system. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. 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.

  6. 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

  7. 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

  8. Systematic secretome analyses of rice leaf and seed callus suspension-cultured cells: workflow development and establishment of high-density two-dimensional gel reference maps.

    Science.gov (United States)

    Jung, Young-Ho; Jeong, Seung-Hee; Kim, So Hee; Singh, Raksha; Lee, Jae-Eun; Cho, Yoon-Seong; Agrawal, Ganesh Kumar; Rakwal, Randeep; Jwa, Nam-Soo

    2008-12-01

    Secreted proteins control a multitude of biological and physiological processes in multicellular organisms such as plants. Identification of secreted proteins in reference plants like Arabidopsis and rice under normal growth conditions and adverse environmental conditions will help better understand the secretory pathways. Here, we have performed a systematic in planta and in vitro analyses of proteins secreted by rice leaves (in planta) and seed callus suspension-cultured cells (SCCs; in vitro), respectively, using a combination of biochemical and two-dimensional gel electrophoresis (2-DGE) coupled with liquid chromatography mass spectrometry analyses. Secreted proteins prepared from either leaves or SCCs medium were essentially free from contamination of intracellular proteins as judged by biochemical and Western blot analyses. 2-DGE analyses of secreted proteins collectively identified 222 protein spots with only 6 protein spots common to both in planta and in vitro derived data sets. Data were used to establish high-resolution and high-density 2-D gel reference maps for both in planta and in vitro secreted proteins. Identified proteins belonged to 11 (in planta) and 6 (in vitro) functional classes. Proteins involved in carbon metabolism (33%) and cell wall metabolism having plant defense mechanism (18%) were highly represented in the in planta secreted proteins accounting for 51% of total identified proteins, whereas proteins of cell wall metabolism having plant defense mechanism (64%) were predominant in the in vitro secreted proteins. Interestingly, secreted proteins possessing signal peptides were significantly lower in an in planta (27%) prepared secreted protein population than in vitro (76%) as predicted by SignalP prediction tool, implying the notion that plant might possess yet unidentified secretory pathway(s) in addition to the classical endoplasmic reticulum/Golgi pathway. Taken together, this systematic study provides evidence for (i) significant

  9. 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

  10. 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

  11. Agarose Gel Electrophoresis Reveals Structural Fluidity of a Phage T3 DNA Packaging Intermediate

    Science.gov (United States)

    Serwer, Philip; Wright, Elena T.

    2012-01-01

    We find a new aspect of DNA packaging-associated structural fluidity for phage T3 capsids. The procedure is (1) glutaraldehyde cross-linking of in vivo DNA packaging intermediates for stabilization of structure and then (2) determining of effective radius by two-dimensional agarose gel electrophoresis (2d-AGE). The intermediates are capsids with incompletely packaged DNA (ipDNA) and without an external DNA segment; these intermediates are called ipDNA-capsids. We initially increase production of ipDNA-capsids by raising NaCl concentration during in vivo DNA packaging. By 2d-AGE, we find a new state of contracted shell for some particles of one previously identified ipDNA-capsid. The contracted shell-state is found when ipDNA length/mature DNA length (F) is above 0.17, but not at lower F. Some contracted-shell ipDNA-capsids have the phage tail; others do not. The contracted-shell ipDNA-capsids are explained by premature DNA maturation cleavage that makes accessible a contracted-shell intermediate of a cycle of the T3 DNA packaging motor. The analysis of ipDNA-capsids, rather than intermediates with uncleaved DNA, provides a simplifying strategy for a complete biochemical analysis of in vivo DNA packaging. PMID:22222979

  12. 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...

  13. Validation of a PicoGreen-based DNA quantification integrated in an RNA extraction method for two-dimensional and three-dimensional cell cultures.

    Science.gov (United States)

    Chen, Yantian; Sonnaert, Maarten; Roberts, Scott J; Luyten, Frank P; Schrooten, Jan

    2012-06-01

    DNA measurement and RNA extraction are two frequently used methods for cell characterization. In the conventional protocols, they require similar, but separate samples and in most cases, different pretreatments. The few combined protocols that exist still include time-consuming steps. Hence, to establish an efficient combined RNA extraction and DNA measurement protocol for two-dimensional (2D) and three-dimensional (3D) cell cultures, a PicoGreen-based DNA measurement was integrated in an existing RNA extraction protocol. It was validated by analysis of the influence of different lysis buffers, RLT, RA1, or Trizol, used for RNA extraction on the measured DNA concentration. The DNA cell yield was evaluated both in cell suspensions (2D) and on 3D cell-seeded scaffolds. Results showed that the different RNA lysis buffers caused a concentration-dependent perturbation of the PicoGreen signal. The measured DNA concentrations in 2D and 3D using RLT and RA1 buffer were comparable, also to the positive control. We, therefore, concluded that RNA extraction protocols using RA1 or RLT buffer allow the integration of a DNA quantification step without the buffer influencing the results. Hence, the combined DNA measurement and RNA extraction offer an alternative for DNA measurement techniques that is time and sample saving, for both 2D cell cultures and specific 3D constructs.

  14. Swelling properties of cross-linked DNA gels.

    Science.gov (United States)

    Costa, Diana; Miguel, M Graça; Lindman, Björn

    2010-07-12

    This work represents our contribution to the field of physical chemistry of DNA gels, and concerns the synthesis and study of novel chemically cross-linked DNA gels. The use of covalent DNA gels is a very promising way to study DNA-cosolute interactions, as well as the dynamic behaviour of DNA and cationic compacting agents, like lipids, surfactants and polycations. Manipulating DNA in new ways, like DNA networks, allows a better understanding and characterization of DNA-cosolute complexes at the molecular level, and also allows us to follow the assembly structures of these complexes. The use of responsive polymer gels for targeted delivery of toxic and/or labile drugs has, during the past few years, shown to be a promising concept. The features found in the proposed system would find applications in a broader field of gel/drug interaction, for the development of controlled release and targeted delivery devices.

  15. Electrophoresis of DNA in agarose gels, polyacrylamide gels and in free solution

    Science.gov (United States)

    Stellwagen, Nancy C.

    2009-01-01

    This review describes the electrophoresis of curved and normal DNA molecules in agarose gels, polyacrylamide gels and in free solution. These studies were undertaken to clarify why curved DNA molecules migrate anomalously slowly in polyacrylamide gels but not in agarose gels. Two milestone papers are cited, in which Ferguson plots were used to estimate the effective pore size of agarose and polyacrylamide gels. Subsequent studies on the effect of the electric field on agarose and polyacrylamide gel matrices, DNA interactions with the two gel matrices, and the effect of curvature on the free solution mobility of DNA are also described. The combined results suggest that the anomalously slow mobilities observed for curved DNA molecules in polyacrylamide gels are due primarily to preferential interactions of curved DNAs with the polyacrylamide gel matrix; the restrictive pore size of the matrix is of lesser importance. In free solution, DNA mobilities increase with increasing molecular mass until leveling off at a plateau value of (3.17 ± 0.01) × 10-4 cm2/Vs in 40 mM Tris-acetate-EDTA buffer at 20°C. Curved DNA molecules migrate anomalously slowly in free solution as well as in polyacrylamide gels, explaining why the Ferguson plots of curved and normal DNAs containing the same number of base pairs extrapolate to different mobilities at zero gel concentration. PMID:19517510

  16. 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.

  17. Agarose gel electrophoresis for the separation of DNA fragments.

    Science.gov (United States)

    Lee, Pei Yun; Costumbrado, John; Hsu, Chih-Yuan; Kim, Yong Hoon

    2012-04-20

    Agarose gel electrophoresis is the most effective way of separating DNA fragments of varying sizes ranging from 100 bp to 25 kb(1). Agarose is isolated from the seaweed genera Gelidium and Gracilaria, and consists of repeated agarobiose (L- and D-galactose) subunits(2). During gelation, agarose polymers associate non-covalently and form a network of bundles whose pore sizes determine a gel's molecular sieving properties. The use of agarose gel electrophoresis revolutionized the separation of DNA. Prior to the adoption of agarose gels, DNA was primarily separated using sucrose density gradient centrifugation, which only provided an approximation of size. To separate DNA using agarose gel electrophoresis, the DNA is loaded into pre-cast wells in the gel and a current applied. The phosphate backbone of the DNA (and RNA) molecule is negatively charged, therefore when placed in an electric field, DNA fragments will migrate to the positively charged anode. Because DNA has a uniform mass/charge ratio, DNA molecules are separated by size within an agarose gel in a pattern such that the distance traveled is inversely proportional to the log of its molecular weight(3). The leading model for DNA movement through an agarose gel is "biased reptation", whereby the leading edge moves forward and pulls the rest of the molecule along(4). The rate of migration of a DNA molecule through a gel is determined by the following: 1) size of DNA molecule; 2) agarose concentration; 3) DNA conformation(5); 4) voltage applied, 5) presence of ethidium bromide, 6) type of agarose and 7) electrophoresis buffer. After separation, the DNA molecules can be visualized under uv light after staining with an appropriate dye. By following this protocol, students should be able to: Understand the mechanism by which DNA fragments are separated within a gel matrix Understand how conformation of the DNA molecule will determine its mobility through a gel matrix Identify an agarose solution of appropriate

  18. DNA- and AC electric field-assisted assembly of two-dimensional colloidal photonic crystals and their controlled defect insertion

    Science.gov (United States)

    Kim, Sejong

    Photonic crystals (PC) are structures in which the refractive index is a periodic function in space. The ability of photonic crystals to localize and manipulate electromagnetic waves has attracted considerable attention from the scientific community. The self-assembly of monodisperse micrometer scale colloidal spheres into hexagonal closed-packed colloidal crystals provides a simple, fast, and cheap materials chemistry approach to PCs. Employing DNA supramolecular recognition, 2-dimensional (2D) photonic crystal monolayer was fabricated with monodisperse polystyrene colloidal microspheres. Amine-terminated DNA oligomers were covalently attached onto carboxy-decorated microspheres and enabled their DNA-functionalization while preserving their colloidal stability and organization properties. Following a capillary-force-assisted organization of DNA-decorated microspheres into close-packed 2D opaline arrays, the first monolayer was immobilized by DNA hybridization. Insertion of vacancies at predetermined sites within the lattice of colloidal crystals is a prerequisite in order to realize high-quality, opaline-based photonic devices. The previously obtained DNA-hybridization type binding of 2D-opaline arrays provides a heat-sensitive "adhesive" between substrate and microspheres within a surrounding aqueous medium that enables tuning the hybridization strength of DNA linker as well as a mechanism to facilitate the removal of unbound microspheres. Focusing a laser beam onto a single microsphere of the opaline array induces localized heating that enables the microsphere to detach, leaving behind vacancies. By repeating this process, line vacancies were successfully obtained. The effects of salt concentration, laser power, light-absorbing dyes, DNA length and refractive index mismatch were investigated and found to correlate with heat-induced DNA dehybridization. In addition, AC (alternating current) electrokinetic force was also utilized to obtain assembly of colloidal

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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...

  5. Stability of capillary gels for automated sequencing of DNA.

    Science.gov (United States)

    Swerdlow, H; Dew-Jager, K E; Brady, K; Grey, R; Dovichi, N J; Gesteland, R

    1992-08-01

    Recent interest in capillary gel electrophoresis has been fueled by the Human Genome Project and other large-scale sequencing projects. Advances in gel polymerization techniques and detector design have enabled sequencing of DNA directly in capillaries. Efforts to exploit this technology have been hampered by problems with the reproducibility and stability of gels. Gel instability manifests itself during electrophoresis as a decrease in the current passing through the capillary under a constant voltage. Upon subsequent microscopic examination, bubbles are often visible at or near the injection (cathodic) end of the capillary gel. Gels have been prepared with the polyacrylamide matrix covalently attached to the silica walls of the capillary. These gels, although more stable, still suffer from problems with bubbles. The use of actual DNA sequencing samples also adversely affects gel stability. We examined the mechanisms underlying these disruptive processes by employing polyacrylamide gel-filled capillaries in which the gel was not attached to the capillary wall. Three sources of gel instability were identified. Bubbles occurring in the absence of sample introduction were attributed to electroosmotic force; replacing the denaturant urea with formamide was shown to reduce the frequency of these bubbles. The slow, steady decline in current through capillary sequencing gels interferes with the ability to detect other gel problems. This phenomenon was shown to be a result of ionic depletion at the gel-liquid interface. The decline was ameliorated by adding denaturant and acrylamide monomers to the buffer reservoirs. Sample-induced problems were shown to be due to the presence of template DNA; elimination of the template allowed sample loading to occur without complications.(ABSTRACT TRUNCATED AT 250 WORDS)

  6. Inexpensive and Safe DNA Gel Electrophoresis Using Household Materials

    Science.gov (United States)

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

    2012-01-01

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

  7. Inexpensive and Safe DNA Gel Electrophoresis Using Household Materials

    Science.gov (United States)

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

    2012-01-01

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

  8. Improved recovery of DNA from polyacrylamide gels after in situ DNA footprinting

    NARCIS (Netherlands)

    van Keulen, G; Meijer, WG

    Methods used to date for the isolation of DNA from polyacrylamide gels are elution based, time-consuming and with low yield in DNA. This paper describes an improved system employing polyacrylamide gels made of a meltable matrix. The new system was successfully applied to in situ DNA footprinting

  9. Improved recovery of DNA from polyacrylamide gels after in situ DNA footprinting

    NARCIS (Netherlands)

    van Keulen, G; Meijer, WG

    2003-01-01

    Methods used to date for the isolation of DNA from polyacrylamide gels are elution based, time-consuming and with low yield in DNA. This paper describes an improved system employing polyacrylamide gels made of a meltable matrix. The new system was successfully applied to in situ DNA footprinting fol

  10. 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.

  11. 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.

  12. 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.

  13. DNA gel electrophoresis: the reptation model(s).

    Science.gov (United States)

    Slater, Gary W

    2009-06-01

    DNA gel electrophoresis has been the most important experimental tool to separate DNA fragments for several decades. The introduction of PFGE in the 1980s and capillary gel electrophoresis in the 1990s made it possible to study, map and sequence entire genomes. Explaining how very large DNA molecules move in a gel and why PFGE is needed to separate them has been an active field of research ever since the launch of the journal Electrophoresis. This article presents a personal and historical overview of the development of the theory of gel electrophoresis, focusing on the reptation model, the band broadening mechanisms, and finally the factors that limit the read length and the resolution of electrophoresis-based sequencing systems. I conclude with a short discussion of some of the questions that remain unanswered.

  14. A proteomics strategy to discover beta-glucosidases from Aspergillus fumigatus with two-dimensional page in-gel activity assay and tandem mass spectrometry.

    Science.gov (United States)

    Kim, Kee-Hong; Brown, Kimberly M; Harris, Paul V; Langston, James A; Cherry, Joel R

    2007-12-01

    Economically competitive production of ethanol from lignocellulosic biomass by enzymatic hydrolysis and fermentation is currently limited, in part, by the relatively high cost and low efficiency of the enzymes required to hydrolyze cellulose to fermentable sugars. Discovery of novel cellulases with greater activity could be a critical step in overcoming this cost barrier. beta-Glucosidase catalyzes the final step in conversion of glucose polymers to glucose. Despite the importance, only a few beta-glucosidases are commercially available, and more efficient ones are clearly needed. We developed a proteomics strategy aiming to discover beta-glucosidases present in the secreted proteome of the cellulose-degrading fungus Aspergillus fumigatus. With the use of partial or complete protein denaturing conditions, the secretory proteome was fractionated in a 2DGE format and beta-glucosidase activity was detected in the gel after infusion with a substrate analogue that fluoresces upon hydrolysis. Fluorescing spots were subjected to tryptic-digestion, and identification as beta-glucosidases was confirmed by tandem mass spectrometry. Two novel beta-glucosidases of A. fumigatus were identified by this in situ activity staining method, and the gene coding for a novel beta-glucosidase ( EAL88289 ) was cloned and heterologously expressed. The expressed beta-glucosidase showed far superior heat stability to the previously characterized beta-glucosidases of Aspergillus niger and Aspergillus oryzae. Improved heat stability is important for development of the next generation of saccharifying enzymes capable of performing fast cellulose hydrolysis reactions at elevated temperatures, thereby lowering the cost of bioethanol production. The in situ activity staining approach described here would be a useful tool for cataloguing and assessing the efficiency of beta-glucosidases in a high throughput fashion.

  15. 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.

  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. Rapid DNA sequencing by horizontal ultrathin gel electrophoresis.

    Science.gov (United States)

    Brumley, R L; Smith, L M

    1991-01-01

    A horizontal polyacrylamide gel electrophoresis apparatus has been developed that decreases the time required to separate the DNA fragments produced in enzymatic sequencing reactions. The configuration of this apparatus and the use of circulating coolant directly under the glass plates result in heat exchange that is approximately nine times more efficient than passive thermal transfer methods commonly used. Bubble-free gels as thin as 25 microns can be routinely cast on this device. The application to these ultrathin gels of electric fields up to 250 volts/cm permits the rapid separation of multiple DNA sequencing reactions in parallel. When used in conjunction with 32P-based autoradiography, the DNA bands appear substantially sharper than those obtained in conventional electrophoresis. This increased sharpness permits shorter autoradiographic exposure times and longer sequence reads. Images PMID:1870968

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  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. 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.

  6. Cloning of DNA fragments: ligation reactions in agarose gel.

    Science.gov (United States)

    Furtado, Agnelo

    2014-01-01

    Ligation reactions to ligate a desired DNA fragment into a vector can be challenging to beginners and especially if the amount of the insert is limiting. Although additives known as crowding agents, such as PEG 8000, added to the ligation mixes can increase the success one has with ligation reactions, in practice the amount of insert used in the ligation can determine the success or the failure of the ligation reaction. The method described here, which uses insert DNA in gel slice added directly into the ligation reaction, has two benefits: (a) using agarose as the crowding agent and (b) reducing steps of insert purification. The use of rapid ligation buffer and incubation of the ligation reaction at room temperature greatly increase the efficiency of the ligation reaction even for blunt-ended ligation.

  7. Scalable lithography from Natural DNA Patterns via polyacrylamide gel

    Science.gov (United States)

    Qu, Jiehao; Hou, Xianliang; Fan, Wanchao; Xi, Guanghui; Diao, Hongyan; Liu, Xiangdon

    2015-12-01

    A facile strategy for fabricating scalable stamps has been developed using cross-linked polyacrylamide gel (PAMG) that controllably and precisely shrinks and swells with water content. Aligned patterns of natural DNA molecules were prepared by evaporative self-assembly on a PMMA substrate, and were transferred to unsaturated polyester resin (UPR) to form a negative replica. The negative was used to pattern the linear structures onto the surface of water-swollen PAMG, and the pattern sizes on the PAMG stamp were customized by adjusting the water content of the PAMG. As a result, consistent reproduction of DNA patterns could be achieved with feature sizes that can be controlled over the range of 40%-200% of the original pattern dimensions. This methodology is novel and may pave a new avenue for manufacturing stamp-based functional nanostructures in a simple and cost-effective manner on a large scale.

  8. A zinc(II)-based two-dimensional MOF for sensitive and selective sensing of HIV-1 ds-DNA sequences

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Hai-Qing; Qiu, Gui-Hua; Liang, Zhen [Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515 (China); Li, Min-Min [The First Affiliated Hospital of Jinan University, Guangzhou 510515 (China); Sun, Bin; Qin, Liang; Yang, Shui-Ping; Chen, Wen-Hua [Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515 (China); Chen, Jin-Xiang, E-mail: jxchen@smu.edu.cn [Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515 (China)

    2016-05-30

    Coordination reaction of a known three-dimensional (3D) polymer precursor {Na_3[Na_9(Cbdcp)_6(H_2O)_1_8]}{sub n} (A, Cbdcp = N-(4-carboxybenzyl)-(3,5-dicarboxyl)pyridinium) with Zn(NO{sub 3}){sub 2}·6H{sub 2}O in H{sub 2}O or H{sub 2}O/DMF at 100 °C and in the presence of aspirin, 5-fluorouracil (5-FU) as modulators, trans-1,2-bis(4-pyridyl)ethylene (bpe) or 1,2-bis(4-pyridyl)ethane (bpea) as ancillary ligands afforded six novel Zn(II)-based metal-organic frameworks (MOFs), that is, {[Zn(Cbdcp)(H_2O)_3]·H_2O}{sub n} (1, 1D zigzag chain), {[Zn(HCbdcp)_2]·H_2O}{sub n} (2, 2D sheet), {[Zn(Cbdcp)(bpe)_1_/_2]·2H_2O}{sub n} (3, 3D polymer), {[Zn(Cbdcp)(bpe)_1_/_2]·2H_2O}{sub n} (4, 2D network), {[Zn(Cbdcp)(bpea)_1_/_2]·2H_2O}{sub n} (5, 3D polymer) and {[Zn(Cbdcp)(bpea)_1_/_2]·2H_2O}{sub n} (6, 2D network). Among them, compound 2 contains aromatic rings, positively charged pyridinium, Zn{sup 2+} cation centers and carboxylic acid groups lined up on the 2D sheet structure with a certain extended surface exposure. The unique structure of 2 facilitates effective association with carboxyfluorescein (FAM) labeled probe single stranded DNA (probe ss-DNA, delineates as P-DNA) to yield a P-DNA@2 system, and leads to fluorescence quenching of FAM via a photoinduced electron transfer process. The P-DNA@2 system is effective and reliable for the detection of human immunodeficiency virus 1 ds-DNA (HIV ds-DNA) sequences and capable of distinguishing complementary HIV ds-DNA from mismatched target sequences with the detection limit as low as 10 pM (S/N = 3). - Graphical abstract: Six water-stable zinc(II) zwitterionic carboxylate compounds with 1D chain, 2D and 3D networks were synthesized. Compound 2 can interact with the probe DNA through noncovalent bonds to form P-DNA@2 system. This system can be used as an effective, fluorescent sensing platform for the detection of HIV ds-DNA with the detection limit as low as 10 pM. - Highlights: • Six water-stable zinc

  9. 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.

  10. MSH2 and MLH1 mutations in sporadic replication error-positive colorectal carcinoma as assessed by two-dimensional DNA electrophoresis

    NARCIS (Netherlands)

    Wu, Y; NystromLahti, M; Osinga, J; Looman, MWG; Peltomaki, P; Aaltonen, LA; delaChapelle, A; Hofstra, RMW; Buys, CHCM

    1997-01-01

    Replication errors (RER) are frequently seen in both sporadic and hereditary forms of colorectal cancer. In hereditary nonpolyposis colorectal cancer (HNPCC), RER is associated with defects in DNA mismatch repair genes. Two of these genes, MSH2 and MLH1, account for a major share of this cancer synd

  11. Surveying and benchmarking techniques to analyse DNA gel fingerprint images.

    Science.gov (United States)

    Heras, Jónathan; Domínguez, César; Mata, Eloy; Pascual, Vico

    2016-11-01

    DNA fingerprinting is a genetic typing technique that allows the analysis of the genomic relatedness between samples, and the comparison of DNA patterns. The analysis of DNA gel fingerprint images usually consists of five consecutive steps: image pre-processing, lane segmentation, band detection, normalization and fingerprint comparison. In this article, we firstly survey the main methods that have been applied in the literature in each of these stages. Secondly, we focus on lane-segmentation and band-detection algorithms-as they are the steps that usually require user-intervention-and detect the seven core algorithms used for both tasks. Subsequently, we present a benchmark that includes a data set of images, the gold standards associated with those images and the tools to measure the performance of lane-segmentation and band-detection algorithms. Finally, we implement the core algorithms used both for lane segmentation and band detection, and evaluate their performance using our benchmark. As a conclusion of that study, we obtain that the average profile algorithm is the best starting point for lane segmentation and band detection.

  12. 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...

  13. 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.

  14. A Quick, Cost-Free Method of Purification of DNA Fragments from Agarose Gel

    Directory of Open Access Journals (Sweden)

    Yuan Sun, Kannappan Sriramajayam, Dianzhong Luo, D. Joshua Liao

    2012-01-01

    Full Text Available In this short communication we report a quick, cost-free method of purification of DNA fragments from agarose gel. Unlike those procedures that involve commercial kits, this method uses glass wool or absorbent cotton to filter agarose gel during a quick spinning-down of DNA, thus significantly simplifying the routine practice of many molecular biologists and decreasing the cost.

  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. 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.

  18. 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...

  19. 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.

  20. Automatic DNA Diagnosis for 1D Gel Electrophoresis Images using Bio-image Processing Technique.

    Science.gov (United States)

    Intarapanich, Apichart; Kaewkamnerd, Saowaluck; Shaw, Philip J; Ukosakit, Kittipat; Tragoonrung, Somvong; Tongsima, Sissades

    2015-01-01

    DNA gel electrophoresis is a molecular biology technique for separating different sizes of DNA fragments. Applications of DNA gel electrophoresis include DNA fingerprinting (genetic diagnosis), size estimation of DNA, and DNA separation for Southern blotting. Accurate interpretation of DNA banding patterns from electrophoretic images can be laborious and error prone when a large number of bands are interrogated manually. Although many bio-imaging techniques have been proposed, none of them can fully automate the typing of DNA owing to the complexities of migration patterns typically obtained. We developed an image-processing tool that automatically calls genotypes from DNA gel electrophoresis images. The image processing workflow comprises three main steps: 1) lane segmentation, 2) extraction of DNA bands and 3) band genotyping classification. The tool was originally intended to facilitate large-scale genotyping analysis of sugarcane cultivars. We tested the proposed tool on 10 gel images (433 cultivars) obtained from polyacrylamide gel electrophoresis (PAGE) of PCR amplicons for detecting intron length polymorphisms (ILP) on one locus of the sugarcanes. These gel images demonstrated many challenges in automated lane/band segmentation in image processing including lane distortion, band deformity, high degree of noise in the background, and bands that are very close together (doublets). Using the proposed bio-imaging workflow, lanes and DNA bands contained within are properly segmented, even for adjacent bands with aberrant migration that cannot be separated by conventional techniques. The software, called GELect, automatically performs genotype calling on each lane by comparing with an all-banding reference, which was created by clustering the existing bands into the non-redundant set of reference bands. The automated genotype calling results were verified by independent manual typing by molecular biologists. This work presents an automated genotyping tool from DNA

  1. Reconstruction of central carbon metabolism in Sulfolobus solfataricus using a two-dimensional gel electrophoresis map, stable isotope labelling and DNA microarray analysis

    NARCIS (Netherlands)

    Snijders, B.P.L.; Walther, J.; Peter, S.; Kinnman, I.; Vos, de M.J.G.; Werken, van de H.J.G.; Brouns, S.J.J.; Oost, van der J.; Wright, P.C.

    2006-01-01

    In the last decade, an increasing number of sequenced archaeal genomes have become available, opening up the possibility for functional genomic analyses. Here, we reconstructed the central carbon metabolism in the hyperthermophilic crenarchaeon Sulfolobus solfataricus (glycolysis, gluconeogenesis an

  2. Reconstruction of central carbon metabolism in Sulfolobus solfataricus using a two-dimensional gel electrophoresis map, stable isotope labelling and DNA microarray analysis

    NARCIS (Netherlands)

    Snijders, B.P.L.; Walther, J.; Peter, S.; Kinnman, I.; Vos, de M.J.G.; Werken, van de H.J.G.; Brouns, S.J.J.; Oost, van der J.; Wright, P.C.

    2006-01-01

    In the last decade, an increasing number of sequenced archaeal genomes have become available, opening up the possibility for functional genomic analyses. Here, we reconstructed the central carbon metabolism in the hyperthermophilic crenarchaeon Sulfolobus solfataricus (glycolysis, gluconeogenesis

  3. LINKAGE ANALYSIS BY 2-DIMENSIONAL DNA TYPING

    NARCIS (Netherlands)

    MEERMAN, GJT; MULLAART, E; VANDERMEULEN, MA; DENDAAS, JHG; MOROLLI, B; UITTERLINDEN, AG; 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

  4. 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.

  5. 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.

  6. 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.

  7. DNA recovery from agarose gels with a simple centrifuge-driven sephadex filtration

    Institute of Scientific and Technical Information of China (English)

    Niu Chen; Li Yun

    2006-01-01

    Conventional methods of DNA recovery from agarose gel generally require expensive equipment, extended elution times,or considerable handling of the sample after elution. We developed a simple protocol for a quick and effective recovery of DNA from agarose gels with good yield and quality. Using a Sephadex resin filled spin column, DNA fragments of 500 bp to 6 kb in an agarose gel slice were easily recovered by a 2 min centrifugation. The recovery efficiencies were over 40%-50% and the eluted DNA can be used directly for downstream application, such as polymerase chain reactions (PCR) and restriction enzyme digestion. This method could also be used to recover large DNA fragment (48 kb) without degradation. The use of Sephadex helps to remove small molecular impurities from agarose and it also reduces the chance of clogging the column filter caused by direct contact with agarose.

  8. 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.

  9. Improved high-throughput DNA fragment analyzer employing horizontal ultrathin gel electrophoresis

    Science.gov (United States)

    Brumley, Robert L., Jr.; Luckey, John A.

    1996-04-01

    We are currently developing a significantly improved gel electrophoresis and detection system that will allow more than an order of magnitude enhancement in the speed of DNA fragment analysis. This system is based upon the technique of horizontal ultrathin gel electrophoresis (HUGE) which employs denaturing polyacrylamide gels that are 75 microns thick. Because of the thinness of the gel, very high electric field strengths may be applied without deleterious thermal effects on resolution. Our proprietary fluorescence detector that scans the gel during electrophoresis allows for the simultaneous detection of up to four fluorophores. Because of the efficiency of the system of light collection, the gel can be scanned at speeds fast enough to generate high resolution gel images despite the high speed of separations. In addition, we are able to increase sample density by collecting 500 datapoints across the width of the gel. The resulting instrument has the capability to separate and resolve single-stranded DNA molecules that are between 25 and 300 bases in length from each of 60 lanes in less than 45 minutes. With the advent of 96 lane gels and attendant automation, this instrument will have the ability to analyze 18,432 genotypes per day.

  10. Development of bufferless gel electrophoresis chip for easy preparation and rapid DNA separation.

    Science.gov (United States)

    Oleksandrov, Sergiy; Aman, Abdurazak; Lim, Wanyoung; Kim, Younghee; Bae, Nam Ho; Lee, Kyoung G; Lee, Seok Jae; Park, Sungsu

    2017-09-27

    This work presents a handy, fast, and compact bufferless gel electrophoresis chip (BGEC), which consists of precast agarose gel confined in a disposable plastic body with electrodes. It does not require large volumes of buffer to fill reservoirs, or the process of immersing the gel in the buffer. It withstands voltages up to 28.4 V/cm, thereby allowing DNA separation within 10 minutes with a similar separation capability to the standard gel electrophoresis. The results suggest that our BGEC is highly suitable for in situ gel electrophoresis in forensic, epidemiological settings and crime scenes where standard gel electrophoresis equipment cannot be brought in while quick results are needed. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  11. 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.

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

    Science.gov (United States)

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

    2016-09-01

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

  13. New visible and selective DNA staining method in gels with tetrazolium salts.

    Science.gov (United States)

    Paredes, Aaron J; Naranjo-Palma, Tatiana; Alfaro-Valdés, Hilda M; Barriga, Andrés; Babul, Jorge; Wilson, Christian A M

    2017-01-15

    DNA staining in gels has historically been carried out using silver staining and fluorescent dyes like ethidium bromide and SYBR Green I (SGI). Using fluorescent dyes allows recovery of the analyte, but requires instruments such as a transilluminator or fluorimeter to visualize the DNA. Here we described a new and simple method that allows DNA visualization to the naked eye by generating a colored precipitate. It works by soaking the acrylamide or agarose DNA gel in SGI and nitro blue tetrazolium (NBT) solution that, when exposed to sunlight, produces a purple insoluble formazan precipitate that remains in the gel after exposure to light. A calibration curve made with a DNA standard established a detection limit of approximately 180 pg/band at 500 bp. Selectivity of this assay was determined using different biomolecules, demonstrating a high selectivity for DNA. Integrity and functionality of the DNA recovered from gels was determined by enzymatic cutting with a restriction enzyme and by transforming competent cells after the different staining methods, respectively. Our method showed the best performance among the dyes employed. Based on its specificity, low cost and its adequacy for field work, this new methodology has enormous potential benefits to research and industry.

  14. Sequence-specific nucleic acid mobility using a reversible block copolymer gel matrix and DNA amphiphiles (lipid-DNA) in capillary and microfluidic electrophoretic separations

    NARCIS (Netherlands)

    Wagler, Patrick; Minero, Gabriel Antonio S.; Tangen, Uwe; de Vries, Jan Willem; Prusty, Deepak; Kwak, Minseok; Herrmann, Andreas; McCaskill, John S.

    2015-01-01

    Reversible noncovalent but sequence-dependent attachment of DNA to gels is shown to allow programmable mobility processing of DNA populations. The covalent attachment of DNA oligomers to polyacrylamide gels using acrydite-modified oligonucleotides has enabled sequence-specific mobility assays for

  15. Sequence-specific nucleic acid mobility using a reversible block copolymer gel matrix and DNA amphiphiles (lipid-DNA) in capillary and microfluidic electrophoretic separations

    NARCIS (Netherlands)

    Wagler, Patrick; Minero, Gabriel Antonio S.; Tangen, Uwe; de Vries, Jan Willem; Prusty, Deepak; Kwak, Minseok; Herrmann, Andreas; McCaskill, John S.

    2015-01-01

    Reversible noncovalent but sequence-dependent attachment of DNA to gels is shown to allow programmable mobility processing of DNA populations. The covalent attachment of DNA oligomers to polyacrylamide gels using acrydite-modified oligonucleotides has enabled sequence-specific mobility assays for DN

  16. 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.

  17. 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.

  18. A CCD-based system for the detection of DNA in electrophoresis gels by UV absorption

    Science.gov (United States)

    Mahon, Alex R.; MacDonald, John H.; Ott, Robert J.; Mainwood, Alison

    1999-06-01

    A method and apparatus for the detection and quantification of large fragments of unlabelled nucleic acids in agarose gels is presented. The technique is based on ultraviolet (UV) absorption by nucleotides. A deuterium source illuminates individual sample lanes of an electrophoresis gel via an array of optical fibres. As DNA bands pass through the illuminated region of the gel the amount of UV light transmitted is reduced because of absorption by the DNA. During electrophoresis the regions of DNA are detected on-line using a UV-sensitive charge coupled device (CCD). As the absorption coefficient is proportional to the mass of DNA the technique is inherently quantitative. The mass of DNA in a region of the gel is approximately proportional to the integrated signal in the corresponding section of the CCD image. This system currently has a detection limit of less than 1.25 ng compared with 2-10 ng for the most popular conventional technique, ethidium bromide (EtBr) staining. In addition the DNA sample remains in its native state. The removal of the carcinogenic dye from the detection procedure greatly reduces associated biological hazards.

  19. Using in situ rheology to characterize the microstructure in photopolymerized polyacrylamide gels for DNA electrophoresis.

    Science.gov (United States)

    Wang, Jian; Ugaz, Victor M

    2006-09-01

    Photopolymerized cross-linked polyacrylamide hydrogels are attractive sieving matrix formulations for DNA electrophoresis owing to their rapid polymerization times and the potential to locally tailor the gel pore structure through spatial variation of illumination intensity. This capability is especially important in microfluidic systems, where photopolymerization allows gel matrices to be precisely positioned within complex microchannel networks. Separation performance is also directly related to the nanoscale gel pore structure, which is in turn strongly influenced by polymerization kinetics. Unfortunately, detailed studies of the interplay among polymerization kinetics, mechanical properties, and structural morphology are lacking in photopolymerized hydrogel systems. In this paper, we address this issue by performing a series of in situ dynamic small-amplitude oscillatory shear measurements during photopolymerization of cross-linked polyacrylamide electrophoresis gels to investigate the relationship between rheology and parameters associated with the gelation environment including UV intensity, monomer and cross-linker composition, and reaction temperature. In general, we find that the storage modulus G' increases with increasing initial monomer concentration, cross-linker concentration, and polymerization temperature. The steady-state value of G', however, exhibits a more complex dependence on UV intensity that varies with gel concentration. A simple model based on rubber elasticity theory is used to obtain estimates of the average gel pore size that are in surprisingly good agreement with corresponding data obtained from analysis of DNA electrophoretic mobility in gels cast under identical polymerization conditions.

  20. The influence of ionic strength on DNA diffusion in gel networks

    Science.gov (United States)

    Fu, Yuanxi; Jee, Ah-Young; Kim, Hyeong-Ju; Granick, Steve

    Cations are known to reduce the rigidity of the DNA molecules by screening the negative charge along the sugar phosphate backbone. This was established by optical tweezer pulling experiment of immobilized DNA strands. However, little is known regarding the influence of ions on the motion of DNA molecules as they thread through network meshes. We imaged in real time the Brownian diffusion of fluorescent labeled lambda-DNA in an agarose gel network in the presence of salt with monovalent or multivalent cations. Each movie was analyzed using home-written program to yield a trajectory of center of the mass and the accompanying history of the shape fluctuations. One preliminary finding is that ionic strength has a profound influence on the slope of the trace of mean square displacement (MSD) versus time. The influence of ionic strength on DNA diffusion in gel networks.

  1. Recovery of DNA from Agarose Gel with Home-made Silica Milk

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    An usefulness of silica milk made with waste ultraviolet light tube for recovery of DNA fragment from agarose gel was represented. The glass milk is a water suspension of 50% fine silica powder prepared by grinding the crushed waste ultraviolet light tube with a porcelain mortar.It was showed that one microliter of the glass milk could bind more than 1 μg of DNA fragment,and DNA fragment in length from 125 bp to 23 kb could be efficiently recovered from agarose gel. The bound DNA could be eluted from the particle of SiO2 in the glass milk with a yield of about 60%-80%.The eluted DNA could be used in all manipulations in molecular cloning.

  2. Electrokinetic injection of DNA from gel micropads: basis for coupling polony technology with CE separation.

    Science.gov (United States)

    Kosobokova, Olga; Gavrilov, Dmitri N; Khozikov, Vyacheslav; Stepukhovich, Andrey; Tsupryk, Andriy; Pan'kov, Sergey; Somova, Olga; Abanshin, Nikolai; Gudkov, Georgiy; Tcherevishnik, Marina; Gorfinkel, Vera

    2007-11-01

    We propose a novel method for electrokinetic injection of DNA samples into capillaries from nanoliter gel micropads, deposited on glass slides, which are coated with electroconducting film. Theoretical and experimental proof is presented for the proposed method. The method allows efficient and highly precise injection without physical contact between the gel pad and the capillary. Read length of more than 700 bp at Q20 has been reproducibly demonstrated in fused-silica capillaries using the proposed injection technique. Based on the obtained results we discuss a novel DNA sequencing system which combines DNA amplification and cycle sequencing in arrays of subnanoliter gel micropads and high-throughput electrophoretic separation in monolith multicapillary arrays.

  3. 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.

  4. Scalable lithography from Natural DNA Patterns via polyacrylamide gel

    National Research Council Canada - National Science Library

    Qu, JieHao; Hou, XianLiang; Fan, WanChao; Xi, GuangHui; Diao, HongYan; Liu, XiangDon

    2015-01-01

    ...) that controllably and precisely shrinks and swells with water content. Aligned patterns of natural DNA molecules were prepared by evaporative self-assembly on a PMMA substrate, and were transferred to unsaturated polyester resin (UPR...

  5. Optimization of separation and detection schemes for DNA with pulsed field slab gel and capillary electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    McGregor, David A. [Iowa State Univ., Ames, IA (United States)

    1993-07-01

    The purpose of the Human Genome Project is outlined followed by a discussion of electrophoresis in slab gels and capillaries and its application to deoxyribonucleic acid (DNA). Techniques used to modify electroosmotic flow in capillaries are addressed. Several separation and detection schemes for DNA via gel and capillary electrophoresis are described. Emphasis is placed on the elucidation of DNA fragment size in real time and shortening separation times to approximate real time monitoring. The migration of DNA fragment bands through a slab gel can be monitored by UV absorption at 254 nm and imaged by a charge coupled device (CCD) camera. Background correction and immediate viewing of band positions to interactively change the field program in pulsed-field gel electrophoresis are possible throughout the separation. The use of absorption removes the need for staining or radioisotope labeling thereby simplifying sample preparation and reducing hazardous waste generation. This leaves the DNA in its native state and further analysis can be performed without de-staining. The optimization of several parameters considerably reduces total analysis time. DNA from 2 kb to 850 kb can be separated in 3 hours on a 7 cm gel with interactive control of the pulse time, which is 10 times faster than the use of a constant field program. The separation of ΦX174RF DNA-HaeIII fragments is studied in a 0.5% methyl cellulose polymer solution as a function of temperature and applied voltage. The migration times decreased with both increasing temperature and increasing field strength, as expected. The relative migration rates of the fragments do not change with temperature but are affected by the applied field. Conditions were established for the separation of the 271/281 bp fragments, even without the addition of intercalating agents. At 700 V/cm and 20°C, all fragments are separated in less than 4 minutes with an average plate number of 2.5 million per meter.

  6. 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

  7. 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....

  8. Trapping and breaking of in vivo nicked DNA during pulsed field gel electrophoresis.

    Science.gov (United States)

    Khan, Sharik R; Kuzminov, Andrei

    2013-12-15

    Pulsed field gel electrophoresis (PFGE) offers a high-resolution approach to quantify chromosomal fragmentation in bacteria, measured as percentage of chromosomal DNA entering the gel. The degree of separation in pulsed field gel (PFG) depends on the size of DNA as well as various conditions of electrophoresis such as electric field strength, time of electrophoresis, switch time, and buffer composition. Here we describe a new parameter, the structural integrity of the sample DNA itself, that influences its migration through PFGs. We show that subchromosomal fragments containing both spontaneous and DNA damage-induced nicks are prone to breakage during PFGE. Such breakage at single-strand interruptions results in artifactual decrease in molecular weight of linear DNA making accurate determination of the number of double-strand breaks difficult. Although breakage of nicked subchromosomal fragments is field strength independent, some high-molecular-weight subchromosomal fragments are also trapped within wells under the standard PFGE conditions. This trapping can be minimized by lowering the field strength and increasing the time of electrophoresis. We discuss how breakage of nicked DNA may be mechanistically linked to trapping. Our results suggest how to optimize conditions for PFGE when quantifying chromosomal fragmentation induced by DNA damage. Copyright © 2013 Elsevier Inc. All rights reserved.

  9. Measurement of DNA damage in individual cells using the Single Cell Gel Electrophoresis (Comet) assay.

    Science.gov (United States)

    Hartley, Janet M; Spanswick, Victoria J; Hartley, John A

    2011-01-01

    The Single Cell Gel Electrophoresis (Comet) assay is a simple, versatile and sensitive method for measuring DNA damage in individual cells, allowing the determination of heterogeneity of response within a cell population. The basic alkaline technique described is for the determination of DNA strand break damage and its repair at a single cell level. Specific modifications to the method use a lower pH ('neutral' assay), or allow the measurement of DNA interstrand cross-links. It can be further adapted to, for example, study specific DNA repair mechanisms, be combined with fluorescent in situ hybridisation, or incorporate lesion specific enzymes.

  10. Single nucleus versus single-cell gel electrophoresis: kinetics of DNA track formation.

    Science.gov (United States)

    Afanasieva, Katerina; Chopei, Marianna; Sivolob, Andrei

    2015-04-01

    Single-cell gel electrophoresis, or the comet assay, is usually performed with nucleoids prepared after a lysis of either whole cells (more often) or isolated cell nuclei (rarely). Electrophoretic properties of the second type of nucleoids have never been investigated carefully. We measured the kinetics of the DNA exit from nuclei-derived nucleoids in comparison with cell-derived nucleoids. The results show that general organization of the nuclei-derived nucleoids is not changed very much in comparison with nucleoids commonly obtained from whole cells. At the same time, in contrast to the cell-derived nucleoids, for which the exit is stepwise and cooperative, the DNA exit from the nuclei-derived nucleoids can be described by a simple monomolecular kinetics. This difference is probably due to agarose penetration into nuclei (but not into cells) before polymerization of the agarose gel. We suggest that single-nucleus gel electrophoresis may be a way for the comet assay standardization.

  11. Gel electrophoresis of DNA partially denatured at the ends: what are the dominant conformations?

    Science.gov (United States)

    Sean, David; Slater, Gary W

    2013-03-01

    Gel electrophoresis of a partially denatured dsDNA fragment is studied using Langevin Dynamics computer simulations. For simplicity, the denatured ssDNA sections are placed at the ends of the fragment in a symmetrical fashion. A squid-like conformation is found to sometimes cause the fragment to completely block in the gel. In fact, this conformation is the principal cause of the steep reduction in mobility observed in the simulations. As the field is increased, it is found that the occurrence of this conformation dominates the migration dynamics. Although the squid conformation seems to be more stable at high fields, the field can eventually force the fragments to thread through the gel pores regardless. We qualitatively explore the behavior of this squid-like conformation across a range of fields and degrees of denaturation, and we discuss the relevance of our findings for TGGE. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. 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.

  13. 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.

  14. 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.

  15. Technical report. Video imaging of ethidium bromide-stained DNA gels with surface UV illumination.

    Science.gov (United States)

    Solioz, M

    1994-06-01

    We describe here the use of surface UV illumination to record ethidium bromide-stained DNA gels with a video camera. This mode of illumination allows the use of a standard video camera equipped with a red filter and results in a high signal strength. The assembly of a low-cost video system on this basis is described. It uses the public domain software called Image on a Macintosh computer and PostScript laser printer or a thermal printer to generate hard copies. The setup is sensitive enough to detect 500 pg of DNA on an ethidium bromide-stained DNA gel. The UV illumination method described here can also greatly improve the sensitivity of existing video recording equipment.

  16. Trapping and breaking of in vivo nicked DNA during pulsed-field gel electrophoresis

    Science.gov (United States)

    Khan, Sharik R.; Kuzminov, Andrei

    2013-01-01

    Pulsed field gel electrophoresis (PFGE) offers a high-resolution approach to quantify chromosomal fragmentation in bacteria, measured as percent of chromosomal DNA entering the gel. The degree of separation in PFG depends upon the size of DNA, as well as various conditions of electrophoresis, such as electric field strength (FS), time of electrophoresis, switch time and buffer composition. Here we describe a new parameter, the structural integrity of the sample DNA itself, that influences its migration through PFGs. We show that sub-chromosomal fragments containing both spontaneous and DNA damage-induced nicks are prone to breakage during PFGE. Such breakage at single strand interruptions results in artefactual decrease in molecular weight of linear DNA making accurate determination of the number of double strand breaks difficult. While breakage of nicked sub-chromosomal fragments is FS-independent, some high molecular weight sub-chromosomal fragments are also trapped within wells under the standard PFGE conditions. This trapping can be minimized by lowering the field strength and increasing the time of electrophoresis. We discuss how breakage of nicked DNA may be mechanistically linked to trapping. Our results suggest how to optimize conditions for PFGE when quantifying chromosomal fragmentation induced by DNA damage. PMID:23770235

  17. 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.

  18. 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.

  19. Combining ligation reaction and capillary gel electrophoresis to obtain reliable long DNA probes.

    Science.gov (United States)

    García-Cañas, Virginia; Mondello, Monica; Cifuentes, Alejandro

    2011-05-01

    New DNA amplification methods are continuously developed for sensitive detection and quantification of specific DNA target sequences for, e.g. clinical, environmental or food applications. These new applications often require the use of long DNA oligonucleotides as probes for target sequences hybridization. Depending on the molecular technique, the length of DNA probes ranges from 40 to 450 nucleotides, solid-phase chemical synthesis being the strategy generally used for their production. However, the fidelity of chemical synthesis of DNA decreases for larger DNA probes. Defects in the oligonucleotide sequence result in the loss of hybridization efficiency, affecting the sensitivity and selectivity of the amplification method. In this work, an enzymatic procedure has been developed as an alternative to solid-phase chemical synthesis for the production of long oligonucleotides. The enzymatic procedure for probe production was based on ligation of short DNA sequences. Long DNA probes were obtained from smaller oligonucleotides together with a short sequence that acts as bridge stabilizing the molecular complex for DNA ligation. The ligation reactions were monitored by capillary gel electrophoresis with laser-induced fluorescence detection (CGE-LIF) using a bare fused-silica capillary. The capillary gel electrophoresis-LIF method demonstrated to be very useful and informative for the characterization of the ligation reaction, providing important information about the nature of some impurities, as well as for the fine optimization of the ligation conditions (i.e. ligation cycles, oligonucleotide and enzyme concentration). As a result, the yield and quality of the ligation product were highly improved. The in-lab prepared DNA probes were used in a novel multiplex ligation-dependent genome amplification (MLGA) method for the detection of genetically modified maize in samples. The great possibilities of the whole approach were demonstrated by the specific and sensitive

  20. 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.

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

    Institute of Scientific and Technical Information of China (English)

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

    2004-01-01

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

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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...

  7. Investigating DNA Migration in Pulsed Fields Using a Miniaturized Field Inversion Gel Electrophoresis System

    Science.gov (United States)

    Chen, Xiaojia; Ugaz, Victor M.

    2010-01-01

    Pulsed field gel electrophoresis (PFGE) is a well-established technique for fractionation of DNA fragments ranging from kilobases to megabases in length. But many of these separations require an undesirable combination of long experiment times (often approaching tens of hours) and application of high voltages (often approaching tens of kV). Here we present a simple miniaturized field inversion gel electrophoresis (FIGE) apparatus capable of separating DNA fragments up to 32.5 kb in length within 3 hours using a modest applied potential of 20 V. The device is small enough to be imaged under a fluorescence microscope, permitting the migrating DNA bands to be observed during the course of the separation run. We use this capability to investigate how separation performance is affected by parameters including the ratio of forward and backward voltage, pulse time, and temperature. We also characterize the dependence of DNA mobility on fragment size N, and observe a scaling in the vicinity of N−0.5 over the size range investigated. The high speed, low power consumption, and simple design of this system may help enable future studies of DNA migration in PFGE to be performed quickly and inexpensively. PMID:19053074

  8. Unhooking dynamics of U-shaped DNA molecule undergoing gel electrophoresis.

    Science.gov (United States)

    Song, L; Maestre, M F

    1991-08-01

    It has been found that DNA molecules are often hooked around obstacles in a U-shaped configuration in gel electrophoresis. To understand the dynamics of the unhooking of U-shaped DNA molecules undergoing gel electrophoresis, we have examined the length changes of the longer and shorter arms of the U-shape as a function of time. Two types of unhooking have been found. In one type, the length changes of both arms are expontential in time but with different time constants. In another type, the length changes of the shorter arm is exponential and that of the longer one is linear with time. The interpretation is that the extent of stretch of the spring-like DNA chain decreases as the length difference between the two arms increases during the unhooking processes, and that the frictions at the pivot point can be relatively large depending upon the local structure of the gel. The friction coefficient at the pivot point is estimated to be nu 0 = (2.98 +/- 1.42)x10(-5) g/sec.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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

  15. 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

  16. 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...

  17. 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

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

    NARCIS (Netherlands)

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

    1996-01-01

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

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

    NARCIS (Netherlands)

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

    1996-01-01

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

  20. Utilization of DNA as functional materials: preparation of filters containing DNA insolubilized with alginic acid gel.

    Science.gov (United States)

    Iwata, K; Sawadaishi, T; Nishimura, S I; Tokura, S; Nishi, N

    1996-02-01

    Thin films composed of DNA and alginic acid were prepared by casting their mixed solution on glass plate followed by coagulation with aqueous solution of calcium chloride. DNA could be conveniently insolubilized by this method. DNA in the films adsorbed intercalating materials, such as ethidium bromide. This phenomenon was successfully applied to the preparation of filters for the selective removal or accumulation of harmful intercalating pollutants.

  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. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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....

  11. 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.

  12. 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.

  13. 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.

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

    Science.gov (United States)

    Duke, Thomas; Viovy, Jean Louis

    1994-03-01

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

  15. Genetic profiling of Klebsiella pneumoniae: comparison of pulsed field gel electrophoresis and random amplified polymorphic DNA

    Science.gov (United States)

    Ashayeri-Panah, Mitra; Eftekhar, Fereshteh; Ghamsari, Maryam Mobarak; Parvin, Mahmood; Feizabadi, Mohammad Mehdi

    2013-01-01

    In this study, the discriminatory power of pulsed field gel electrophoresis (PFGE) and random amplified polymorphic DNA (RAPD) methods for subtyping of 54 clinical isolates of Klebsiella pneumoniae were compared. All isolates were typeable by RAPD, while 3.6% of them were not typeable by PFGE. The repeatability of both typing methods were 100% with satisfying reproducibility (≥ 95%). Although the discriminatory power of PFGE was greater than RAPD, both methods showed sufficient discriminatory power (DI > 0.95) which reflects the heterogeneity among the K. pneumoniae isolates. An optimized RAPD protocol is less technically demanding and time consuming that makes it a reliable typing method and competitive with PFGE. PMID:24516423

  16. Determination of DNA methylation by COBRA: a comparative study of CGE with LIF detection and conventional gel electrophoresis.

    Science.gov (United States)

    Goedecke, Simon; Schlosser, Sabrina; Mühlisch, Jörg; Hempel, Georg; Frühwald, Michael C; Wünsch, Bernhard

    2009-09-01

    DNA methylation as an epigenetic modification of the human genome is under emphatic investigation. Several studies have demonstrated a role of DNA methylation in oncogenesis. In conjunction with histone modifications, DNA methylation may cause the formation of heterochromatin and thus mediate the inactivation of gene transcription. It is important to develop methods that allow for an accurate quantification of the amount of DNA methylation in particular DNA regions, to gain information concerning the threshold of methylation levels necessary for gene inactivation. In this article, a CGE method with on-column LIF detection using SYBR Green is compared with a conventional slab-gel electrophoresis. We thus investigate the validity to analyze DNA methylation in the samples of a combined bisulfite restriction analysis. It is demonstrated that CGE is superior to gel electrophoresis in means of linearity, precision, accuracy, automatization (high throughput), and sample consumption. However, gel electrophoresis is easier to perform (simple devices, no PC usage), and the running costs are comparatively low. A further advantage of CGE is the sparse use of toxic compounds (MeOH and SYBR Green), whereas gel electrophoresis is performed in polyacrylamide gels with ethidium bromide staining.

  17. 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.

  18. Faster, safer, and better DNA purification by ultracentrifugation using GelRed stain and development of mismatch oligo DNA for genome walking.

    Science.gov (United States)

    Kasajima, Ichiro; Ohtsubo, Norihiro; Sasaki, Katsutomo

    2014-01-01

    Purification of plant DNA involves lengthy ultracentrifugation using ethidium bromide. Here, ultracentrifugation method is improved by staining with GelRed. The resulting method is faster, safer and of higher sensitivity. Purified DNA quality was confirmed by treatment with restriction enzymes and isolation of gene promoters. New type of long adaptor with mismatch sequence was also developed for promoter isolation.

  19. Weakly disordered two-dimensional Frenkel excitons

    Science.gov (United States)

    Boukahil, A.; Zettili, Nouredine

    2004-03-01

    We report the results of studies of the optical properties of weakly disordered two- dimensional Frenkel excitons in the Coherent Potential Approximation (CPA). An approximate complex Green's function for a square lattice with nearest neighbor interactions is used in the self-consistent equation to determine the coherent potential. It is shown that the Density of States is very much affected by the logarithmic singularities in the Green's function. Our CPA results are in excellent agreement with previous investigations by Schreiber and Toyozawa using the Monte Carlo simulation.

  20. 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.

  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. Two-dimensional ranking of Wikipedia articles

    CERN Document Server

    Zhirov, A O; Shepelyansky, D L

    2010-01-01

    The Library of Babel, described by Jorge Luis Borges, stores an enormous amount of information. The Library exists {\\it 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. 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. 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.

  4. Sums of two-dimensional spectral triples

    DEFF Research Database (Denmark)

    Christensen, Erik; Ivan, Cristina

    2007-01-01

    construct a sum of two dimensional modules which reflects some aspects of the topological dimensions of the compact metric space, but this will only give the metric back approximately. At the end we make an explicit computation of the last module for the unit interval in. The metric is recovered exactly......, the Dixmier trace induces a multiple of the Lebesgue integral but the growth of the number of eigenvalues is different from the one found for the standard differential operator on the unit interval....

  5. 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....

  6. Dynamics of film. [two dimensional continua theory

    Science.gov (United States)

    Zak, M.

    1979-01-01

    The general theory of films as two-dimensional continua are elaborated upon. As physical realizations of such a model this paper examines: inextensible films, elastic films, and nets. The suggested dynamic equations have enabled us to find out the characteristic speeds of wave propagation of the invariants of external and internal geometry and formulate the criteria of instability of their shape. Also included herein is a detailed account of the equation describing the film motions beyond the limits of the shape stability accompanied by the formation of wrinkles. The theory is illustrated by examples.

  7. DNA-poly(vinyl alcohol) gel matrices: release properties are strongly dependent on electrolytes and cationic surfactants.

    Science.gov (United States)

    Valente, Artur J M; Cruz, Sandra M A; Murtinho, Dina M B; Miguel, M Graça; Muniz, Edvani C

    2013-01-01

    The release of DNA from cryogel PVA-DNA gel matrices to different electrolyte aqueous solutions was investigated. The rate of release and the distribution coefficient of DNA have been quantified by using a first order kinetic law equation, developed in the frame of a partition-based model. The release of DNA from gels to 1:1 sodium and nitrate salts shows that the transport properties are dependent on the ability of anions/cations to solubilise the DNA in the aqueous phase which, with the exception of bromide, can be related to the Hofmeister series; in the presence of multivalent electrolytes, or increasing the ionic strength, the condensation of DNA inside the gel, followed by a phase separation as seen by scanning electron microscopy, induces the retention of DNA inside the polymer matrix. The DNA condensation and/or phase separation, which contribute to a decrease in the water volume fraction inside the gel, determined by swelling degree experiments, also lead to a decrease in the rate constant of DNA release; such decrease can be justified by the difficulty of the molecular aggregate to move through out the polymeric structure. The DNA release is also dependent on the pH of the bulk solution. The effect of uni- and di-valent cationic surfactants on the release properties of DNA was also evaluated. Our findings suggest that the kinetics of DNA release depends on a complex balance between different structural properties of the surfactants, namely charge, bulkiness of the headgroup and alkyl chain length.

  8. Two-dimensional gauge theoretic supergravities

    Science.gov (United States)

    Cangemi, D.; Leblanc, M.

    1994-05-01

    We investigate two-dimensional supergravity theories, which can be built from a topological and gauge invariant action defined on an ordinary surface. One is the N = 1 supersymmetric extension of the Jackiw-Teitelboim model presented by Chamseddine in a superspace formalism. We complement the proof of Montano, Aoaki and Sonnenschein that this extension is topological and gauge invariant, based on the graded de Sitter algebra. Not only do the equations of motion correspond to the supergravity ones and do gauge transformations encompass local supersymmetries, but we also identify the ∫-theory with the superfield formalism action written by Chamseddine. Next, we show that the N = 1 supersymmetric extension of string-inspired two-dimensional dilaton gravity put forward by Park and Strominger cannot be written as a ∫-theory. As an alternative, we propose two topological and gauge theories that are based on a graded extension of the extended Poincaré algebra and satisfy a vanishing-curvature condition. Both models are supersymmetric extensions of the string-inspired dilaton gravity.

  9. Two-Dimensional Theory of Scientific Representation

    Directory of Open Access Journals (Sweden)

    A Yaghmaie

    2013-03-01

    Full Text Available Scientific representation is an interesting topic for philosophers of science, many of whom have recently explored it from different points of view. There are currently two competing approaches to the issue: cognitive and non-cognitive, and each of them claims its own merits over the other. This article tries to provide a hybrid theory of scientific representation, called Two-Dimensional Theory of Scientific Representation, which has the merits of the two accounts and is free of their shortcomings. To do this, we will argue that although scientific representation needs to use the notion of intentionality, such a notion is defined and realized in a simply structural form contrary to what cognitive approach says about intentionality. After a short introduction, the second part of the paper is devoted to introducing theories of scientific representation briefly. In the third part, the structural accounts of representation will be criticized. The next step is to introduce the two-dimensional theory which involves two key components: fixing and structural fitness. It will be argued that fitness is an objective and non-intentional relation, while fixing is intentional.

  10. Two-dimensional shape memory graphene oxide

    Science.gov (United States)

    Chang, Zhenyue; Deng, Junkai; Chandrakumara, Ganaka G.; Yan, Wenyi; Liu, Jefferson Zhe

    2016-06-01

    Driven by the increasing demand for micro-/nano-technologies, stimuli-responsive shape memory materials at nanoscale have recently attracted great research interests. However, by reducing the size of conventional shape memory materials down to approximately nanometre range, the shape memory effect diminishes. Here, using density functional theory calculations, we report the discovery of a shape memory effect in a two-dimensional atomically thin graphene oxide crystal with ordered epoxy groups, namely C8O. A maximum recoverable strain of 14.5% is achieved as a result of reversible phase transition between two intrinsically stable phases. Our calculations conclude co-existence of the two stable phases in a coherent crystal lattice, giving rise to the possibility of constructing multiple temporary shapes in a single material, thus, enabling highly desirable programmability. With an atomic thickness, excellent shape memory mechanical properties and electric field stimulus, the discovery of a two-dimensional shape memory graphene oxide opens a path for the development of exceptional micro-/nano-electromechanical devices.

  11. Existence and Stability of Two-Dimensional Compact-Like Discrete Breathers in Discrete Two-Dimensional Monatomic Square Lattices

    Institute of Scientific and Technical Information of China (English)

    XU Quan; TIAN Qiang

    2007-01-01

    Two-dimensional compact-like discrete breathers in discrete two-dimensional monatomic square lattices are investigated by discussing a generafized discrete two-dimensional monatomic model.It is proven that the twodimensional compact-like discrete breathers exist not only in two-dimensional soft Ф4 potentials but also in hard two-dimensional Ф4 potentials and pure two-dimensional K4 lattices.The measurements of the two-dimensional compact-like discrete breather cores in soft and hard two-dimensional Ф4 potential are determined by coupling parameter K4,while those in pure two-dimensional K4 lattices have no coupling with parameter K4.The stabilities of the two-dimensional compact-like discrete breathers correlate closely to the coupling parameter K4 and the boundary condition of lattices.

  12. Optimal excitation of two dimensional Holmboe instabilities

    CERN Document Server

    Constantinou, Navid C

    2010-01-01

    Highly stratified shear layers are rendered unstable even at high stratifications by Holmboe instabilities when the density stratification is concentrated in a small region of the shear layer. These instabilities may cause mixing in highly stratified environments. However these instabilities occur in tongues for a limited range of parameters. We perform Generalized Stability analysis of the two dimensional perturbation dynamics of an inviscid Boussinesq stratified shear layer and show that Holmboe instabilities at high Richardson numbers can be excited by their adjoints at amplitudes that are orders of magnitude larger than by introducing initially the unstable mode itself. We also determine the optimal growth that obtains for parameters for which there is no instability. We find that there is potential for large transient growth regardless of whether the background flow is exponentially stable or not and that the characteristic structure of the Holmboe instability asymptotically emerges for parameter values ...

  13. Phonon hydrodynamics in two-dimensional materials.

    Science.gov (United States)

    Cepellotti, Andrea; Fugallo, Giorgia; Paulatto, Lorenzo; Lazzeri, Michele; Mauri, Francesco; Marzari, Nicola

    2015-03-06

    The conduction of heat in two dimensions displays a wealth of fascinating phenomena of key relevance to the scientific understanding and technological applications of graphene and related materials. Here, we use density-functional perturbation theory and an exact, variational solution of the Boltzmann transport equation to study fully from first-principles phonon transport and heat conductivity in graphene, boron nitride, molybdenum disulphide and the functionalized derivatives graphane and fluorographene. In all these materials, and at variance with typical three-dimensional solids, normal processes keep dominating over Umklapp scattering well-above cryogenic conditions, extending to room temperature and more. As a result, novel regimes emerge, with Poiseuille and Ziman hydrodynamics, hitherto typically confined to ultra-low temperatures, characterizing transport at ordinary conditions. Most remarkably, several of these two-dimensional materials admit wave-like heat diffusion, with second sound present at room temperature and above in graphene, boron nitride and graphane.

  14. Probabilistic Universality in two-dimensional Dynamics

    CERN Document Server

    Lyubich, Mikhail

    2011-01-01

    In this paper we continue to explore infinitely renormalizable H\\'enon maps with small Jacobian. It was shown in [CLM] that contrary to the one-dimensional intuition, the Cantor attractor of such a map is non-rigid and the conjugacy with the one-dimensional Cantor attractor is at most 1/2-H\\"older. Another formulation of this phenomenon is that the scaling structure of the H\\'enon Cantor attractor differs from its one-dimensional counterpart. However, in this paper we prove that the weight assigned by the canonical invariant measure to these bad spots tends to zero on microscopic scales. This phenomenon is called {\\it Probabilistic Universality}. It implies, in particular, that the Hausdorff dimension of the canonical measure is universal. In this way, universality and rigidity phenomena of one-dimensional dynamics assume a probabilistic nature in the two-dimensional world.

  15. Two-dimensional position sensitive neutron detector

    Indian Academy of Sciences (India)

    A M Shaikh; S S Desai; A K Patra

    2004-08-01

    A two-dimensional position sensitive neutron detector has been developed. The detector is a 3He + Kr filled multiwire proportional counter with charge division position readout and has a sensitive area of 345 mm × 345 mm, pixel size 5 mm × 5 mm, active depth 25 mm and is designed for efficiency of 70% for 4 Å neutrons. The detector is tested with 0.5 bar 3He + 1.5 bar krypton gas mixture in active chamber and 2 bar 4He in compensating chamber. The pulse height spectrum recorded at an anode potential of 2000 V shows energy resolution of ∼ 25% for the 764 keV peak. A spatial resolution of 8 mm × 6 mm is achieved. The detector is suitable for SANS studies in the range of 0.02–0.25 Å-1.

  16. 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.

  17. 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.

  18. Janus Spectra in Two-Dimensional Flows

    Science.gov (United States)

    Liu, Chien-Chia; Cerbus, Rory T.; Chakraborty, Pinaki

    2016-09-01

    In large-scale atmospheric flows, soap-film flows, and other two-dimensional flows, the exponent of the turbulent energy spectra, α , may theoretically take either of two distinct values, 3 or 5 /3 , but measurements downstream of obstacles have invariably revealed α =3 . Here we report experiments on soap-film flows where downstream of obstacles there exists a sizable interval in which α transitions from 3 to 5 /3 for the streamwise fluctuations but remains equal to 3 for the transverse fluctuations, as if two mutually independent turbulent fields of disparate dynamics were concurrently active within the flow. This species of turbulent energy spectra, which we term the Janus spectra, has never been observed or predicted theoretically. Our results may open up new vistas in the study of turbulence and geophysical flows.

  19. 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.

  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. 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.

  3. Equivalency of two-dimensional algebras

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Gildemar Carneiro dos; Pomponet Filho, Balbino Jose S. [Universidade Federal da Bahia (UFBA), BA (Brazil). Inst. de Fisica

    2011-07-01

    Full text: Let us consider a vector z = xi + yj over the field of real numbers, whose basis (i,j) satisfy a given algebra. Any property of this algebra will be reflected in any function of z, so we can state that the knowledge of the properties of an algebra leads to more general conclusions than the knowledge of the properties of a function. However structural properties of an algebra do not change when this algebra suffers a linear transformation, though the structural constants defining this algebra do change. We say that two algebras are equivalent to each other whenever they are related by a linear transformation. In this case, we have found that some relations between the structural constants are sufficient to recognize whether or not an algebra is equivalent to another. In spite that the basis transform linearly, the structural constants change like a third order tensor, but some combinations of these tensors result in a linear transformation, allowing to write the entries of the transformation matrix as function of the structural constants. Eventually, a systematic way to find the transformation matrix between these equivalent algebras is obtained. In this sense, we have performed the thorough classification of associative commutative two-dimensional algebras, and find that even non-division algebra may be helpful in solving non-linear dynamic systems. The Mandelbrot set was used to have a pictorial view of each algebra, since equivalent algebras result in the same pattern. Presently we have succeeded in classifying some non-associative two-dimensional algebras, a task more difficult than for associative one. (author)

  4. 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

  5. Unpacking of a Crumpled Wire from Two-Dimensional Cavities.

    Directory of Open Access Journals (Sweden)

    Thiago A Sobral

    Full Text Available The physics of tightly packed structures of a wire and other threadlike materials confined in cavities has been explored in recent years in connection with crumpled systems and a number of topics ranging from applications to DNA packing in viral capsids and surgical interventions with catheter to analogies with the electron gas at finite temperature and with theories of two-dimensional quantum gravity. When a long piece of wire is injected into two-dimensional cavities, it bends and originates in the jammed limit a series of closed structures that we call loops. In this work we study the extraction of a crumpled tightly packed wire from a circular cavity aiming to remove loops individually. The size of each removed loop, the maximum value of the force needed to unpack each loop, and the total length of the extracted wire were measured and related to an exponential growth and a mean field model consistent with the literature of crumpled wires. Scaling laws for this process are reported and the relationship between the processes of packing and unpacking of wire is commented upon.

  6. Unpacking of a Crumpled Wire from Two-Dimensional Cavities.

    Science.gov (United States)

    Sobral, Thiago A; Gomes, Marcelo A F; Machado, Núbia R; Brito, Valdemiro P

    2015-01-01

    The physics of tightly packed structures of a wire and other threadlike materials confined in cavities has been explored in recent years in connection with crumpled systems and a number of topics ranging from applications to DNA packing in viral capsids and surgical interventions with catheter to analogies with the electron gas at finite temperature and with theories of two-dimensional quantum gravity. When a long piece of wire is injected into two-dimensional cavities, it bends and originates in the jammed limit a series of closed structures that we call loops. In this work we study the extraction of a crumpled tightly packed wire from a circular cavity aiming to remove loops individually. The size of each removed loop, the maximum value of the force needed to unpack each loop, and the total length of the extracted wire were measured and related to an exponential growth and a mean field model consistent with the literature of crumpled wires. Scaling laws for this process are reported and the relationship between the processes of packing and unpacking of wire is commented upon.

  7. Size-selected genomic libraries: the distribution and size-fractionation of restricted genomic DNA fragments by gel electrophoresis.

    Science.gov (United States)

    Gondo, Y

    1995-02-01

    By using one-dimensional genome scanning, it is possible to directly identify the restricted genomic DNA fragment that reflects the site of genetic change. The subsequent strategies to obtain the molecular clones of the corresponding restriction fragment are usually as follows: (i) the restriction of a mass quantity of an appropriate genomic DNA, (ii) the size-fractionation of the restricted DNA on a preparative electrophoresis gel in order to enrich the corresponding restriction fragment, (iii) the construction of the size-selected libraries from the fractionated genomic DNA, and (iv) the screening of the library to obtain an objective clone which is identified on the analytical genome scanning gel. A knowledge of the size distribution pattern of restriction fragments of the genomic DNA makes it possible to calculate the heterogeneity or complexity of the restriction fragment in each size-fraction. This manuscript first describes the distribution of the restriction fragments with respect to their length. Some examples of the practical application of this theory to genome scanning is then discussed using presumptive genome scanning gels. The way to calculate such DNA complexities in the prepared size-fractionated samples is also demonstrated. Such information should greatly facilitate the design of experimental strategies for the cloning of a certain size of genomic DNA after digestion with restriction enzyme(s) as is the case with genome scanning.

  8. Structural analysis of mitochondrial DNA molecules from fungi and plants using moving pictures and pulsed-field gel electrophoresis.

    Science.gov (United States)

    Bendich, A J

    1996-02-02

    The size and structure of mitochondrial DNA (mtDNA) molecules was investigated by conventional and pulsed-field gel electrophoresis (PFGE) and by analyzing moving pictures during electrophoresis of individual fluorescently labelled mtDNA molecules. Little or no mtDNA that migrated into the gel was found in circular form for fungi (Schizosaccharomyces pombe, Saccharomyces cerevisiae and Neurospora crassa) or plants (Brassica hirta, tobacco, voodoo lily and maize). Most mtDNA migrated as a smear of linear DNA sizes from about 50 to 100 or 250 kilobases (kb), depending on the species, irrespective of the size of the mitochondrial genome over a range of 0.06 to 570 kb. S. cerevisiae, B. hirta and tobacco also yielded a linear mtDNA fraction containing molecules > 1000 kb in size. About half the mtDNA remained in the well of the gel after PFGE. Moving pictures revealed that this well-bound (wb) mtDNA contained molecules larger than the genome size in linear form for all species (except N. crassa) and in multi-fibered, comet-like forms for most of the wb mtDNA of N. crassa and Sc. pombe. A minor amount of the wb mtDNA with visually interpretable structure was circular: circle sizes were both larger and smaller than the 80-kb genome of S. cerevisiae, larger than the 19-kb genome of Sc. pombe and smaller than the 208-kb and 570-kb genomes of B. hirta and maize, respectively. About 25 to 75% of the wb mtDNA from cultured tobacco cells was found in circles smaller than its genome size. Partial digestion of Sc. pombe mtDNA with restriction endonucleases that cleave once per genome revealed gel bands at about 38 kb and 19 kb with a smear of sizes between the bands and below the 19-kb band, suggesting a head-to-tail genomic concatemer as the most prominent form in extracted mtDNA. A pattern of bands with smears was also found for complete digests (with multiply cleaving enzymes) of mtDNA from Sc. pombe, S. cerevisiae and N. crassa, but bands without smears were found for

  9. 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.

  10. Two-dimensional screening of the Wageningen chicken BAC library.

    Science.gov (United States)

    Crooijmans, R P; Vrebalov, J; Dijkhof, R J; van der Poel, J J; Groenen, M A

    2000-05-01

    We have constructed a Bacterial Artificial Chromosome (BAC) library that provides 5.5-fold redundant coverage of the chicken genome. The library was made by cloning partial HindIII-digested high-molecular-weight (HMW) DNA of a female White Leghorn chicken into the HindIII site of the vector pECBAC1. Several modifications of standard protocols were necessary to clone efficiently large partial HindIII DNA fragments. The library consists of 49,920 clones arranged in 130 384-well plates. An average insert size of 134 kb was estimated from the analysis of 152 randomly selected BAC clones. The average number of NotI restriction sites per clone was 0.77. After individual growth, DNA was isolated of the pooled clones of each 384-well plate, and subsequently DNA of each plate was isolated from the individual row and column pools. Screening of the Wageningen chicken BAC library was performed by two-dimensional PCR with 125 microsatellite markers. For 124 markers at least one BAC clone was obtained. FISH experiments of 108 BAC clones revealed chimerism in less than 1%. The number of different BAC clones per marker present in the BAC library was examined for 35 markers which resulted in a total of 167 different BAC clones. Per marker the number of BAC clones varied from 1 to 11, with an average of 4.77. The chicken BAC library constitutes an invaluable tool for positional cloning and for comparative mapping studies.

  11. Genetic profiling of Klebsiella pneumoniae: comparison of pulsed field gel electrophoresis and random amplified polymorphic DNA

    Directory of Open Access Journals (Sweden)

    Mitra Ashayeri-Panah

    2013-09-01

    Full Text Available In this study, the discriminatory power of pulsed field gel electrophoresis (PFGE and random amplified polymorphic DNA (RAPD methods for subtyping of 54 clinical isolates of Klebsiella pneumoniae were compared. All isolates were typeable by RAPD, while 3.6% of them were not typeable by PFGE. The repeatability of both typing methods were 100% with satisfying reproducibility (≥ 95%. Although the discriminatory power of PFGE was greater than RAPD, both methods showed sufficient discriminatory power (DI > 0.95 which reflects the heterogeneity among the K. pneumoniae isolates. An optimized RAPD protocol is less technically demanding and time consuming that makes it a reliable typing method and competitive with PFGE.

  12. On numerical evaluation of two-dimensional phase integrals

    DEFF Research Database (Denmark)

    Lessow, H.; Rusch, W.; Schjær-Jacobsen, Hans

    1975-01-01

    The relative advantages of several common numerical integration algorithms used in computing two-dimensional phase integrals are evaluated.......The relative advantages of several common numerical integration algorithms used in computing two-dimensional phase integrals are evaluated....

  13. 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.

  14. Janus spectra in two-dimensional flows

    CERN Document Server

    Liu, Chien-Chia; Chakraborty, Pinaki

    2016-01-01

    In theory, large-scale atmospheric flows, soap-film flows and other two-dimensional flows may host two distinct types of turbulent energy spectra---in one, $\\alpha$, the spectral exponent of velocity fluctuations, equals $3$ and the fluctuations are dissipated at the small scales, and in the other, $\\alpha=5/3$ and the fluctuations are dissipated at the large scales---but measurements downstream of obstacles have invariably revealed $\\alpha = 3$. Here we report experiments on soap-film flows where downstream of obstacles there exists a sizable interval in which $\\alpha$ has transitioned from $3$ to $5/3$ for the streamwise fluctuations but remains equal to $3$ for the transverse fluctuations, as if two mutually independent turbulent fields of disparate dynamics were concurrently active within the flow. This species of turbulent energy spectra, which we term the Janus spectra, has never been observed or predicted theoretically. Our results may open up new vistas in the study of turbulence and geophysical flows...

  15. Two-dimensional hexagonal semiconductors beyond graphene

    Science.gov (United States)

    Nguyen, Bich Ha; Hieu Nguyen, Van

    2016-12-01

    The rapid and successful development of the research on graphene and graphene-based nanostructures has been substantially enlarged to include many other two-dimensional hexagonal semiconductors (THS): phosphorene, silicene, germanene, hexagonal boron nitride (h-BN) and transition metal dichalcogenides (TMDCs) such as MoS2, MoSe2, WS2, WSe2 as well as the van der Waals heterostructures of various THSs (including graphene). The present article is a review of recent works on THSs beyond graphene and van der Waals heterostructures composed of different pairs of all THSs. One among the priorities of new THSs compared to graphene is the presence of a non-vanishing energy bandgap which opened up the ability to fabricate a large number of electronic, optoelectronic and photonic devices on the basis of these new materials and their van der Waals heterostructures. Moreover, a significant progress in the research on TMDCs was the discovery of valley degree of freedom. The results of research on valley degree of freedom and the development of a new technology based on valley degree of freedom-valleytronics are also presented. Thus the scientific contents of the basic research and practical applications os THSs are very rich and extremely promising.

  16. Two-Dimensional Phononic Crystals: Disorder Matters.

    Science.gov (United States)

    Wagner, Markus R; Graczykowski, Bartlomiej; Reparaz, Juan Sebastian; El Sachat, Alexandros; Sledzinska, Marianna; Alzina, Francesc; Sotomayor Torres, Clivia M

    2016-09-14

    The design and fabrication of phononic crystals (PnCs) hold the key to control the propagation of heat and sound at the nanoscale. However, there is a lack of experimental studies addressing the impact of order/disorder on the phononic properties of PnCs. Here, we present a comparative investigation of the influence of disorder on the hypersonic and thermal properties of two-dimensional PnCs. PnCs of ordered and disordered lattices are fabricated of circular holes with equal filling fractions in free-standing Si membranes. Ultrafast pump and probe spectroscopy (asynchronous optical sampling) and Raman thermometry based on a novel two-laser approach are used to study the phononic properties in the gigahertz (GHz) and terahertz (THz) regime, respectively. Finite element method simulations of the phonon dispersion relation and three-dimensional displacement fields furthermore enable the unique identification of the different hypersonic vibrations. The increase of surface roughness and the introduction of short-range disorder are shown to modify the phonon dispersion and phonon coherence in the hypersonic (GHz) range without affecting the room-temperature thermal conductivity. On the basis of these findings, we suggest a criteria for predicting phonon coherence as a function of roughness and disorder.

  17. Two-dimensional topological photonic systems

    Science.gov (United States)

    Sun, Xiao-Chen; He, Cheng; Liu, Xiao-Ping; Lu, Ming-Hui; Zhu, Shi-Ning; Chen, Yan-Feng

    2017-09-01

    The topological phase of matter, originally proposed and first demonstrated in fermionic electronic systems, has drawn considerable research attention in the past decades due to its robust transport of edge states and its potential with respect to future quantum information, communication, and computation. Recently, searching for such a unique material phase in bosonic systems has become a hot research topic worldwide. So far, many bosonic topological models and methods for realizing them have been discovered in photonic systems, acoustic systems, mechanical systems, etc. These discoveries have certainly yielded vast opportunities in designing material phases and related properties in the topological domain. In this review, we first focus on some of the representative photonic topological models and employ the underlying Dirac model to analyze the edge states and geometric phase. On the basis of these models, three common types of two-dimensional topological photonic systems are discussed: 1) photonic quantum Hall effect with broken time-reversal symmetry; 2) photonic topological insulator and the associated pseudo-time-reversal symmetry-protected mechanism; 3) time/space periodically modulated photonic Floquet topological insulator. Finally, we provide a summary and extension of this emerging field, including a brief introduction to the Weyl point in three-dimensional systems.

  18. Radiation effects on two-dimensional materials

    Energy Technology Data Exchange (ETDEWEB)

    Walker, R.C. II; Robinson, J.A. [Department of Materials Science, Penn State, University Park, PA (United States); Center for Two-Dimensional Layered Materials, Penn State, University Park, PA (United States); Shi, T. [Department of Mechanical and Nuclear Engineering, Penn State, University Park, PA (United States); Department of Nuclear Engineering and Radiological Sciences, University of Michigan, Ann Arbor, MI (United States); Silva, E.C. [GlobalFoundries, Malta, NY (United States); Jovanovic, I. [Department of Nuclear Engineering and Radiological Sciences, University of Michigan, Ann Arbor, MI (United States)

    2016-12-15

    The effects of electromagnetic and particle irradiation on two-dimensional materials (2DMs) are discussed in this review. Radiation creates defects that impact the structure and electronic performance of materials. Determining the impact of these defects is important for developing 2DM-based devices for use in high-radiation environments, such as space or nuclear reactors. As such, most experimental studies have been focused on determining total ionizing dose damage to 2DMs and devices. Total dose experiments using X-rays, gamma rays, electrons, protons, and heavy ions are summarized in this review. We briefly discuss the possibility of investigating single event effects in 2DMs based on initial ion beam irradiation experiments and the development of 2DM-based integrated circuits. Additionally, beneficial uses of irradiation such as ion implantation to dope materials or electron-beam and helium-beam etching to shape materials have begun to be used on 2DMs and are reviewed as well. For non-ionizing radiation, such as low-energy photons, we review the literature on 2DM-based photo-detection from terahertz to UV. The majority of photo-detecting devices operate in the visible and UV range, and for this reason they are the focus of this review. However, we review the progress in developing 2DMs for detecting infrared and terahertz radiation. (copyright 2016 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  19. 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.

  20. Asymptotics for Two-dimensional Atoms

    DEFF Research Database (Denmark)

    Nam, Phan Thanh; Portmann, Fabian; Solovej, Jan Philip

    2012-01-01

    We prove that the ground state energy of an atom confined to two dimensions with an infinitely heavy nucleus of charge $Z>0$ and $N$ quantum electrons of charge -1 is $E(N,Z)=-{1/2}Z^2\\ln Z+(E^{\\TF}(\\lambda)+{1/2}c^{\\rm H})Z^2+o(Z^2)$ when $Z\\to \\infty$ and $N/Z\\to \\lambda$, where $E^{\\TF}(\\lambd......We prove that the ground state energy of an atom confined to two dimensions with an infinitely heavy nucleus of charge $Z>0$ and $N$ quantum electrons of charge -1 is $E(N,Z)=-{1/2}Z^2\\ln Z+(E^{\\TF}(\\lambda)+{1/2}c^{\\rm H})Z^2+o(Z^2)$ when $Z\\to \\infty$ and $N/Z\\to \\lambda$, where $E......^{\\TF}(\\lambda)$ is given by a Thomas-Fermi type variational problem and $c^{\\rm H}\\approx -2.2339$ is an explicit constant. We also show that the radius of a two-dimensional neutral atom is unbounded when $Z\\to \\infty$, which is contrary to the expected behavior of three-dimensional atoms....

  1. 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.

  2. In vitro genotypic variation of Campylobacter coli documented by pulsed-field gel electrophoretic DNA profiling, implications for epidemiological studies

    DEFF Research Database (Denmark)

    On, Stephen L.W.

    1998-01-01

    Six isolates of Campylobacter coli from different pig herds were subcultured up to 50 times over a 6-month period and DNA samples suitable for pulsed-field gel electrophoretic (PFGE) profiling prepared at regular (1, 20, 40 and 50 passages) intervals. In 5/6 strains, changes in the banding patter...

  3. AraUTP-Affi-Gel 10: a novel affinity absorbent for the specific purification of DNA polymerase alpha-primase.

    Science.gov (United States)

    Izuta, S; Saneyoshi, M

    1988-10-01

    For the specific purification of eukaryotic DNA-dependent DNA polymerase alpha, we prepared two novel affinity resins bearing 5-(E)-(4-aminostyryl) araUTP as a ligand. One of them was araUTP-Sepharose 4B which was coupled directly with the ligand and the other was araUTP-Affi-Gel 10 which was coupled with the ligand through a spacer. No DNA polymerase alpha-primase activity from cherry salmon (Oncorhynchus masou) testes was bound on the araUTP-Sepharose 4B in all cases examined. On the other hand, the araUTP-Affi-Gel 10 retains this enzyme activity when poly(dA) or poly(dA)-oligo(dT)12-18 is present. The retained enzyme activity was sharply eluted around 100-mM KCl concentrations as a single peak, and this fraction showed a specific activity of about 170,000 units/mg as alpha-polymerase activity. The highly purified DNA polymerase alpha-primase isolated using the araUTP-Affi-Gel 10 contained only three polypeptides, which showed Mr values of 120,000, 62,000, and 58,000, respectively, as judged using sodium dodecyl sulfate-polyacrylamide gel electrophoresis.

  4. Measurement of oxidatively-induced clustered DNA lesions using a novel adaptation of single cell gel electrophoresis (comet assay).

    Science.gov (United States)

    Georgakilas, Alexandros G; Holt, Stewart M; Hair, Jessica M; Loftin, Charles W

    2010-12-01

    The two basic groups of complex DNA damage are double-strand breaks (DSBs) and non-DSB oxidatively-induced clustered DNA lesions (OCDLs). The single-cell gel electrophoresis (SCGE) or comet assay has been widely used for the detection of low levels of various types of DNA lesions including single-strand breaks (SSBs), DSBs, and oxidized bases per individual cell. There are limited data on the use of the comet assay for the detection of non-DSB clustered DNA lesions using different repair enzymes as enzymatic probes. This unit discusses a novel adaptation of the comet assay used to measure these unique types of lesions. Until now OCDL yields have been measured using primarily pulsed-field agarose gel electrophoresis. The advantages offered by the current approach are: (1) measurement of OCDL levels per individual cell; (2) use of a small number of cells (∼10,000) and relatively low doses of ionizing radiation (1 to 2 Gy) or low levels of oxidative stress, which are not compatible with standard agarose gel electrophoresis; and finally, (3) the assay is fast and allows direct comparison with pulsed-field gel electrophoresis results.

  5. 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} .

  6. Two-dimensional materials and their prospects in transistor electronics.

    Science.gov (United States)

    Schwierz, F; Pezoldt, J; Granzner, R

    2015-05-14

    During the past decade, two-dimensional materials have attracted incredible interest from the electronic device community. The first two-dimensional material studied in detail was graphene and, since 2007, it has intensively been explored as a material for electronic devices, in particular, transistors. While graphene transistors are still on the agenda, researchers have extended their work to two-dimensional materials beyond graphene and the number of two-dimensional materials under examination has literally exploded recently. Meanwhile several hundreds of different two-dimensional materials are known, a substantial part of them is considered useful for transistors, and experimental transistors with channels of different two-dimensional materials have been demonstrated. In spite of the rapid progress in the field, the prospects of two-dimensional transistors still remain vague and optimistic opinions face rather reserved assessments. The intention of the present paper is to shed more light on the merits and drawbacks of two-dimensional materials for transistor electronics and to add a few more facets to the ongoing discussion on the prospects of two-dimensional transistors. To this end, we compose a wish list of properties for a good transistor channel material and examine to what extent the two-dimensional materials fulfill the criteria of the list. The state-of-the-art two-dimensional transistors are reviewed and a balanced view of both the pros and cons of these devices is provided.

  7. Methods for two-dimensional cell confinement.

    Science.gov (United States)

    Le Berre, Maël; Zlotek-Zlotkiewicz, Ewa; Bonazzi, Daria; Lautenschlaeger, Franziska; Piel, Matthieu

    2014-01-01

    Protocols described in this chapter relate to a method to dynamically confine cells in two dimensions with various microenvironments. It can be used to impose on cells a given height, with an accuracy of less than 100 nm on large surfaces (cm(2)). The method is based on the gentle application of a modified glass coverslip onto a standard cell culture. Depending on the preparation, this confinement slide can impose on the cells a given geometry but also an environment of controlled stiffness, controlled adhesion, or a more complex environment. An advantage is that the method is compatible with most optical microscopy technologies and molecular biology protocols allowing advanced analysis of confined cells. In this chapter, we first explain the principle and issues of using these slides to confine cells in a controlled geometry and describe their fabrication. Finally, we discuss how the nature of the confinement slide can vary and provide an alternative method to confine cells with gels of controlled rigidity.

  8. 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

  9. 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

  10. Electrophoretic analysis of proteins from Mycoplasma capricolum and related serotypes using extracts from intact cells and from minicells containing cloned mycoplasma DNA

    DEFF Research Database (Denmark)

    Andersen, H; Christiansen, Gunna; Christiansen, C

    1984-01-01

    The acidic proteins of six different mycoplasma serotypes causing bovine or caprine pleuropneumonia were compared by two-dimensional gel electrophoresis of extracts of 35S-labelled cells. The organisms investigated were Mycoplasma mycoides subsp. mycoides (PG1), M. mycoides subsp. mycoides (Y...... proteins in the two-dimensional gels. In Escherichia coli minicells, DNA from strain PG50 cloned in the vector pBR325 gave rise to incorporation of radioactive label into proteins which were identified as mycoplasma proteins by two-dimensional electrophoresis and immunoprecipitation....

  11. Electronic nanobiosensors based on two-dimensional materials

    Science.gov (United States)

    Ping, Jinglei

    Atomically-thick two-dimensional (2D) nanomaterials have tremendous potential to be applied as transduction elements in biosensors and bioelectronics. We developed scalable methods for synthesis and large-area transfer of two-dimensional nanomaterials, particularly graphene and metal dichalcogenides (so called ``MX2'' materials). We also developed versatile fabrication methods for large arrays of field-effect transistors (FETs) and micro-electrodes with these nanomaterials based on either conventional photolithography or innovative approaches that minimize contamination of the 2D layer. By functionalizing the FETs with a computationally redesigned water-soluble mu-opioid receptor, we created selective and sensitive biosensors suitable for detection of the drug target naltrexone and the neuropeptide enkephalin at pg/mL concentrations. We also constructed DNA-functionalized biosensors and nano-particle decorated biosensors by applying related bio-nano integration techniques. Our methodology paves the way for multiplexed nanosensor arrays with all-electronic readout suitable for inexpensive point-of-care diagnostics, drug-development and biomedical research. With graphene field-effect transistors, we investigated the graphene/solution interface and developed a quantitative model for the effect of ionic screening on the graphene carrier density based on theories of the electric double layer. Finally, we have developed a technique for measuring low-level Faradaic charge-transfer current (fA) across the graphene/solution interface via real-time charge monitoring of graphene microelectrodes in ionic solution. This technique enables the development of flexible and transparent pH sensors that are promising for in vivo applications. The author acknowledges the support from the Defense Advanced Research Projects Agency (DARPA) and the U. S. Army Research Office under Grant Number W911NF1010093.

  12. 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.

  13. 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.

  14. 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.

  15. Investigation on interaction of DNA and several cationic surfactants with different head groups by spectroscopy, gel electrophoresis and viscosity technologies.

    Science.gov (United States)

    Guo, Qing; Zhang, Zhaohong; Song, Youtao; Liu, Shuo; Gao, Wei; Qiao, Heng; Guo, Lili; Wang, Jun

    2017-02-01

    In this study, the interaction between DNA and several cationic surfactants with different head groups such as ethyl hexadecyl dimethyl ammonium bromide (EHDAB), hexadecyl dimethyl benzyl ammonium chloride (HDBAC), and cetyl pyridinium bromide (CPB) were investigated by UV-vis absorption, fluorescence and circular dichroism (CD) spectroscopy, gel electrophoresis, and viscosity technologies. The results show that these cationic surfactants can interact with DNA and major binding modes are electrostatic and hydrophobic. Also, CPB and HDBAC molecules interact with DNA by partial intercalation, and CPB has slightly stronger intercalation than HDBAC, while EHDAB interacts with DNA by non-intercalation. The different head groups of the surfactant molecules can influence the interaction strength. CPB has the stronger interaction with DNA than the others. Moreover, surfactant concentration, the ratio of DNA and fluorescence probe, ionic strength can influence the interaction. The surfactants may interact with DNA by the competition reactions with BR for DNA-BR. The increase of ionic strength may favor the surface binding between DNA and surfactants to some extent. This work provides deep mechanistic insight on the toxicity of cationic surfactants with different head groups to DNA molecules.

  16. The convolution theorem for two-dimensional continuous wavelet transform

    Institute of Scientific and Technical Information of China (English)

    ZHANG CHI

    2013-01-01

    In this paper , application of two -dimensional continuous wavelet transform to image processes is studied. We first show that the convolution and correlation of two continuous wavelets satisfy the required admissibility and regularity conditions ,and then we derive the convolution and correlation theorem for two-dimensional continuous wavelet transform. Finally, we present numerical example showing the usefulness of applying the convolution theorem for two -dimensional continuous wavelet transform to perform image restoration in the presence of additive noise.

  17. Open microfluidic gel electrophoresis: Rapid and low cost separation and analysis of DNA at the nanoliter scale.

    Science.gov (United States)

    Gutzweiler, Ludwig; Gleichmann, Tobias; Tanguy, Laurent; Koltay, Peter; Zengerle, Roland; Riegger, Lutz

    2017-07-01

    Gel electrophoresis is one of the most applied and standardized tools for separation and analysis of macromolecules and their fragments in academic research and in industry. In this work we present a novel approach for conducting on-demand electrophoretic separations of DNA molecules in open microfluidic (OM) systems on planar polymer substrates. The approach combines advantages of slab gel, capillary- and chip-based methods offering low consumable costs (gel line acting as separation channel interconnecting the reservoirs and sample injected into the line via non-contact droplet dispensing and thus enabling the precise control of the injection plug and sample concentration. Evaporation is prevented by covering aqueous structures with PCR-grade mineral oil while maintaining surface temperature at 15°C. The liquid gel line exhibits a semi-circular cross section of adaptable width (∼200-600 μm) and height (∼30-80 μm) as well as a typical length of 15-55 mm. Layout of such liquid structures is adaptable on-demand not requiring time consuming and repetitive fabrication steps. The approach was successfully demonstrated by the separation of a standard label-free DNA ladder (100-1000 bp) at 100 V/cm via in-line staining and laser induced fluorescent end-point detection using an automated prototype. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Staining-free gel electrophoresis-based multiplex enzyme assay using DNA and peptide dual-functionalized gold nanoparticles.

    Science.gov (United States)

    Zhao, Wenting; Yao, Chunlei; Luo, Xiaoteng; Lin, Li; Hsing, I-Ming

    2012-04-01

    We report a simple staining-free gel electrophoresis method to simultaneously probe protease and nuclease. Utilizing gold nanoparticles (Au-NPs) dual-functionalized with DNA and peptide, the presence and concentration of nuclease and protease are determined concurrently from the relative position and intensity of the bands in the staining-free gel electrophoresis. The use of Au-NPs eliminates the need for staining processes and enables naked eye detection, while a mononucleotide-mediated approach facilitates the synthesis of DNA/peptide conjugated Au-NPs and simplifies the operation procedures. Multiplex detection and quantification of DNase I and trypsin are successfully demonstrated. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Lack of DNA damage induced by fluoride on mouse lymphoma and human fibroblast cells by single cell gel (comet) assay

    OpenAIRE

    Ribeiro,Daniel Araki; Alves de Lima, Patrícia Lepage; Marques, Mariângela Esther Alencar; Salvadori,Daisy Maria Favero

    2006-01-01

    Fluoride has widely been used in Dentistry because it is a specific and effective caries prophylactic agent. However, excess fluoride may represent a hazard to human health, especially by causing injury on genetic apparatus. Genotoxicity tests constitute an important part of cancer research for risk assessment of potential carcinogens. In this study, the potential DNA damage associated with exposure to fluoride was assessed by the single cell gel (comet) assay in vitro. Mouse lymphoma and hum...

  20. Comparison of three methods of DNA extraction in endocervical specimens for Chlamydia trachomatis infection by spectrophotometry, agarose gel, and PCR.

    Science.gov (United States)

    Jenab, Anahita; Roghanian, Rasoul; Golbang, Naser; Golbang, Pouran; Chamani-Tabriz, Leili

    2010-06-01

    Chlamydia trachomatis is the major cause of sexually transmitted disease in the world. The aim of this study was to determine the best method of DNA extraction for detecting C. trachomatis by polymerase chain reaction (PCR) in sexually active women (n = 80) attending Shahid Beheshti Hospital in Isfahan, Iran. Endocervical swabs were collected from 80 women, 22 of whom were asymptomatic and 58 symptomatic. Three different DNA extraction methods were used in this study (phenol-chlorophorm, proteinase K, and boiling). DNA yield was evaluated by spectrophotometry, agarose gel, and PCR. The internal control was assayed by beta-globin primers (PCO4, GH20). The DNA cryptic plasmid was selected as the target for C. trachomatis and samples were examined by PCR using specific KL1 and KL2 primers. It was shown that DNA extraction by boiling was the most sensitive with the highest yield of DNA. Of the 80 samples, 17 (21.25%) showed positivity for C. trachomatis by PCR. The highest rate of C. trachomatis infection was found in the group aged between 35 and 45 years old and those who used withdrawal or an intrauterine device as methods of contraception. It was demonstrated that DNA extraction by boiling was the least expensive and a very rapid method that gave the highest DNA yield. The infection rate in the sexually active women, including symptomatic and asymptomatic, was 21.25%, with a presumably high prevalence compared with other studies done in this field.

  1. The Chandrasekhar's Equation for Two-Dimensional Hypothetical White Dwarfs

    CERN Document Server

    De, Sanchari

    2014-01-01

    In this article we have extended the original work of Chandrasekhar on the structure of white dwarfs to the two-dimensional case. Although such two-dimensional stellar objects are hypothetical in nature, we strongly believe that the work presented in this article may be prescribed as Master of Science level class problem for the students in physics.

  2. Beginning Introductory Physics with Two-Dimensional Motion

    Science.gov (United States)

    Huggins, Elisha

    2009-01-01

    During the session on "Introductory College Physics Textbooks" at the 2007 Summer Meeting of the AAPT, there was a brief discussion about whether introductory physics should begin with one-dimensional motion or two-dimensional motion. Here we present the case that by starting with two-dimensional motion, we are able to introduce a considerable…

  3. Spatiotemporal surface solitons in two-dimensional photonic lattices.

    Science.gov (United States)

    Mihalache, Dumitru; Mazilu, Dumitru; Lederer, Falk; Kivshar, Yuri S

    2007-11-01

    We analyze spatiotemporal light localization in truncated two-dimensional photonic lattices and demonstrate the existence of two-dimensional surface light bullets localized in the lattice corners or the edges. We study the families of the spatiotemporal surface solitons and their properties such as bistability and compare them with the modes located deep inside the photonic lattice.

  4. Mechanics of Apparent Horizon in Two Dimensional Dilaton Gravity

    CERN Document Server

    Cai, Rong-Gen

    2016-01-01

    In this article, we give a definition of apparent horizon in a two dimensional general dilaton gravity theory. With this definition, we construct the mechanics of the apparent horizon by introducing a quasi-local energy of the theory. Our discussion generalizes the apparent horizons mechanics in general spherically symmetric spactimes in four or higher dimensions to the two dimensional dilaton gravity case.

  5. Topological aspect of disclinations in two-dimensional crystals

    Institute of Scientific and Technical Information of China (English)

    Qi Wei-Kai; Zhu Tao; Chen Yong; Ren Ji-Rong

    2009-01-01

    By using topological current theory, this paper studies the inner topological structure of disclinations during the melting of two-dimensional systems. From two-dimensional elasticity theory, it finds that there are topological currents for topological defects in homogeneous equation. The evolution of disclinations is studied, and the branch conditions for generating, annihilating, crossing, splitting and merging of disclinations are given.

  6. 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.

  7. Invariant Subspaces of the Two-Dimensional Nonlinear Evolution Equations

    Directory of Open Access Journals (Sweden)

    Chunrong Zhu

    2016-11-01

    Full Text Available In this paper, we develop the symmetry-related methods to study invariant subspaces of the two-dimensional nonlinear differential operators. The conditional Lie–Bäcklund symmetry and Lie point symmetry methods are used to construct invariant subspaces of two-dimensional differential operators. We first apply the multiple conditional Lie–Bäcklund symmetries to derive invariant subspaces of the two-dimensional operators. As an application, the invariant subspaces for a class of two-dimensional nonlinear quadratic operators are provided. Furthermore, the invariant subspace method in one-dimensional space combined with the Lie symmetry reduction method and the change of variables is used to obtain invariant subspaces of the two-dimensional nonlinear operators.

  8. 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.

  9. Two-dimensional discrete gap breathers in a two-dimensional discrete diatomic Klein-Gordon lattice

    Institute of Scientific and Technical Information of China (English)

    XU Quan; QIANG Tian

    2009-01-01

    We study the existence and stability of two-dimensional discrete breathers in a two-dimensional discrete diatomic Klein-Gordon lattice consisting of alternating light and heavy atoms, with nearest-neighbor harmonic coupling.Localized solutions to the corresponding nonlinear differential equations with frequencies inside the gap of the linear wave spectrum, i.e. two-dimensional gap breathers, are investigated numerically. The numerical results of the corresponding algebraic equations demonstrate the possibility of the existence of two-dimensional gap breathers with three types of symmetries, i.e., symmetric, twin-antisymmetric and single-antisymmetric. Their stability depends on the nonlinear on-site potential (soft or hard), the interaction potential (attractive or repulsive)and the center of the two-dimensional gap breather (on a light or a heavy atom).

  10. 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.

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

    Institute of Scientific and Technical Information of China (English)

    ZHOU Pei; LIU Baofeng; LU Yitong

    2005-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

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

  13. 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...

  14. Two Dimensional Hydrodynamic Analysis of the Moose Creek Floodway

    Science.gov (United States)

    2012-09-01

    ER D C/ CH L TR -1 2 -2 0 Two Dimensional Hydrodynamic Analysis of the Moose Creek Floodway C oa st al a n d H yd ra u lic s La b or at...distribution is unlimited. ERDC/CHL TR-12-20 September 2012 Two Dimensional Hydrodynamic Analysis of the Moose Creek Floodway Stephen H. Scott, Jeremy A...A two-dimensional Adaptive Hydraulics (AdH) hydrodynamic model was developed to simulate the Moose Creek Floodway. The Floodway is located

  15. RESEARCH ON TWO-DIMENSIONAL LDA FOR FACE RECOGNITION

    Institute of Scientific and Technical Information of China (English)

    Han Ke; Zhu Xiuchang

    2006-01-01

    The letter presents an improved two-dimensional linear discriminant analysis method for feature extraction. Compared with the current two-dimensional methods for feature extraction, the improved two-dimensional linear discriminant analysis method makes full use of not only the row and the column direction information of face images but also the discriminant information among different classes. The method is evaluated using the Nanjing University of Science and Technology (NUST) 603 face database and the Aleix Martinez and Robert Benavente (AR) face database. Experimental results show that the method in the letter is feasible and effective.

  16. ONE-DIMENSIONAL AND TWO-DIMENSIONAL LEADERSHIP STYLES

    Directory of Open Access Journals (Sweden)

    Nikola Stefanović

    2007-06-01

    Full Text Available In order to motivate their group members to perform certain tasks, leaders use different leadership styles. These styles are based on leaders' backgrounds, knowledge, values, experiences, and expectations. The one-dimensional styles, used by many world leaders, are autocratic and democratic styles. These styles lie on the two opposite sides of the leadership spectrum. In order to precisely define the leadership styles on the spectrum between the autocratic leadership style and the democratic leadership style, leadership theory researchers use two dimensional matrices. The two-dimensional matrices define leadership styles on the basis of different parameters. By using these parameters, one can identify two-dimensional styles.

  17. 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.

  18. Application of single-cell gel electrophoresis (comet) assay for assessing levels of DNA damage in canine and feline leukocytes.

    Science.gov (United States)

    Heaton, Paul R; Ransley, Raymond; Charlton, Chris J; Mann, Sarah J; Stevenson, Joy; Smith, Brigitte H E; Rawlings, John M; Harper, E Jean

    2002-06-01

    Increasing evidence suggests involvement of free-radical species in the development of oxidative DNA damage, the consequences of which have been implicated in a number of degenerative disorders associated with the aging process. Here we report the application of a single-cell gel electrophoresis (comet) assay for assessing levels of DNA damage in canine and feline leukocytes. Leukocytes were collected from 24 healthy adult cats and dogs and subjected to DNA damage ex vivo by exposure to a range of hydrogen peroxide (H(2)O(2)) concentrations (0-250 micromol/L). The optimal concentration of H(2)O(2) to induce a significant increase in DNA damage was 100 micromol/L for both canine and feline leukocyte samples. Levels of DNA damage were assessed and quantified by visual and computer image analysis. The results obtained showed high correlations between visual scoring and computer image analysis for feline samples (percentage DNA in tail, R(2) > 0.99; tail moment, R(2) > 0.95; tail length, R(2) > 0.90) and canine samples (percentage DNA in tail, R(2) > 0.97; tail moment, R(2) > 0.95; tail length, R(2) > 0.91). In conclusion, this method provides a way of assessing levels of DNA damage utilizing visual and/or computer image analysis in the feline and canine systems. With the capacity of the comet assay to be able to measure end products of free-radical reactions, it is a useful tool for determining the optimal effects of dietary antioxidants on a reliable biomarker of oxidative stress such as cellular DNA status in cats and dogs.

  19. Rapid isolation of plasmid DNA by LiCl-ethidium bromide treatment and gel filtration.

    Science.gov (United States)

    Kondo, T; Mukai, M; Kondo, Y

    1991-10-01

    We established a simple and rapid plasmid DNA purification method. Crude plasmid DNA preparations are treated with 4 M LiCl in the presence of 0.6 mg/ml ethidium bromide to precipitate RNA and proteins contained in the DNA preparations. After removal of RNA and protein precipitates, the supernatant is filtered through a Sepharose CL6B column to remove low-molecular-weight contaminants. This procedure takes only 30 min and provides pure plasmid DNA preparations that consist mainly of covalently closed circular plasmid DNA but have no detectable RNA and protein. The purified DNA preparations are susceptible to various six- and four-base-recognition restriction endonucleases, T4 DNA ligase, the Klenow fragment of DNA polymerase I, and T7 and Taq DNA polymerase. Since no special equipment is needed for this purification method, 20 or more samples of microgram to milligram levels can be treated in parallel.

  20. A study of two-dimensional magnetic polaron

    Institute of Scientific and Technical Information of China (English)

    LIU; Tao; ZHANG; Huaihong; FENG; Mang; WANG; Kelin

    2006-01-01

    By using the variational method and anneal simulation, we study in this paper the self-trapped magnetic polaron (STMP) in two-dimensional anti-ferromagnetic material and the bound magnetic polaron (BMP) in ferromagnetic material. Schwinger angular momentum theory is applied to changing the problem into a coupling problem of carriers and two types of Bosons. Our calculation shows that there are single-peak and multi-peak structures in the two-dimensional STMP. For the ferromagnetic material, the properties of the two-dimensional BMP are almost the same as that in one-dimensional case; but for the anti-ferromagnetic material, the two-dimensional STMP structure is much richer than the one-dimensional case.

  1. UPWIND DISCONTINUOUS GALERKIN METHODS FOR TWO DIMENSIONAL NEUTRON TRANSPORT EQUATIONS

    Institute of Scientific and Technical Information of China (English)

    袁光伟; 沈智军; 闫伟

    2003-01-01

    In this paper the upwind discontinuous Galerkin methods with triangle meshes for two dimensional neutron transport equations will be studied.The stability for both of the semi-discrete and full-discrete method will be proved.

  2. Two-Dimensionally-Modulated, Magnetic Structure of Neodymium Metal

    DEFF Research Database (Denmark)

    Lebech, Bente; Bak, P.

    1979-01-01

    The incipient magnetic order of dhcp Nd is described by a two-dimensional, incommensurably modulated structure ("triple-q" structure). The ordering is accompanied by a lattice distortion that forms a similar pattern....

  3. Entanglement Entropy for time dependent two dimensional holographic superconductor

    CERN Document Server

    Mazhari, N S; Myrzakulov, Kairat; Myrzakulov, R

    2016-01-01

    We studied entanglement entropy for a time dependent two dimensional holographic superconductor. We showed that the conserved charge of the system plays the role of the critical parameter to have condensation.

  4. Decoherence in a Landau Quantized Two Dimensional Electron Gas

    Directory of Open Access Journals (Sweden)

    McGill Stephen A.

    2013-03-01

    Full Text Available We have studied the dynamics of a high mobility two-dimensional electron gas as a function of temperature. The presence of satellite reflections in the sample and magnet can be modeled in the time-domain.

  5. Quantization of Two-Dimensional Gravity with Dynamical Torsion

    CERN Document Server

    Lavrov, P M

    1999-01-01

    We consider two-dimensional gravity with dynamical torsion in the Batalin - Vilkovisky and Batalin - Lavrov - Tyutin formalisms of gauge theories quantization as well as in the background field method.

  6. Spatiotemporal dissipative solitons in two-dimensional photonic lattices.

    Science.gov (United States)

    Mihalache, Dumitru; Mazilu, Dumitru; Lederer, Falk; Kivshar, Yuri S

    2008-11-01

    We analyze spatiotemporal dissipative solitons in two-dimensional photonic lattices in the presence of gain and loss. In the framework of the continuous-discrete cubic-quintic Ginzburg-Landau model, we demonstrate the existence of novel classes of two-dimensional spatiotemporal dissipative lattice solitons, which also include surface solitons located in the corners or at the edges of the truncated two-dimensional photonic lattice. We find the domains of existence and stability of such spatiotemporal dissipative solitons in the relevant parameter space, for both on-site and intersite lattice solitons. We show that the on-site solitons are stable in the whole domain of their existence, whereas most of the intersite solitons are unstable. We describe the scenarios of the instability-induced dynamics of dissipative solitons in two-dimensional lattices.

  7. Bound states of two-dimensional relativistic harmonic oscillators

    Institute of Scientific and Technical Information of China (English)

    Qiang Wen-Chao

    2004-01-01

    We give the exact normalized bound state wavefunctions and energy expressions of the Klein-Gordon and Dirac equations with equal scalar and vector harmonic oscillator potentials in the two-dimensional space.

  8. A two-dimensional polymer prepared by organic synthesis.

    Science.gov (United States)

    Kissel, Patrick; Erni, Rolf; Schweizer, W Bernd; Rossell, Marta D; King, Benjamin T; Bauer, Thomas; Götzinger, Stephan; Schlüter, A Dieter; Sakamoto, Junji

    2012-02-05

    Synthetic polymers are widely used materials, as attested by a production of more than 200 millions of tons per year, and are typically composed of linear repeat units. They may also be branched or irregularly crosslinked. Here, we introduce a two-dimensional polymer with internal periodicity composed of areal repeat units. This is an extension of Staudinger's polymerization concept (to form macromolecules by covalently linking repeat units together), but in two dimensions. A well-known example of such a two-dimensional polymer is graphene, but its thermolytic synthesis precludes molecular design on demand. Here, we have rationally synthesized an ordered, non-equilibrium two-dimensional polymer far beyond molecular dimensions. The procedure includes the crystallization of a specifically designed photoreactive monomer into a layered structure, a photo-polymerization step within the crystal and a solvent-induced delamination step that isolates individual two-dimensional polymers as free-standing, monolayered molecular sheets.

  9. Second invariant for two-dimensional classical super systems

    Indian Academy of Sciences (India)

    S C Mishra; Roshan Lal; Veena Mishra

    2003-10-01

    Construction of superpotentials for two-dimensional classical super systems (for ≥ 2) is carried out. Some interesting potentials have been studied in their super form and also their integrability.

  10. Evaluation of radio-induced DNA damage and their repair in human lymphocytes by comet assay or single cell gel electrophoresis; Avaliacao do dano radioinduzido no DNA e reparo em linfocitos humanos pelo metodo do cometa (single cell gel electrophoresis)

    Energy Technology Data Exchange (ETDEWEB)

    Nascimento, Patricia A. do; Suzuki, Miriam F.; Okazaki, Kayo [Instituto de Pesquisas Energeticas e Nucleares (IPEN), Sao Paulo, SP (Brazil)

    1997-12-01

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

  11. Extreme paths in oriented two-dimensional percolation

    OpenAIRE

    Andjel, E. D.; Gray, L. F.

    2016-01-01

    International audience; A useful result about leftmost and rightmost paths in two dimensional bond percolation is proved. This result was introduced without proof in \\cite{G} in the context of the contact process in continuous time. As discussed here, it also holds for several related models, including the discrete time contact process and two dimensional site percolation. Among the consequences are a natural monotonicity in the probability of percolation between different sites and a somewha...

  12. Two Dimensional Nucleation Process by Monte Carlo Simulation

    OpenAIRE

    T., Irisawa; K., Matsumoto; Y., Arima; T., Kan; Computer Center, Gakushuin University; Department of Physics, Gakushuin University

    1997-01-01

    Two dimensional nucleation process on substrate is investigated by Monte Carlo simulation, and the critical nucleus size and its waiting time are measured with a high accuracy. In order to measure the critical nucleus with a high accuracy, we calculate the attachment and the detachment rate to the nucleus directly, and define the critical nucleus size when both rate are equal. Using the kinematical nucleation theory by Nishioka, it is found that, our obtained kinematical two dimensional criti...

  13. Controlled Interactions between Two Dimensional Layered Inorganic Nanosheets and Polymers

    Science.gov (United States)

    2016-06-15

    polymers . 2. Introduction . Research objectives: This research aims to study the physical (van der Waals forces: crystal epitaxy and π-π...AFRL-AFOSR-JP-TR-2016-0071 Controlled Interactions between Two Dimensional Layered Inorganic Nanosheets and Polymers Cheolmin Park YONSEI UNIVERSITY...Interactions between Two Dimensional Layered Inorganic Nanosheets and Polymers 5a.  CONTRACT NUMBER 5b.  GRANT NUMBER FA2386-14-1-4054 5c.  PROGRAM ELEMENT

  14. Two-Dimensional Weak Pseudomanifolds on Eight Vertices

    Indian Academy of Sciences (India)

    Basudeb Datta; Nandini Nilakantan

    2002-05-01

    We explicitly determine all the two-dimensional weak pseudomanifolds on 8 vertices. We prove that there are (up to isomorphism) exactly 95 such weak pseudomanifolds, 44 of which are combinatorial 2-manifolds. These 95 weak pseudomanifolds triangulate 16 topological spaces. As a consequence, we prove that there are exactly three 8-vertex two-dimensional orientable pseudomanifolds which allow degree three maps to the 4-vertex 2-sphere.

  15. Two-Dimensional Materials for Sensing: Graphene and Beyond

    Directory of Open Access Journals (Sweden)

    Seba Sara Varghese

    2015-09-01

    Full Text Available Two-dimensional materials have attracted great scientific attention due to their unusual and fascinating properties for use in electronics, spintronics, photovoltaics, medicine, composites, etc. Graphene, transition metal dichalcogenides such as MoS2, phosphorene, etc., which belong to the family of two-dimensional materials, have shown great promise for gas sensing applications due to their high surface-to-volume ratio, low noise and sensitivity of electronic properties to the changes in the surroundings. Two-dimensional nanostructured semiconducting metal oxide based gas sensors have also been recognized as successful gas detection devices. This review aims to provide the latest advancements in the field of gas sensors based on various two-dimensional materials with the main focus on sensor performance metrics such as sensitivity, specificity, detection limit, response time, and reversibility. Both experimental and theoretical studies on the gas sensing properties of graphene and other two-dimensional materials beyond graphene are also discussed. The article concludes with the current challenges and future prospects for two-dimensional materials in gas sensor applications.

  16. Development of a bi-functional silica monolith for electro-osmotic pumping and DNA clean-up/extraction using gel-supported reagents in a microfluidic device.

    Science.gov (United States)

    Oakley, Jennifer A; Shaw, Kirsty J; Docker, Peter T; Dyer, Charlotte E; Greenman, John; Greenway, Gillian M; Haswell, Stephen J

    2009-06-07

    A silica monolith used to support both electro-osmotic pumping (EOP) and the extraction/elution of DNA coupled with gel-supported reagents is described. The benefits of the combined EOP extraction/elution system were illustrated by combining DNA extraction and gene amplification using the polymerase chain reaction (PCR) process. All the reagents necessary for both processes were supported within pre-loaded gels that allow the reagents to be stored at 4 degrees C for up to four weeks in the microfluidic device. When carrying out an analysis the crude sample only needed to be hydrodynamically introduced into the device which was connected to an external computer controlled power supply via platinum wire electrodes. DNA was extracted with 65% efficiency after loading lysed cells onto a silica monolith. Ethanol contained within an agarose gel matrix was then used to wash unwanted debris away from the sample by EOP (100 V cm(-1) for 5 min). The retained DNA was subsequently eluted from the monolith by water contained in a second agarose gel, again by EOP using an electric field of 100 V cm(-1) for 5 min, and transferred into the PCR reagent containing gel. The eluted DNA in solution was successfully amplified by PCR, confirming that the concept of a complete self-contained microfluidic device could be realised for DNA sample clean up and amplification, using a simple pumping and on-chip reagent storage methodology.

  17. DNA gel electrophoretic and microaut oradiographic studies on apoptosisin bone tumor cells after exposure with 153Sm-EDTMP

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    The apoptosis in bone tumor cells is studied after 153Sm-EDTMP irradiation.Fragmented DNA is analyzed by agarose gel electrophoresis.Experimental observations show that 153Sm-EDTMP exposureinduces the internucleosomal DNA damage in bone tumor cells the DNAladder pattern formation in bone tumor cells is shown.At the same time,the microautoradiographic study indicates that 153153Sm-EDTMP could permeate through cell membrane and displays membrane-seeking condensation in bone tumor cells.Soon afterwards 153Sm-EDTMP could be phagocytized by the tumor cells and distributed in cytoplasm as well as nucleus in the form of phagosome.With the prolongation of observing time, the membrane-bounded apoptotic bodies are observed.

  18. Tracking dynamics of two-dimensional continuous attractor neural networks

    Science.gov (United States)

    Fung, C. C. Alan; Wong, K. Y. Michael; Wu, Si

    2009-12-01

    We introduce an analytically solvable model of two-dimensional continuous attractor neural networks (CANNs). The synaptic input and the neuronal response form Gaussian bumps in the absence of external stimuli, and enable the network to track external stimuli by its translational displacement in the two-dimensional space. Basis functions of the two-dimensional quantum harmonic oscillator in polar coordinates are introduced to describe the distortion modes of the Gaussian bump. The perturbative method is applied to analyze its dynamics. Testing the method by considering the network behavior when the external stimulus abruptly changes its position, we obtain results of the reaction time and the amplitudes of various distortion modes, with excellent agreement with simulation results.

  19. Electronics and optoelectronics of two-dimensional transition metal dichalcogenides.

    Science.gov (United States)

    Wang, Qing Hua; Kalantar-Zadeh, Kourosh; Kis, Andras; Coleman, Jonathan N; Strano, Michael S

    2012-11-01

    The remarkable properties of graphene have renewed interest in inorganic, two-dimensional materials with unique electronic and optical attributes. Transition metal dichalcogenides (TMDCs) are layered materials with strong in-plane bonding and weak out-of-plane interactions enabling exfoliation into two-dimensional layers of single unit cell thickness. Although TMDCs have been studied for decades, recent advances in nanoscale materials characterization and device fabrication have opened up new opportunities for two-dimensional layers of thin TMDCs in nanoelectronics and optoelectronics. TMDCs such as MoS(2), MoSe(2), WS(2) and WSe(2) have sizable bandgaps that change from indirect to direct in single layers, allowing applications such as transistors, photodetectors and electroluminescent devices. We review the historical development of TMDCs, methods for preparing atomically thin layers, their electronic and optical properties, and prospects for future advances in electronics and optoelectronics.

  20. Hamiltonian formalism of two-dimensional Vlasov kinetic equation.

    Science.gov (United States)

    Pavlov, Maxim V

    2014-12-08

    In this paper, the two-dimensional Benney system describing long wave propagation of a finite depth fluid motion and the multi-dimensional Russo-Smereka kinetic equation describing a bubbly flow are considered. The Hamiltonian approach established by J. Gibbons for the one-dimensional Vlasov kinetic equation is extended to a multi-dimensional case. A local Hamiltonian structure associated with the hydrodynamic lattice of moments derived by D. J. Benney is constructed. A relationship between this hydrodynamic lattice of moments and the two-dimensional Vlasov kinetic equation is found. In the two-dimensional case, a Hamiltonian hydrodynamic lattice for the Russo-Smereka kinetic model is constructed. Simple hydrodynamic reductions are presented.

  1. Control Operator for the Two-Dimensional Energized Wave Equation

    Directory of Open Access Journals (Sweden)

    Sunday Augustus REJU

    2006-07-01

    Full Text Available This paper studies the analytical model for the construction of the two-dimensional Energized wave equation. The control operator is given in term of space and time t independent variables. The integral quadratic objective cost functional is subject to the constraint of two-dimensional Energized diffusion, Heat and a source. The operator that shall be obtained extends the Conjugate Gradient method (ECGM as developed by Hestenes et al (1952, [1]. The new operator enables the computation of the penalty cost, optimal controls and state trajectories of the two-dimensional energized wave equation when apply to the Conjugate Gradient methods in (Waziri & Reju, LEJPT & LJS, Issues 9, 2006, [2-4] to appear in this series.

  2. 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...

  3. A two-dimensional spin liquid in quantum kagome ice.

    Science.gov (United States)

    Carrasquilla, Juan; Hao, Zhihao; Melko, Roger G

    2015-06-22

    Actively sought since the turn of the century, two-dimensional quantum spin liquids (QSLs) are exotic phases of matter where magnetic moments remain disordered even at zero temperature. Despite ongoing searches, QSLs remain elusive, due to a lack of concrete knowledge of the microscopic mechanisms that inhibit magnetic order in materials. Here we study a model for a broad class of frustrated magnetic rare-earth pyrochlore materials called quantum spin ices. When subject to an external magnetic field along the [111] crystallographic direction, the resulting interactions contain a mix of geometric frustration and quantum fluctuations in decoupled two-dimensional kagome planes. Using quantum Monte Carlo simulations, we identify a set of interactions sufficient to promote a groundstate with no magnetic long-range order, and a gap to excitations, consistent with a Z2 spin liquid phase. This suggests an experimental procedure to search for two-dimensional QSLs within a class of pyrochlore quantum spin ice materials.

  4. Spectral Radiative Properties of Two-Dimensional Rough Surfaces

    Science.gov (United States)

    Xuan, Yimin; Han, Yuge; Zhou, Yue

    2012-12-01

    Spectral radiative properties of two-dimensional rough surfaces are important for both academic research and practical applications. Besides material properties, surface structures have impact on the spectral radiative properties of rough surfaces. Based on the finite difference time domain algorithm, this paper studies the spectral energy propagation process on a two-dimensional rough surface and analyzes the effect of different factors such as the surface structure, angle, and polarization state of the incident wave on the spectral radiative properties of the two-dimensional rough surface. To quantitatively investigate the spatial distribution of energy reflected from the rough surface, the concept of the bidirectional reflectance distribution function is introduced. Correlation analysis between the reflectance and different impact factors is conducted to evaluate the influence degree. Comparison between the theoretical and experimental data is given to elucidate the accuracy of the computational code. This study is beneficial to optimizing the surface structures of optoelectronic devices such as solar cells.

  5. Two dimensional convolute integers for machine vision and image recognition

    Science.gov (United States)

    Edwards, Thomas R.

    1988-01-01

    Machine vision and image recognition require sophisticated image processing prior to the application of Artificial Intelligence. Two Dimensional Convolute Integer Technology is an innovative mathematical approach for addressing machine vision and image recognition. This new technology generates a family of digital operators for addressing optical images and related two dimensional data sets. The operators are regression generated, integer valued, zero phase shifting, convoluting, frequency sensitive, two dimensional low pass, high pass and band pass filters that are mathematically equivalent to surface fitted partial derivatives. These operators are applied non-recursively either as classical convolutions (replacement point values), interstitial point generators (bandwidth broadening or resolution enhancement), or as missing value calculators (compensation for dead array element values). These operators show frequency sensitive feature selection scale invariant properties. Such tasks as boundary/edge enhancement and noise or small size pixel disturbance removal can readily be accomplished. For feature selection tight band pass operators are essential. Results from test cases are given.

  6. Optical modulators with two-dimensional layered materials

    CERN Document Server

    Sun, Zhipei; Wang, Feng

    2016-01-01

    Light modulation is an essential operation in photonics and optoelectronics. With existing and emerging technologies increasingly demanding compact, efficient, fast and broadband optical modulators, high-performance light modulation solutions are becoming indispensable. The recent realization that two-dimensional layered materials could modulate light with superior performance has prompted intense research and significant advances, paving the way for realistic applications. In this review, we cover the state-of-the-art of optical modulators based on two-dimensional layered materials including graphene, transition metal dichalcogenides and black phosphorus. We discuss recent advances employing hybrid structures, such as two-dimensional heterostructures, plasmonic structures, and silicon/fibre integrated structures. We also take a look at future perspectives and discuss the potential of yet relatively unexplored mechanisms such as magneto-optic and acousto-optic modulation.

  7. Discovery of protein- and DNA-imperceptible nanoparticle hard coating using gel-based reaction tuning.

    Science.gov (United States)

    Welsher, Kevin; McManus, Simon A; Hsia, Chih-Hao; Yin, Shuhui; Yang, Haw

    2015-01-21

    The seemingly inevitable protein corona appears to be an insurmountable obstacle to wider application of functional nanomaterials in biotechnology. The accumulation of serum proteins can block targeting functionalities and alter the in vivo fate of these nanomaterials. Here we demonstrate a method to generate non-stick, robustly passivated functional nanoparticles (NPs) using a tailored silica coating. We apply agarose gel electrophoresis to sensitively evaluate protein binding to NPs with different surface chemistry. Using gel banding and retardation as a read-out for protein adsorption, we optimize the surface chemistry to yield a mixed charge surface which displays remarkable binding resistance to a wide range of serum proteins and nucleic acids. The hard silica shell also protects the functional NP core in harsh environments (down to pH 1) while still showing the ability to be targeted for cellular uptake with little or no non-specific binding.

  8. Variety of molecular conformation of plasmid pUC18 DNA and solenoidally supercoiled DNA

    Institute of Scientific and Technical Information of China (English)

    黄熙泰; 王照清; 吴永文; 樊廷玉; 王树荣; 王勖焜

    1996-01-01

    The plasmid pUC18 DNA isolated from Escherichia coli HB101 were analyzed by two-dimensional agarose gel electrophoresis and hybridization. The results show that the DNA sample can be separated into six groups of different structural components. The plectonemically and solenoidally supercoiled pUC18 DNA coexist in it. These two different conformations of supercoiled DNA are interchangeable with the circumstances (ionic strength and type, etc.). The amount of solenoidally supercoiled pUC18 DNA in the samples can be changed by treatment of DNA topoisome rases. Under an electron microscope, the solenoidal supercoiling DNA has a round shape with an average diameter of 45 nm. The facts suggest that solenoidaUy supercoiled DNA be a structural entity independent of histones. The polymorphism of DNA structure may be important to packing of DNA in vivo.

  9. Two-dimensional superconductors with atomic-scale thickness

    Science.gov (United States)

    Uchihashi, Takashi

    2017-01-01

    Recent progress in two-dimensional superconductors with atomic-scale thickness is reviewed mainly from the experimental point of view. The superconducting systems treated here involve a variety of materials and forms: elemental metal ultrathin films and atomic layers on semiconductor surfaces; interfaces and superlattices of heterostructures made of cuprates, perovskite oxides, and rare-earth metal heavy-fermion compounds; interfaces of electric-double-layer transistors; graphene and atomic sheets of transition metal dichalcogenide; iron selenide and organic conductors on oxide and metal surfaces, respectively. Unique phenomena arising from the ultimate two dimensionality of the system and the physics behind them are discussed.

  10. 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.

  11. Singular analysis of two-dimensional bifurcation system

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Bifurcation properties of two-dimensional bifurcation system are studied in this paper.Universal unfolding and transition sets of the bifurcation equations are obtained.The whole parametric plane is divided into several different persistent regions according to the type of motion,and the different qualitative bifurcation diagrams in different persistent regions are given.The bifurcation properties of the two-dimensional bifurcation system are compared with its reduced one-dimensional system.It is found that the system which is reduced to one dimension has lost many bifurcation properties.

  12. Critical Behaviour of a Two-Dimensional Random Antiferromagnet

    DEFF Research Database (Denmark)

    Als-Nielsen, Jens Aage; Birgeneau, R. J.; Guggenheim, H. J.

    1976-01-01

    A neutron scattering study of the order parameter, correlation length and staggered susceptibility of the two-dimensional random antiferromagnet Rb2Mn0.5Ni0.5F4 is reported. The system is found to exhibit a well-defined phase transition with critical exponents identical to those of the isomorphou...... pure materials K2NiF4 and K2MnF4. Thus, in these systems, which have the asymptotic critical behaviour of the two-dimensional Ising model, randomness has no measurable effect on the phase-transition behaviour....

  13. Nonlinear excitations in two-dimensional molecular structures with impurities

    DEFF Research Database (Denmark)

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

    1995-01-01

    We study the nonlinear dynamics of electronic excitations interacting with acoustic phonons in two-dimensional molecular structures with impurities. We show that the problem is reduced to the nonlinear Schrodinger equation with a varying coefficient. The latter represents the influence of the imp......We study the nonlinear dynamics of electronic excitations interacting with acoustic phonons in two-dimensional molecular structures with impurities. We show that the problem is reduced to the nonlinear Schrodinger equation with a varying coefficient. The latter represents the influence...... excitations. Analytical results are in good agreement with numerical simulations of the nonlinear Schrodinger equation....

  14. Vortices in the Two-Dimensional Simple Exclusion Process

    Science.gov (United States)

    Bodineau, T.; Derrida, B.; Lebowitz, Joel L.

    2008-06-01

    We show that the fluctuations of the partial current in two dimensional diffusive systems are dominated by vortices leading to a different scaling from the one predicted by the hydrodynamic large deviation theory. This is supported by exact computations of the variance of partial current fluctuations for the symmetric simple exclusion process on general graphs. On a two-dimensional torus, our exact expressions are compared to the results of numerical simulations. They confirm the logarithmic dependence on the system size of the fluctuations of the partial flux. The impact of the vortices on the validity of the fluctuation relation for partial currents is also discussed in an Appendix.

  15. Two-dimensional hazard estimation for longevity analysis

    DEFF Research Database (Denmark)

    Fledelius, Peter; Guillen, M.; Nielsen, J.P.

    2004-01-01

    the two-dimensional mortality surface. Furthermore we look at aggregated synthetic population metrics as 'population life expectancy' and 'population survival probability'. For Danish women these metrics indicate decreasing mortality with respect to chronological time. The metrics can not directly be used......We investigate developments in Danish mortality based on data from 1974-1998 working in a two-dimensional model with chronological time and age as the two dimensions. The analyses are done with non-parametric kernel hazard estimation techniques. The only assumption is that the mortality surface...... for analysis of economic implications arising from mortality changes....

  16. Field analysis of two-dimensional focusing grating couplers

    Science.gov (United States)

    Borsboom, P.-P.; Frankena, H. J.

    1995-05-01

    A different technique was developed by which several two-dimensional dielectric optical gratings, consisting 100 or more corrugations, were treated in a numerical reliable approach. The numerical examples that were presented were restricted to gratings made up of sequences of waveguide sections symmetric about the x = 0 plane. The newly developed method was effectively used to investigate the field produced by a two-dimensional focusing grating coupler. Focal-region fields were determined for three symmetrical gratings with 19, 50, and 124 corrugations. For focusing grating coupler with limited length, high-frequency intensity variations were noted in the focal region.

  17. Dynamics of vortex interactions in two-dimensional flows

    DEFF Research Database (Denmark)

    Juul Rasmussen, J.; Nielsen, A.H.; Naulin, V.

    2002-01-01

    a critical value, a(c). Using the Weiss-field, a(c) is estimated for vortex patches. Introducing an effective radius for vortices with distributed vorticity, we find that 3.3 a(c) ...The dynamics and interaction of like-signed vortex structures in two dimensional flows are investigated by means of direct numerical solutions of the two-dimensional Navier-Stokes equations. Two vortices with distributed vorticity merge when their distance relative to their radius, d/R-0l. is below...

  18. Two-dimensional assignment with merged measurements using Langrangrian relaxation

    Science.gov (United States)

    Briers, Mark; Maskell, Simon; Philpott, Mark

    2004-01-01

    Closely spaced targets can result in merged measurements, which complicate data association. Such merged measurements violate any assumption that each measurement relates to a single target. As a result, it is not possible to use the auction algorithm in its simplest form (or other two-dimensional assignment algorithms) to solve the two-dimensional target-to-measurement assignment problem. We propose an approach that uses the auction algorithm together with Lagrangian relaxation to incorporate the additional constraints resulting from the presence of merged measurements. We conclude with some simulated results displaying the concepts introduced, and discuss the application of this research within a particle filter context.

  19. Two-dimensional lattice Boltzmann model for magnetohydrodynamics.

    Science.gov (United States)

    Schaffenberger, Werner; Hanslmeier, Arnold

    2002-10-01

    We present a lattice Boltzmann model for the simulation of two-dimensional magnetohydro dynamic (MHD) flows. The model is an extension of a hydrodynamic lattice Boltzman model with 9 velocities on a square lattice resulting in a model with 17 velocities. Earlier lattice Boltzmann models for two-dimensional MHD used a bidirectional streaming rule. However, the use of such a bidirectional streaming rule is not necessary. In our model, the standard streaming rule is used, allowing smaller viscosities. To control the viscosity and the resistivity independently, a matrix collision operator is used. The model is then applied to the Hartmann flow, giving reasonable results.

  20. Quasinormal frequencies of asymptotically flat two-dimensional black holes

    CERN Document Server

    Lopez-Ortega, A

    2011-01-01

    We discuss whether the minimally coupled massless Klein-Gordon and Dirac fields have well defined quasinormal modes in single horizon, asymptotically flat two-dimensional black holes. To get the result we solve the equations of motion in the massless limit and we also calculate the effective potentials of Schrodinger type equations. Furthermore we calculate exactly the quasinormal frequencies of the Dirac field propagating in the two-dimensional uncharged Witten black hole. We compare our results on its quasinormal frequencies with other already published.

  1. Spin dynamics in a two-dimensional quantum gas

    DEFF Research Database (Denmark)

    Pedersen, Poul Lindholm; Gajdacz, Miroslav; Deuretzbacher, Frank

    2014-01-01

    We have investigated spin dynamics in a two-dimensional quantum gas. Through spin-changing collisions, two clouds with opposite spin orientations are spontaneously created in a Bose-Einstein condensate. After ballistic expansion, both clouds acquire ring-shaped density distributions with superimp......We have investigated spin dynamics in a two-dimensional quantum gas. Through spin-changing collisions, two clouds with opposite spin orientations are spontaneously created in a Bose-Einstein condensate. After ballistic expansion, both clouds acquire ring-shaped density distributions...

  2. Replication of Bovine Papillomavirus Type 1 (BPV-1) DNA in Saccharomyces cerevisiae following Infection with BPV-1 Virions

    OpenAIRE

    Zhao, Kong-Nan; Frazer, Ian H

    2002-01-01

    Saccharomyces cerevisiae protoplasts exposed to bovine papillomavirus type 1 (BPV-1) virions demonstrated uptake of virions on electron microscopy. S. cerevisiae cells looked larger after exposure to BPV-1 virions, and cell wall regeneration was delayed. Southern blot hybridization of Hirt DNA from cells exposed to BPV-1 virions demonstrated BPV-1 DNA, which could be detected over 80 days of culture and at least 13 rounds of division. Two-dimensional gel analysis of Hirt DNA showed replicativ...

  3. On some classes of two-dimensional local models in discrete two-dimensional monatomic FPU lattice with cubic and quartic potential

    Institute of Scientific and Technical Information of China (English)

    Xu Quan; Tian Qiang

    2009-01-01

    This paper discusses the two-dimensional discrete monatomic Fermi-Pasta-Ulam lattice, by using the method of multiple-scale and the quasi-discreteness approach. By taking into account the interaction between the atoms in the lattice and their nearest neighbours, it obtains some classes of two-dimensional local models as follows: two-dimensional bright and dark discrete soliton trains, two-dimensional bright and dark line discrete breathers, and two-dimensional bright and dark discrete breather.

  4. Feasibility of a DNA-Based Combinatorial Array Recognition Surface (CARS) in a Polyacrylamide Gel Matrix

    Science.gov (United States)

    2007-12-12

    the phosphate backbone. wherever p.·J.Ttial hybrids naturally occur, via Taq DNA ligase (16). Ligation may not have been entirely necessary for the...CARS libraries, noncontiguous pieces can be ligaled togclher willi Taq DNA ligase . The lOp half o(lhe figure iIIu51Tates Ihe appearance o( a I-D CARS...cluding dideoxynucleotides. were from a "Si lver Sequence" kit purchased from Promega Corporation (Madison. WI). ThermliS aquaticus (Taq) DNA ligase was

  5. Mapping two-dimensional polar active fluids to two-dimensional soap and one-dimensional sandblasting

    Science.gov (United States)

    Chen, Leiming; Lee, Chiu Fan; Toner, John

    2016-07-01

    Active fluids and growing interfaces are two well-studied but very different non-equilibrium systems. Each exhibits non-equilibrium behaviour distinct from that of their equilibrium counterparts. Here we demonstrate a surprising connection between these two: the ordered phase of incompressible polar active fluids in two spatial dimensions without momentum conservation, and growing one-dimensional interfaces (that is, the 1+1-dimensional Kardar-Parisi-Zhang equation), in fact belong to the same universality class. This universality class also includes two equilibrium systems: two-dimensional smectic liquid crystals, and a peculiar kind of constrained two-dimensional ferromagnet. We use these connections to show that two-dimensional incompressible flocks are robust against fluctuations, and exhibit universal long-ranged, anisotropic spatio-temporal correlations of those fluctuations. We also thereby determine the exact values of the anisotropy exponent ζ and the roughness exponents χx,y that characterize these correlations.

  6. Mechanism of Lactobacillus casei Zhang domesticated strain against acid stress by two-dimensional fluorescence difference in gel electrophoresis analysis%应用双向荧光差异凝胶技术解析干酪乳杆菌Lactobacillus casei Zhang驯化菌株耐酸胁迫机制

    Institute of Scientific and Technical Information of China (English)

    张娟; 吴重德; 张梦汝; 堵国成; 陈坚

    2012-01-01

    The domesticated strain of Lactobacillus casei Zhang with outstanding acid stress resistance was obtained after the adaptive evolution. The intracellular microenvironment analysis found that the domesticated strain can maintain a higher phosphoenolpyruvate-sugar transfer enzyme activity in the acid stress process, and showed higher H+-ATPase activity and intracellular ATP concentration. Proteomics analysis investigated that the acid treatment led to expression changes of cell protein. Compared with the wild strain, the domesticated strain maintained higher metabolic activity. Meanwhile, the domesticated strain kept its physiological activity by a large number of induced stress proteins such as molecular chaperones GroEL, GrpE, and the cold / heat stress protein CspC / DnaK, which effectively improved the acid stress resistance. This study revealed the physiology of lactic acid bacteria cells under acid stress further, and explored the optimal strategy to promote the performance of lactic acid bacteria against acid stress, thereby provided a novel way to enhance their performance on industrial application.%以干酪乳杆菌Lactobacillus casei Zhang为出发菌株,通过适应性进化获得了干酪乳杆菌酸胁迫抗性驯化菌株.对细胞内微环境的检测发现,驯化菌株在酸胁迫过程中能够维持较高的磷酸烯醇式丙酮酸-糖转移酶系统活力,并具有较高的H+ -ATPase活性以及胞内ATP浓度.蛋白质组学分析结果表明,酸胁迫引发了细胞蛋白表达的变化,与原始菌株相比,驯化菌株保持了更高的代谢活性;同时,驯化菌株通过大量诱导应激蛋白如分子伴侣GroEL、GrpE,冷/热应激蛋白CspC、DnaK等维持了细胞的生理活性,有效提高了细胞对酸胁迫的抵御能力.本研究为进一步揭示酸胁迫下乳酸菌细胞的生理应答机制,探寻促进乳酸菌酸胁迫性能提升的最优策略,进而改善其在生产中的应用性能提供了可借鉴的思路.

  7. Waiting Time Dynamics in Two-Dimensional Infrared Spectroscopy

    NARCIS (Netherlands)

    Jansen, Thomas L. C.; Knoester, Jasper

    We review recent work on the waiting time dynamics of coherent two-dimensional infrared (2DIR) spectroscopy. This dynamics can reveal chemical and physical processes that take place on the femto- and picosecond time scale, which is faster than the time scale that may be probed by, for example,

  8. The partition function of two-dimensional string theory

    Science.gov (United States)

    Dijkgraaf, Robbert; Moore, Gregory; Plesser, Ronen

    1993-04-01

    We derive a compact and explicit expression for the generating functional of all correlation functions of tachyon operators in two-dimensional string theory. This expression makes manifest relations of the c = 1 system to KP flow nd W 1 + ∞ constraints. Moreover we derive a Kontsevich-Penner integral representation of this generating functional.

  9. The partition function of two-dimensional string theory

    Energy Technology Data Exchange (ETDEWEB)

    Dijkgraaf, R. (School of Natural Sciences, Inst. for Advanced Study, Princeton, NJ (United States) Dept. of Mathematics, Univ. Amsterdam (Netherlands)); Moore, G.; Plesser, R. (Dept. of Physics, Yale Univ., New Haven, CT (United States))

    1993-04-12

    We derive a compact and explicit expression for the generating functional of all correlation functions of tachyon operators in two-dimensional string theory. This expression makes manifest relations of the c=1 system to KP flow and W[sub 1+[infinity

  10. Two-Dimensional Electronic Spectroscopy of a Model Dimer System

    Directory of Open Access Journals (Sweden)

    Prokhorenko V.I.

    2013-03-01

    Full Text Available Two-dimensional spectra of a dimer were measured to determine the timescale for electronic decoherence at room temperature. Anti-correlated beats in the crosspeaks were observed only during the period corresponding to the measured homogeneous lifetime.

  11. Torque magnetometry studies of two-dimensional electron systems

    NARCIS (Netherlands)

    Schaapman, Maaike Ruth

    2004-01-01

    This thesis describes a study of the magnetization two-dimensional electron gases (2DEGs). To detect the typically small magnetization, a sensitive magnetometer with optical angular detection was developed. The magnetometer uses a quadrant detector to measure the rotation of the sample. By mounting

  12. Low-frequency scattering from two-dimensional perfect conductors

    DEFF Research Database (Denmark)

    Hansen, Thorkild; Yaghjian, A.D

    1991-01-01

    Exact expressions have been obtained for the leading terms in the low-frequency expansions of the far fields scattered from three different types of two-dimensional perfect conductors: a cylinder with finite cross section, a cylindrical bump on an infinite ground plane, and a cylindrical dent...

  13. 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

  14. Piezoelectricity and Piezomagnetism: Duality in two-dimensional checkerboards

    Science.gov (United States)

    Fel, Leonid G.

    2002-05-01

    The duality approach in two-dimensional two-component regular checkerboards is extended to piezoelectricity and piezomagnetism. The relation between the effective piezoelectric and piezomagnetic moduli is found for a checkerboard with the p6'mm'-plane symmetry group (dichromatic triangle).

  15. Specification of a Two-Dimensional Test Case

    DEFF Research Database (Denmark)

    Nielsen, Peter Vilhelm

    This paper describes the geometry and other boundary conditions for a test case which can be used to test different two-dimensional CFD codes in the lEA Annex 20 work. The given supply opening is large compared with practical openings. Therefore, this geometry will reduce the need for a high number...... of grid points in the wall jet region....

  16. Operator splitting for two-dimensional incompressible fluid equations

    CERN Document Server

    Holden, Helge; Karper, Trygve K

    2011-01-01

    We analyze splitting algorithms for a class of two-dimensional fluid equations, which includes the incompressible Navier-Stokes equations and the surface quasi-geostrophic equation. Our main result is that the Godunov and Strang splitting methods converge with the expected rates provided the initial data are sufficiently regular.

  17. Chaotic dynamics for two-dimensional tent maps

    Science.gov (United States)

    Pumariño, Antonio; Ángel Rodríguez, José; Carles Tatjer, Joan; Vigil, Enrique

    2015-02-01

    For a two-dimensional extension of the classical one-dimensional family of tent maps, we prove the existence of an open set of parameters for which the respective transformation presents a strange attractor with two positive Lyapounov exponents. Moreover, periodic orbits are dense on this attractor and the attractor supports a unique ergodic invariant probability measure.

  18. 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...

  19. Spin-orbit torques in two-dimensional Rashba ferromagnets

    NARCIS (Netherlands)

    Qaiumzadeh, A.; Duine, R. A.|info:eu-repo/dai/nl/304830127; Titov, M.

    2015-01-01

    Magnetization dynamics in single-domain ferromagnets can be triggered by a charge current if the spin-orbit coupling is sufficiently strong. We apply functional Keldysh theory to investigate spin-orbit torques in metallic two-dimensional Rashba ferromagnets in the presence of spin-dependent

  20. Numerical blowup in two-dimensional Boussinesq equations

    CERN Document Server

    Yin, Zhaohua

    2009-01-01

    In this paper, we perform a three-stage numerical relay to investigate the finite time singularity in the two-dimensional Boussinesq approximation equations. The initial asymmetric condition is the middle-stage output of a $2048^2$ run, the highest resolution in our study is $40960^2$, and some signals of numerical blowup are observed.

  1. Exact two-dimensional superconformal R symmetry and c extremization.

    Science.gov (United States)

    Benini, Francesco; Bobev, Nikolay

    2013-02-08

    We uncover a general principle dubbed c extremization, which determines the exact R symmetry of a two-dimensional unitary superconformal field theory with N=(0,2) supersymmetry. To illustrate its utility, we study superconformal theories obtained by twisted compactifications of four-dimensional N=4 super-Yang-Mills theory on Riemann surfaces and construct their gravity duals.

  2. 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

  3. Topology optimization of two-dimensional elastic wave barriers

    DEFF Research Database (Denmark)

    Van Hoorickx, C.; Sigmund, Ole; Schevenels, M.

    2016-01-01

    Topology optimization is a method that optimally distributes material in a given design domain. In this paper, topology optimization is used to design two-dimensional wave barriers embedded in an elastic halfspace. First, harmonic vibration sources are considered, and stiffened material is insert...

  4. Non perturbative methods in two dimensional quantum field theory

    CERN Document Server

    Abdalla, Elcio; Rothe, Klaus D

    1991-01-01

    This book is a survey of methods used in the study of two-dimensional models in quantum field theory as well as applications of these theories in physics. It covers the subject since the first model, studied in the fifties, up to modern developments in string theories, and includes exact solutions, non-perturbative methods of study, and nonlinear sigma models.

  5. Thermodynamics of Two-Dimensional Black-Holes

    OpenAIRE

    Nappi, Chiara R.; Pasquinucci, Andrea

    1992-01-01

    We explore the thermodynamics of a general class of two dimensional dilatonic black-holes. A simple prescription is given that allows us to compute the mass, entropy and thermodynamic potentials, with results in agreement with those obtained by other methods, when available.

  6. Influence of index contrast in two dimensional photonic crystal lasers

    DEFF Research Database (Denmark)

    Jørgensen, Mette Marie; Petersen, Sidsel Rübner; Christiansen, Mads Brøkner;

    2010-01-01

    The influence of index contrast variations for obtaining single-mode operation and low threshold in dye doped polymer two dimensional photonic crystal (PhC) lasers is investigated. We consider lasers made from Pyrromethene 597 doped Ormocore imprinted with a rectangular lattice PhC having a cavit...

  7. Magnetic order in two-dimensional nanoparticle assemblies

    NARCIS (Netherlands)

    Georgescu, M

    2008-01-01

    This thesis involves a fundamental study of two-dimensional arrays of magnetic nanoparticles using non-contact Atomic Force Microscopy, Magnetic Force Microscopy, and Atomic Force Spectroscopy. The goal is to acquire a better understanding of the interactions between magnetic nanoparticles and the

  8. Dynamical phase transitions in the two-dimensional ANNNI model

    Energy Technology Data Exchange (ETDEWEB)

    Barber, M.N.; Derrida, B.

    1988-06-01

    We study the phase diagram of the two-dimensional anisotropic next-nearest neighbor Ising (ANNNI) model by comparing the time evolution of two distinct spin configurations submitted to the same thermal noise. We clearly se several dynamical transitions between ferromagnetic, paramagnetic, antiphase, and floating phases. These dynamical transitions seem to occur rather close to the transition lines determined previously in the literature.

  9. Two-dimensional static black holes with pointlike sources

    CERN Document Server

    Melis, M

    2004-01-01

    We study the static black hole solutions of generalized two-dimensional dilaton-gravity theories generated by pointlike mass sources, in the hypothesis that the matter is conformally coupled. We also discuss the motion of test particles. Due to conformal coupling, these follow the geodesics of a metric obtained by rescaling the canonical metric with the dilaton.

  10. Magnetic order in two-dimensional nanoparticle assemblies

    NARCIS (Netherlands)

    Georgescu, M

    2008-01-01

    This thesis involves a fundamental study of two-dimensional arrays of magnetic nanoparticles using non-contact Atomic Force Microscopy, Magnetic Force Microscopy, and Atomic Force Spectroscopy. The goal is to acquire a better understanding of the interactions between magnetic nanoparticles and the r

  11. Two-Dimensional Chirality in Three-Dimensional Chemistry.

    Science.gov (United States)

    Wintner, Claude E.

    1983-01-01

    The concept of two-dimensional chirality is used to enhance students' understanding of three-dimensional stereochemistry. This chirality is used as a key to teaching/understanding such concepts as enaniotropism, diastereotopism, pseudoasymmetry, retention/inversion of configuration, and stereochemical results of addition to double bonds. (JN)

  12. Field analysis of two-dimensional focusing grating

    NARCIS (Netherlands)

    Borsboom, P.P.; Frankena, H.J.

    1995-01-01

    The method that we have developed [P-P. Borsboom, Ph.D. dissertation (Delft University of Technology, Delft, The Netherlands); P-P. Borsboom and H. J. Frankena, J. Opt. Soc. Am. A 12, 1134–1141 (1995)] is successfully applied to a two-dimensional focusing grating coupler. The field in the focal regi

  13. Torque magnetometry studies of two-dimensional electron systems

    NARCIS (Netherlands)

    Schaapman, Maaike Ruth

    2004-01-01

    This thesis describes a study of the magnetization two-dimensional electron gases (2DEGs). To detect the typically small magnetization, a sensitive magnetometer with optical angular detection was developed. The magnetometer uses a quadrant detector to measure the rotation of the sample. By mounting

  14. 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

  15. Vibrations of Thin Piezoelectric Shallow Shells: Two-Dimensional Approximation

    Indian Academy of Sciences (India)

    N Sabu

    2003-08-01

    In this paper we consider the eigenvalue problem for piezoelectric shallow shells and we show that, as the thickness of the shell goes to zero, the eigensolutions of the three-dimensional piezoelectric shells converge to the eigensolutions of a two-dimensional eigenvalue problem.

  16. 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...

  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. Easy interpretation of optical two-dimensional correlation spectra

    NARCIS (Netherlands)

    Lazonder, K.; Pshenichnikov, M.S.; Wiersma, D.A.

    2006-01-01

    We demonstrate that the value of the underlying frequency-frequency correlation function can be retrieved from a two-dimensional optical correlation spectrum through a simple relationship. The proposed method yields both intuitive clues and a quantitative measure of the dynamics of the system. The t

  19. Two Dimensional F(R) Horava-Lifshitz Gravity

    CERN Document Server

    Kluson, J

    2016-01-01

    We study two-dimensional F(R) Horava-Lifshitz gravity from the Hamiltonian point of view. We determine constraints structure with emphasis on the careful separation of the second class constraints and global first class constraints. We determine number of physical degrees of freedom and also discuss gauge fixing of the global first class constraints.

  20. Localization of Tight Closure in Two-Dimensional Rings

    Indian Academy of Sciences (India)

    Kamran Divaani-Aazar; Massoud Tousi

    2005-02-01

    It is shown that tight closure commutes with localization in any two-dimensional ring of prime characteristic if either is a Nagata ring or possesses a weak test element. Moreover, it is proved that tight closure commutes with localization at height one prime ideals in any ring of prime characteristic.

  1. Cryptanalysis of the Two-Dimensional Circulation Encryption Algorithm

    Directory of Open Access Journals (Sweden)

    Bart Preneel

    2005-07-01

    Full Text Available We analyze the security of the two-dimensional circulation encryption algorithm (TDCEA, recently published by Chen et al. in this journal. We show that there are several flaws in the algorithm and describe some attacks. We also address performance issues in current cryptographic designs.

  2. New directions in science and technology: two-dimensional crystals

    Energy Technology Data Exchange (ETDEWEB)

    Neto, A H Castro [Graphene Research Centre, National University of Singapore, 2 Science Drive 3, Singapore 117542 (Singapore); Novoselov, K, E-mail: phycastr@nus.edu.sg, E-mail: konstantin.novoselov@manchester.ac.uk [School of Physics and Astronomy, University of Manchester, Oxford Road, Manchester, M13 9PL (United Kingdom)

    2011-08-15

    Graphene is possibly one of the largest and fastest growing fields in condensed matter research. However, graphene is only one example in a large class of two-dimensional crystals with unusual properties. In this paper we briefly review the properties of graphene and look at the exciting possibilities that lie ahead.

  3. Boundary-value problems for two-dimensional canonical systems

    NARCIS (Netherlands)

    Hassi, Seppo; De Snoo, H; Winkler, Henrik

    2000-01-01

    The two-dimensional canonical system Jy' = -lHy where the nonnegative Hamiltonian matrix function H(x) is trace-normed on (0,∞) has been studied in a function-theoretic way by L. de Branges. We show that the Hamiltonian system induces a closed symmetric relation which can be reduced to a, not necess

  4. 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

  5. Dislocation climb in two-dimensional discrete dislocation dynamics

    NARCIS (Netherlands)

    Davoudi, K.M.; Nicola, L.; Vlassak, J.J.

    2012-01-01

    In this paper, dislocation climb is incorporated in a two-dimensional discrete dislocation dynamics model. Calculations are carried out for polycrystalline thin films, passivated on one or both surfaces. Climb allows dislocations to escape from dislocation pile-ups and reduces the strain-hardening r

  6. SAR Processing Based On Two-Dimensional Transfer Function

    Science.gov (United States)

    Chang, Chi-Yung; Jin, Michael Y.; Curlander, John C.

    1994-01-01

    Exact transfer function, ETF, is two-dimensional transfer function that constitutes basis of improved frequency-domain-convolution algorithm for processing synthetic-aperture-radar, SAR data. ETF incorporates terms that account for Doppler effect of motion of radar relative to scanned ground area and for antenna squint angle. Algorithm based on ETF outperforms others.

  7. Sound waves in two-dimensional ducts with sinusoidal walls

    Science.gov (United States)

    Nayfeh, A. H.

    1974-01-01

    The method of multiple scales is used to analyze the wave propagation in two-dimensional hard-walled ducts with sinusoidal walls. For traveling waves, resonance occurs whenever the wall wavenumber is equal to the difference of the wavenumbers of any two duct acoustic modes. The results show that neither of these resonating modes could occur without strongly generating the other.

  8. Confined two-dimensional fermions at finite density

    CERN Document Server

    De Francia, M; Loewe, M; Santangelo, E M; De Francia, M; Falomir, H; Loewe, M; Santangelo, E M

    1995-01-01

    We introduce the chemical potential in a system of two-dimensional massless fermions, confined to a finite region, by imposing twisted boundary conditions in the Euclidean time direction. We explore in this simple model the application of functional techniques which could be used in more complicated situations.

  9. Imperfect two-dimensional topological insulator field-effect transistors

    Science.gov (United States)

    Vandenberghe, William G.; Fischetti, Massimo V.

    2017-01-01

    To overcome the challenge of using two-dimensional materials for nanoelectronic devices, we propose two-dimensional topological insulator field-effect transistors that switch based on the modulation of scattering. We model transistors made of two-dimensional topological insulator ribbons accounting for scattering with phonons and imperfections. In the on-state, the Fermi level lies in the bulk bandgap and the electrons travel ballistically through the topologically protected edge states even in the presence of imperfections. In the off-state the Fermi level moves into the bandgap and electrons suffer from severe back-scattering. An off-current more than two-orders below the on-current is demonstrated and a high on-current is maintained even in the presence of imperfections. At low drain-source bias, the output characteristics are like those of conventional field-effect transistors, at large drain-source bias negative differential resistance is revealed. Complementary n- and p-type devices can be made enabling high-performance and low-power electronic circuits using imperfect two-dimensional topological insulators. PMID:28106059

  10. 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...

  11. Miniature sensor for two-dimensional magnetic field distributions

    NARCIS (Netherlands)

    Fluitman, J.H.J.; Krabbe, H.W.

    1972-01-01

    Describes a simple method of production of a sensor for two-dimensional magnetic field distributions. The sensor consists of a strip of Ni-Fe(81-19), of which the magnetoresistance is utilized. Typical dimensions of the strip, placed at the edge of a glass substrate, are: length 100 mu m, width 2 or

  12. 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

  13. Spontaneous emission in two-dimensional photonic crystal microcavities

    DEFF Research Database (Denmark)

    Søndergaard, Thomas

    2000-01-01

    The properties of the radiation field in a two-dimensional photonic crystal with and without a microcavity introduced are investigated through the concept of the position-dependent photon density of states. The position-dependent rate of spontaneous radiative decay for a two-level atom with random...

  14. Phase conjugated Andreev backscattering in two-dimensional ballistic cavities

    NARCIS (Netherlands)

    Morpurgo, A.F.; Holl, S.; Wees, B.J.van; Klapwijk, T.M; Borghs, G.

    1997-01-01

    We have experimentally investigated transport in two-dimensional ballistic cavities connected to a point contact and to two superconducting electrodes with a tunable macroscopic phase difference. The point contact resistance oscillates as a function of the phase difference in a way which reflects

  15. Two-dimensional manifold with point-like defects

    CERN Document Server

    Gani, Vakhid A; Rubin, Sergei G

    2014-01-01

    We study a class of two-dimensional extra spaces isomorphic to the $S^2$ sphere in the framework of the multidimensional gravitation. We show that there exists a family of stationary metrics that depend on the initial (boundary) conditions. All these geometries have a singular point. We also discuss the possibility for these deformed extra spaces to be considered as dark matter candidates.

  16. Instability of two-dimensional heterotic stringy black holes

    CERN Document Server

    Azreg-Ainou, M

    1999-01-01

    We solve the eigenvalue problem of general relativity for the case of charged black holes in two-dimensional heterotic string theory, derived by McGuigan et al. For the case of $m^{2}>q^{2}$, we find a physically acceptable time-dependent growing mode; thus the black hole is unstable. The extremal case $m^{2}=q^{2}$ is stable.

  17. Two Dimensional Tensor Product B-Spline Wavelet Scaling Functions for the Solution of Two-Dimensional Unsteady Diffusion Equations

    Institute of Scientific and Technical Information of China (English)

    XIONG Lei; LI haijiao; ZHANG Lewen

    2008-01-01

    The fourth-order B spline wavelet scaling functions are used to solve the two-dimensional unsteady diffusion equation. The calculations from a case history indicate that the method provides high accuracy and the computational efficiency is enhanced due to the small matrix derived from this method.The respective features of 3-spline wavelet scaling functions, 4-spline wavelet scaling functions and quasi-wavelet used to solve the two-dimensional unsteady diffusion equation are compared. The proposed method has potential applications in many fields including marine science.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-07-01

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

  19. Pulse Field Gel Electrophoresis.

    Science.gov (United States)

    Sharma-Kuinkel, Batu K; Rude, Thomas H; Fowler, Vance G

    2016-01-01

    Pulse Field Gel Electrophoresis (PFGE) is a powerful genotyping technique used for the separation of large DNA molecules (entire genomic DNA) after digesting it with unique restriction enzymes and applying to a gel matrix under the electric field that periodically changes direction. PFGE is a variation of agarose gel electrophoresis that permits analysis of bacterial DNA fragments over an order of magnitude larger than that with conventional restriction enzyme analysis. It provides a good representation of the entire bacterial chromosome in a single gel with a highly reproducible restriction profile, providing clearly distinct and well-resolved DNA fragments.

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

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

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

  1. Parallel characterization of anaerobic toluene- and ethylbenzene-degrading microbial consortia by PCR-denaturing gradient gel electrophoresis, RNA-DNA membrane hybridization, and DNA microarray technology

    Science.gov (United States)

    Koizumi, Yoshikazu; Kelly, John J.; Nakagawa, Tatsunori; Urakawa, Hidetoshi; El-Fantroussi, Said; Al-Muzaini, Saleh; Fukui, Manabu; Urushigawa, Yoshikuni; Stahl, David A.

    2002-01-01

    A mesophilic toluene-degrading consortium (TDC) and an ethylbenzene-degrading consortium (EDC) were established under sulfate-reducing conditions. These consortia were first characterized by denaturing gradient gel electrophoresis (DGGE) fingerprinting of PCR-amplified 16S rRNA gene fragments, followed by sequencing. The sequences of the major bands (T-1 and E-2) belonging to TDC and EDC, respectively, were affiliated with the family Desulfobacteriaceae. Another major band from EDC (E-1) was related to an uncultured non-sulfate-reducing soil bacterium. Oligonucleotide probes specific for the 16S rRNAs of target organisms corresponding to T-1, E-1, and E-2 were designed, and hybridization conditions were optimized for two analytical formats, membrane and DNA microarray hybridization. Both formats were used to characterize the TDC and EDC, and the results of both were consistent with DGGE analysis. In order to assess the utility of the microarray format for analysis of environmental samples, oil-contaminated sediments from the coast of Kuwait were analyzed. The DNA microarray successfully detected bacterial nucleic acids from these samples, but probes targeting specific groups of sulfate-reducing bacteria did not give positive signals. The results of this study demonstrate the limitations and the potential utility of DNA microarrays for microbial community analysis.

  2. Nano-scale proteomics approach using two-dimensional fibrin zymography combined with fluorescent SYPRO ruby dye.

    Science.gov (United States)

    Choi, Nack-Shick; Yoo, Ki-Hyun; Yoon, Kab-Seog; Maeng, Pil Jae; Kim, Seung-Ho

    2004-05-31

    In general, a SYPRO Ruby dye is well known as a sensitive fluorescence-based method for detecting proteins by one-or two-dimensional SDS-PAGE (1-DE or 2-DE). Based on the SYPRO Ruby dye system, the combined two-dimensional fibrin zymography (2-D FZ) with SYPRO Ruby staining was newly developed to identify the Bacillus sp. proteases. Namely, complex protein mixtures from Bacillus sp. DJ-4, which were screened from Doen-Jang (Korean traditional fermented food), showed activity on the zymogram gel. The gel spots on the SYPRO Ruby gel, which corresponded to the active spots showing on the 2-D FZ gel, were analyzed by a matrix-assisted laser desorption ionization time of flight (MALDI-TOF) mass spectrometric analysis. Five intracellular fibrinolytic enzymes of Bacillus sp. DJ-4 were detected through 2-D FZ. The gel spots on the SYPRO Ruby dye stained 2-D gel corresponding to 2-D FZ were then analyzed by MALID-TOF MS. Three of the five gel spots proved to be quite similar to the ATP-dependent protease, extracellular neutral metalloprotease, and protease of Bacillus subtilis. Also, the extracellular proteases of Bacillus sp. DJ-4 employing this combined system were identified on three gels (e.g., casein, fibrin, and gelatin) and the proteolytic maps were established. This combined system of 2-D zymography and SYPRO Ruby dye should be useful for searching the specific protease from complex protein mixtures of many other sources (e.g., yeast and cancer cell lines).

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

    Institute of Scientific and Technical Information of China (English)

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

    2005-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2012-01-01

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

  5. Stress Wave Propagation in Two-dimensional Buckyball Lattice

    Science.gov (United States)

    Xu, Jun; Zheng, Bowen

    2016-11-01

    Orderly arrayed granular crystals exhibit extraordinary capability to tune stress wave propagation. Granular system of higher dimension renders many more stress wave patterns, showing its great potential for physical and engineering applications. At nanoscale, one-dimensionally arranged buckyball (C60) system has shown the ability to support solitary wave. In this paper, stress wave behaviors of two-dimensional buckyball (C60) lattice are investigated based on square close packing and hexagonal close packing. We show that the square close packed system supports highly directional Nesterenko solitary waves along initially excited chains and hexagonal close packed system tends to distribute the impulse and dissipates impact exponentially. Results of numerical calculations based on a two-dimensional nonlinear spring model are in a good agreement with the results of molecular dynamics simulations. This work enhances the understanding of wave properties and allows manipulations of nanoscale lattice and novel design of shock mitigation and nanoscale energy harvesting devices.

  6. 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.

  7. Entanglement Entropy in Two-Dimensional String Theory.

    Science.gov (United States)

    Hartnoll, Sean A; Mazenc, Edward A

    2015-09-18

    To understand an emergent spacetime is to understand the emergence of locality. Entanglement entropy is a powerful diagnostic of locality, because locality leads to a large amount of short distance entanglement. Two-dimensional string theory is among the very simplest instances of an emergent spatial dimension. We compute the entanglement entropy in the large-N matrix quantum mechanics dual to two-dimensional string theory in the semiclassical limit of weak string coupling. We isolate a logarithmically large, but finite, contribution that corresponds to the short distance entanglement of the tachyon field in the emergent spacetime. From the spacetime point of view, the entanglement is regulated by a nonperturbative "graininess" of space.

  8. Topological defect motifs in two-dimensional Coulomb clusters

    CERN Document Server

    Radzvilavičius, A; 10.1088/0953-8984/23/38/385301

    2012-01-01

    The most energetically favourable arrangement of low-density electrons in an infinite two-dimensional plane is the ordered triangular Wigner lattice. However, in most instances of contemporary interest one deals instead with finite clusters of strongly interacting particles localized in potential traps, for example, in complex plasmas. In the current contribution we study distribution of topological defects in two-dimensional Coulomb clusters with parabolic lateral confinement. The minima hopping algorithm based on molecular dynamics is used to efficiently locate the ground- and low-energy metastable states, and their structure is analyzed by means of the Delaunay triangulation. The size, structure and distribution of geometry-induced lattice imperfections strongly depends on the system size and the energetic state. Besides isolated disclinations and dislocations, classification of defect motifs includes defect compounds --- grain boundaries, rosette defects, vacancies and interstitial particles. Proliferatio...

  9. The Persistence Problem in Two-Dimensional Fluid Turbulence

    CERN Document Server

    Perlekar, Prasad; Mitra, Dhrubaditya; Pandit, Rahul

    2010-01-01

    We present a natural framework for studying the persistence problem in two-dimensional fluid turbulence by using the Okubo-Weiss parameter {\\Lambda} to distinguish between vortical and extensional regions. We then use a direct numerical simulation (DNS) of the two-dimensional, incompressible Navier-Stokes equation with Ekman friction to study probability distribution functions (PDFs) of the persistence times of vortical and extensional regions by employing both Eulerian and Lagrangian measurements. We find that, in the Eulerian case, the persistence-time PDFs have exponential tails; by contrast, this PDF for Lagrangian particles, in vortical regions, has a power-law tail with a universal exponent {\\theta} = 3.1 \\pm 0.2.

  10. On Dirichlet eigenvectors for neutral two-dimensional Markov chains

    CERN Document Server

    Champagnat, Nicolas; Miclo, Laurent

    2012-01-01

    We consider a general class of discrete, two-dimensional Markov chains modeling the dynamics of a population with two types, without mutation or immigration, and neutral in the sense that type has no influence on each individual's birth or death parameters. We prove that all the eigenvectors of the corresponding transition matrix or infinitesimal generator \\Pi\\ can be expressed as the product of "universal" polynomials of two variables, depending on each type's size but not on the specific transitions of the dynamics, and functions depending only on the total population size. These eigenvectors appear to be Dirichlet eigenvectors for \\Pi\\ on the complement of triangular subdomains, and as a consequence the corresponding eigenvalues are ordered in a specific way. As an application, we study the quasistationary behavior of finite, nearly neutral, two-dimensional Markov chains, absorbed in the sense that 0 is an absorbing state for each component of the process.

  11. Statistical mechanics of two-dimensional and geophysical flows

    CERN Document Server

    Bouchet, Freddy

    2011-01-01

    The theoretical study of the self-organization of two-dimensional and geophysical turbulent flows is addressed based on statistical mechanics methods. This review is a self-contained presentation of classical and recent works on this subject; from the statistical mechanics basis of the theory up to applications to Jupiter's troposphere and ocean vortices and jets. Emphasize has been placed on examples with available analytical treatment in order to favor better understanding of the physics and dynamics. The equilibrium microcanonical measure is built from the Liouville theorem. On this theoretical basis, we predict the output of the long time evolution of complex turbulent flows as statistical equilibria. This is applied to make quantitative models of two-dimensional turbulence, the Great Red Spot and other Jovian vortices, ocean jets like the Gulf-Stream, and ocean vortices. We also present recent results for non-equilibrium situations, for the studies of either the relaxation towards equilibrium or non-equi...

  12. Two-dimensional hazard estimation for longevity analysis

    DEFF Research Database (Denmark)

    Fledelius, Peter; Guillen, M.; Nielsen, J.P.

    2004-01-01

    We investigate developments in Danish mortality based on data from 1974-1998 working in a two-dimensional model with chronological time and age as the two dimensions. The analyses are done with non-parametric kernel hazard estimation techniques. The only assumption is that the mortality surface...... the two-dimensional mortality surface. Furthermore we look at aggregated synthetic population metrics as 'population life expectancy' and 'population survival probability'. For Danish women these metrics indicate decreasing mortality with respect to chronological time. The metrics can not directly be used...... for prediction purposes. However, we suggest that life insurance companies use the estimation technique and the cross-validation for bandwidth selection when analyzing their portfolio mortality. The non-parametric approach may give valuable information prior to developing more sophisticated prediction models...

  13. Analysis of one dimensional and two dimensional fuzzy controllers

    Institute of Scientific and Technical Information of China (English)

    Ban Xiaojun; Gao Xiaozhi; Huang Xianlin; Wu Tianbao

    2006-01-01

    The analytical structures and the corresponding mathematical properties of the one dimensional and two dimensional fuzzy controllers are first investigated in detail.The nature of these two kinds of fuzzy controllers is next probed from the perspective of control engineering. For the one dimensional fuzzy controller, it is concluded that this controller is a combination of a saturation element and a nonlinear proportional controller, and the system that employs the one dimensional fuzzy controller is the combination of an open-loop control system and a closedloop control system. For the latter case, it is concluded that it is a hybrid controller, which comprises the saturation part, zero-output part, nonlinear derivative part, nonlinear proportional part, as well as nonlinear proportional-derivative part, and the two dimensional fuzzy controller-based control system is a loop-varying system with varying number of control loops.

  14. 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.

  15. Two Dimensional Lattice Boltzmann Method for Cavity Flow Simulation

    Directory of Open Access Journals (Sweden)

    Panjit MUSIK

    2004-01-01

    Full Text Available This paper presents a simulation of incompressible viscous flow within a two-dimensional square cavity. The objective is to develop a method originated from Lattice Gas (cellular Automata (LGA, which utilises discrete lattice as well as discrete time and can be parallelised easily. Lattice Boltzmann Method (LBM, known as discrete Lattice kinetics which provide an alternative for solving the Navier–Stokes equations and are generally used for fluid simulation, is chosen for the study. A specific two-dimensional nine-velocity square Lattice model (D2Q9 Model is used in the simulation with the velocity at the top of the cavity kept fixed. LBM is an efficient method for reproducing the dynamics of cavity flow and the results which are comparable to those of previous work.

  16. Transport behavior of water molecules through two-dimensional nanopores

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Chongqin; Li, Hui; Meng, Sheng, E-mail: smeng@iphy.ac.cn [Beijing National Laboratory for Condensed Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China)

    2014-11-14

    Water transport through a two-dimensional nanoporous membrane has attracted increasing attention in recent years thanks to great demands in water purification and desalination applications. However, few studies have been reported on the microscopic mechanisms of water transport through structured nanopores, especially at the atomistic scale. Here we investigate the microstructure of water flow through two-dimensional model graphene membrane containing a variety of nanopores of different size by using molecular dynamics simulations. Our results clearly indicate that the continuum flow transits to discrete molecular flow patterns with decreasing pore sizes. While for pores with a diameter ≥15 Å water flux exhibits a linear dependence on the pore area, a nonlinear relationship between water flux and pore area has been identified for smaller pores. We attribute this deviation from linear behavior to the presence of discrete water flow, which is strongly influenced by the water-membrane interaction and hydrogen bonding between water molecules.

  17. Transport behavior of water molecules through two-dimensional nanopores

    Science.gov (United States)

    Zhu, Chongqin; Li, Hui; Meng, Sheng

    2014-11-01

    Water transport through a two-dimensional nanoporous membrane has attracted increasing attention in recent years thanks to great demands in water purification and desalination applications. However, few studies have been reported on the microscopic mechanisms of water transport through structured nanopores, especially at the atomistic scale. Here we investigate the microstructure of water flow through two-dimensional model graphene membrane containing a variety of nanopores of different size by using molecular dynamics simulations. Our results clearly indicate that the continuum flow transits to discrete molecular flow patterns with decreasing pore sizes. While for pores with a diameter ≥15 Å water flux exhibits a linear dependence on the pore area, a nonlinear relationship between water flux and pore area has been identified for smaller pores. We attribute this deviation from linear behavior to the presence of discrete water flow, which is strongly influenced by the water-membrane interaction and hydrogen bonding between water molecules.

  18. Thermodynamics of two-dimensional Yukawa systems across coupling regimes

    Science.gov (United States)

    Kryuchkov, Nikita P.; Khrapak, Sergey A.; Yurchenko, Stanislav O.

    2017-04-01

    Thermodynamics of two-dimensional Yukawa (screened Coulomb or Debye-Hückel) systems is studied systematically using molecular dynamics (MD) simulations. Simulations cover very broad parameter range spanning from weakly coupled gaseous states to strongly coupled fluid and crystalline states. Important thermodynamic quantities, such as internal energy and pressure, are obtained and accurate physically motivated fits are proposed. This allows us to put forward simple practical expressions to describe thermodynamic properties of two-dimensional Yukawa systems. For crystals, in addition to numerical simulations, the recently developed shortest-graph interpolation method is applied to describe pair correlations and hence thermodynamic properties. It is shown that the finite-temperature effects can be accounted for by using simple correction of peaks in the pair correlation function. The corresponding correction coefficients are evaluated using MD simulation. The relevance of the obtained results in the context of colloidal systems, complex (dusty) plasmas, and ions absorbed to interfaces in electrolytes is pointed out.

  19. Topological states in two-dimensional hexagon lattice bilayers

    Science.gov (United States)

    Zhang, Ming-Ming; Xu, Lei; Zhang, Jun

    2016-10-01

    We investigate the topological states of the two-dimensional hexagon lattice bilayer. The system exhibits a quantum valley Hall (QVH) state when the interlayer interaction t⊥ is smaller than the nearest neighbor hopping energy t, and then translates to a trivial band insulator state when t⊥ / t > 1. Interestingly, the system is found to be a single-edge QVH state with t⊥ / t = 1. The topological phase transition also can be presented via changing bias voltage and sublattice potential in the system. The QVH states have different edge modes carrying valley current but no net charge current. The bias voltage and external electric field can be tuned easily in experiments, so the present results will provide potential application in valleytronics based on the two-dimensional hexagon lattice.

  20. CORPORATE VALUATION USING TWO-DIMENSIONAL MONTE CARLO SIMULATION

    Directory of Open Access Journals (Sweden)

    Toth Reka

    2010-12-01

    Full Text Available In this paper, we have presented a corporate valuation model. The model combine several valuation methods in order to get more accurate results. To determine the corporate asset value we have used the Gordon-like two-stage asset valuation model based on the calculation of the free cash flow to the firm. We have used the free cash flow to the firm to determine the corporate market value, which was calculated with use of the Black-Scholes option pricing model in frame of the two-dimensional Monte Carlo simulation method. The combined model and the use of the two-dimensional simulation model provides a better opportunity for the corporate value estimation.

  1. Two-dimensional magnetostriction under vector magnetic characteristic

    Science.gov (United States)

    Wakabayashi, D.; Enokizono, M.

    2015-05-01

    This paper presents two-dimensional magnetostriction of electrical steel sheet under vector magnetic characteristic. In conventional measurement method using Single Sheet Tester, the magnetic flux density, the magnetic field strength, and the magnetostriction have been measured in one direction. However, an angle between the magnetic flux density vector and the magnetic field strength vector exists because the magnetic property is vector quantity. An angle between the magnetic flux density vector and the direction of maximum magnetostriction also exists. We developed a new measurement method, which enables measurement of these angles. The vector magnetic characteristic and the two-dimensional magnetostriction have been measured using the new measurement method. The BH and Bλ curves considering the angles are shown in this paper. The analyzed results considering the angles are also made clear.

  2. Phase separation under two-dimensional Poiseuille flow.

    Science.gov (United States)

    Kiwata, H

    2001-05-01

    The spinodal decomposition of a two-dimensional binary fluid under Poiseuille flow is studied by numerical simulation. We investigated time dependence of domain sizes in directions parallel and perpendicular to the flow. In an effective region of the flow, the power-law growth of a characteristic length in the direction parallel to the flow changes from the diffusive regime with the growth exponent alpha=1/3 to a new regime. The scaling invariance of the growth in the perpendicular direction is destroyed after the diffusive regime. A recurrent prevalence of thick and thin domains which determines log-time periodic oscillations has not been observed in our model. The growth exponents in the infinite system under two-dimensional Poiseuille flow are obtained by the renormalization group.

  3. Two-dimensional localized structures in harmonically forced oscillatory systems

    Science.gov (United States)

    Ma, Y.-P.; Knobloch, E.

    2016-12-01

    Two-dimensional spatially localized structures in the complex Ginzburg-Landau equation with 1:1 resonance are studied near the simultaneous presence of a steady front between two spatially homogeneous equilibria and a supercritical Turing bifurcation on one of them. The bifurcation structures of steady circular fronts and localized target patterns are computed in the Turing-stable and Turing-unstable regimes. In particular, localized target patterns grow along the solution branch via ring insertion at the core in a process reminiscent of defect-mediated snaking in one spatial dimension. Stability of axisymmetric solutions on these branches with respect to axisymmetric and nonaxisymmetric perturbations is determined, and parameter regimes with stable axisymmetric oscillons are identified. Direct numerical simulations reveal novel depinning dynamics of localized target patterns in the radial direction, and of circular and planar localized hexagonal patterns in the fully two-dimensional system.

  4. Enstrophy inertial range dynamics in generalized two-dimensional turbulence

    Science.gov (United States)

    Iwayama, Takahiro; Watanabe, Takeshi

    2016-07-01

    We show that the transition to a k-1 spectrum in the enstrophy inertial range of generalized two-dimensional turbulence can be derived analytically using the eddy damped quasinormal Markovianized (EDQNM) closure. The governing equation for the generalized two-dimensional fluid system includes a nonlinear term with a real parameter α . This parameter controls the relationship between the stream function and generalized vorticity and the nonlocality of the dynamics. An asymptotic analysis accounting for the overwhelming dominance of nonlocal triads allows the k-1 spectrum to be derived based upon a scaling analysis. We thereby provide a detailed analytical explanation for the scaling transition that occurs in the enstrophy inertial range at α =2 in terms of the spectral dynamics of the EDQNM closure, which extends and enhances the usual phenomenological explanations.

  5. Folding two dimensional crystals by swift heavy ion irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Ochedowski, Oliver; Bukowska, Hanna [Fakultät für Physik and CENIDE, Universität Duisburg-Essen, D-47048 Duisburg (Germany); Freire Soler, Victor M. [Fakultät für Physik and CENIDE, Universität Duisburg-Essen, D-47048 Duisburg (Germany); Departament de Fisica Aplicada i Optica, Universitat de Barcelona, E08028 Barcelona (Spain); Brökers, Lara [Fakultät für Physik and CENIDE, Universität Duisburg-Essen, D-47048 Duisburg (Germany); Ban-d' Etat, Brigitte; Lebius, Henning [CIMAP (CEA-CNRS-ENSICAEN-UCBN), 14070 Caen Cedex 5 (France); Schleberger, Marika, E-mail: marika.schleberger@uni-due.de [Fakultät für Physik and CENIDE, Universität Duisburg-Essen, D-47048 Duisburg (Germany)

    2014-12-01

    Ion irradiation of graphene, the showcase model of two dimensional crystals, has been successfully applied to induce various modifications in the graphene crystal. One of these modifications is the formation of origami like foldings in graphene which are created by swift heavy ion irradiation under glancing incidence angle. These foldings can be applied to locally alter the physical properties of graphene like mechanical strength or chemical reactivity. In this work we show that the formation of foldings in two dimensional crystals is not restricted to graphene but can be applied for other materials like MoS{sub 2} and hexagonal BN as well. Further we show that chemical vapour deposited graphene forms foldings after swift heavy ion irradiation while chemical vapour deposited MoS{sub 2} does not.

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

    DEFF Research Database (Denmark)

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

    2002-01-01

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

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

    NARCIS (Netherlands)

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

    1996-01-01

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

  8. Two-dimensional model of elastically coupled molecular motors

    Institute of Scientific and Technical Information of China (English)

    Zhang Hong-Wei; Wen Shu-Tang; Chen Gai-Rong; Li Yu-Xiao; Cao Zhong-Xing; Li Wei

    2012-01-01

    A flashing ratchet model of a two-headed molecular motor in a two-dimensional potential is proposed to simulate the hand-over-hand motion of kinesins.Extensive Langevin simulations of the model are performed.We discuss the dependences of motion and efficiency on the model parameters,including the external force and the temperature.A good qualitative agreement with the expected behavior is observed.

  9. Conductivity of a two-dimensional guiding center plasma.

    Science.gov (United States)

    Montgomery, D.; Tappert, F.

    1972-01-01

    The Kubo method is used to calculate the electrical conductivity of a two-dimensional, strongly magnetized plasma. The particles interact through (logarithmic) electrostatic potentials and move with their guiding center drift velocities (Taylor-McNamara model). The thermal equilibrium dc conductivity can be evaluated analytically, but the ac conductivity involves numerical solution of a differential equation. Both conductivities fall off as the inverse first power of the magnetic field strength.

  10. Minor magnetization loops in two-dimensional dipolar Ising model

    Energy Technology Data Exchange (ETDEWEB)

    Sarjala, M. [Aalto University, Department of Applied Physics, P.O. Box 14100, FI-00076 Aalto (Finland); Seppaelae, E.T., E-mail: eira.seppala@nokia.co [Nokia Research Center, Itaemerenkatu 11-13, FI-00180 Helsinki (Finland); Alava, M.J., E-mail: mikko.alava@tkk.f [Aalto University, Department of Applied Physics, P.O. Box 14100, FI-00076 Aalto (Finland)

    2011-05-15

    The two-dimensional dipolar Ising model is investigated for the relaxation and dynamics of minor magnetization loops. Monte Carlo simulations show that in a stripe phase an exponential decrease can be found for the magnetization maxima of the loops, M{approx}exp(-{alpha}N{sub l}) where N{sub l} is the number of loops. We discuss the limits of this behavior and its relation to the equilibrium phase diagram of the model.

  11. Cryptography Using Multiple Two-Dimensional Chaotic Maps

    Directory of Open Access Journals (Sweden)

    Ibrahim S. I. Abuhaiba

    2012-08-01

    Full Text Available In this paper, a symmetric key block cipher cryptosystem is proposed, involving multiple two-dimensional chaotic maps and using 128-bits external secret key. Computer simulations indicate that the cipher has good diffusion and confusion properties with respect to the plaintext and the key. Moreover, it produces ciphertext with random distribution. The computation time is much less than previous related works. Theoretic analysis verifies its superiority to previous cryptosystems against different types of attacks.

  12. A UNIVERSAL VARIATIONAL FORMULATION FOR TWO DIMENSIONAL FLUID MECHANICS

    Institute of Scientific and Technical Information of China (English)

    何吉欢

    2001-01-01

    A universal variational formulation for two dimensional fluid mechanics is obtained, which is subject to the so-called parameter-constrained equations (the relationship between parameters in two governing equations). By eliminating the constraints, the generalized variational principle (GVPs) can be readily derived from the formulation. The formulation can be applied to any conditions in case the governing equations can be converted into conservative forms. Some illustrative examples are given to testify the effectiveness and simplicity of the method.

  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. Level crossings in complex two-dimensional potentials

    Indian Academy of Sciences (India)

    Qing-Hai Wang

    2009-08-01

    Two-dimensional $\\mathcal{PT}$-symmetric quantum-mechanical systems with the complex cubic potential 12 = 2 + 2 + 2 and the complex Hénon–Heiles potential HH = 2 + 2 + (2 − 3/3) are investigated. Using numerical and perturbative methods, energy spectra are obtained to high levels. Although both potentials respect the $\\mathcal{PT}$ symmetry, the complex energy eigenvalues appear when level crossing happens between same parity eigenstates.

  15. 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.

  16. Lyapunov Computational Method for Two-Dimensional Boussinesq Equation

    CERN Document Server

    Mabrouk, Anouar Ben

    2010-01-01

    A numerical method is developed leading to Lyapunov operators to approximate the solution of two-dimensional Boussinesq equation. It consists of an order reduction method and a finite difference discretization. It is proved to be uniquely solvable and analyzed for local truncation error for consistency. The stability is checked by using Lyapunov criterion and the convergence is studied. Some numerical implementations are provided at the end of the paper to validate the theoretical results.

  17. Complex dynamical invariants for two-dimensional complex potentials

    Indian Academy of Sciences (India)

    J S Virdi; F Chand; C N Kumar; S C Mishra

    2012-08-01

    Complex dynamical invariants are searched out for two-dimensional complex potentials using rationalization method within the framework of an extended complex phase space characterized by $x = x_{1} + ip_{3}. y = x_{2} + ip_{4}, p_{x} = p_{1} + ix_{3}, p_{y} = p_{2} + ix_{4}$. It is found that the cubic oscillator and shifted harmonic oscillator admit quadratic complex invariants. THe obtained invariants may be useful for studying non-Hermitian Hamiltonian systems.

  18. Two-dimensional hydrogen negative ion in a magnetic field

    Institute of Scientific and Technical Information of China (English)

    Xie Wen-Fang

    2004-01-01

    Making use of the adiabatic hyperspherical approach, we report a calculation for the energy spectrum of the ground and low-excited states of a two-dimensional hydrogen negative ion H- in a magnetic field. The results show that the ground and low-excited states of H- in low-dimensional space are more stable than those in three-dimensional space and there may exist more bound states.

  19. 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.

  20. Chronology Protection in Two-Dimensional Dilaton Gravity

    CERN Document Server

    Mishima, T; Mishima, Takashi; Nakamichi, Akika

    1994-01-01

    The global structure of 1 + 1 dimensional compact Universe is studied in two-dimensional model of dilaton gravity. First we give a classical solution corresponding to the spacetime in which a closed time-like curve appears, and show the instability of this spacetime due to the existence of matters. We also observe quantum version of such a spacetime having closed timelike curves never reappear unless the parameters are fine-tuned.