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Sample records for peptide mapping analysis

  1. High throughput peptide mapping method for analysis of site specific monoclonal antibody oxidation.

    PubMed

    Li, Xiaojuan; Xu, Wei; Wang, Yi; Zhao, Jia; Liu, Yan-Hui; Richardson, Daisy; Li, Huijuan; Shameem, Mohammed; Yang, Xiaoyu

    2016-08-19

    Oxidation of therapeutic monoclonal antibodies (mAbs) often occurs on surface exposed methionine and tryptophan residues during their production in cell culture, purification, and storage, and can potentially impact the binding to their targets. Characterization of site specific oxidation is critical for antibody quality control. Antibody oxidation is commonly determined by peptide mapping/LC-MS methods, which normally require a long (up to 24h) digestion step. The prolonged sample preparation procedure could result in oxidation artifacts of susceptible methionine and tryptophan residues. In this paper, we developed a rapid and simple UV based peptide mapping method that incorporates an 8-min trypsin in-solution digestion protocol for analysis of oxidation. This method is able to determine oxidation levels at specific residues of a mAb based on the peptide UV traces within <1h, from either TBHP treated or UV light stressed samples. This is the simplest and fastest method reported thus far for site specific oxidation analysis, and can be applied for routine or high throughput analysis of mAb oxidation during various stability and degradation studies. By using the UV trace, the method allows more accurate measurement than mass spectrometry and can be potentially implemented as a release assay. It has been successfully used to monitor antibody oxidation in real time stability studies. PMID:27432793

  2. CLPM: A Cross-Linked Peptide Mapping Algorithm for Mass Spectrometric Analysis

    PubMed Central

    Tang, Yong; Chen, Yingfeng; Lichti, Cheryl F; Hall, Roger A; Raney, Kevin D; Jennings, Steven F

    2005-01-01

    Background Protein-protein, protein-DNA and protein-RNA interactions are of central importance in biological systems. Quadrapole Time-of-flight (Q-TOF) mass spectrometry is a sensitive, promising tool for studying these interactions. Combining this technique with chemical crosslinking, it is possible to identify the sites of interactions within these complexes. Due to the complexities of the mass spectrometric data of crosslinked proteins, new software is required to analyze the resulting products of these studies. Result We designed a Cross-Linked Peptide Mapping (CLPM) algorithm which takes advantage of all of the information available in the experiment including the amino acid sequence from each protein, the identity of the crosslinker, the identity of the digesting enzyme, the level of missed cleavage, and possible chemical modifications. The algorithm does in silico digestion and crosslinking, calculates all possible mass values and matches the theoretical data to the actual experimental data provided by the mass spectrometry analysis to identify the crosslinked peptides. Conclusion Identifying peptides by their masses can be an efficient starting point for direct sequence confirmation. The CLPM algorithm provides a powerful tool in identifying these potential interaction sites in combination with chemical crosslinking and mass spectrometry. Through this cost-effective approach, subsequent efforts can quickly focus attention on investigating these specific interaction sites. PMID:16026606

  3. Antibodies that neutralize human beta interferon biologic activity recognize a linear epitope: analysis by synthetic peptide mapping.

    PubMed Central

    Redlich, P N; Hoeprich, P D; Colby, C B; Grossberg, S E

    1991-01-01

    The location of biologically relevant epitopes on recombinant human beta interferon in which Ser-17 replaces Cys-17 (rh[Ser17]IFN-beta) was evaluated by testing the immunoreactivity of antibodies against 159 sequential, overlapping octamer peptides. Three monoclonal antibodies (mAbs) that neutralize rh[Ser17]IFN-beta biologic activity, designated A1, A5, and A7, bound to peptides spanning only residues 39-48, whereas nonneutralizing mAb bound less specifically at multiple sites near the amino terminus. The immunoreactivity of peptides spanning residues 40-47 that contained a series of single amino acid substitutions suggested that residues 41-43 (Pro-Glu-Glu) and 46 (Gln) are important for the binding of neutralizing mAbs. The reactivity of mAbs to larger synthetic peptides containing rh[Ser17]IFN-beta sequences from residue 32 through residue 56 was evaluated. All mAbs except A7 reacted with synthetic peptides representing rh[Ser17]IFN-beta residues 32-47, 40-56, and 32-56, but only mAbs A1 and A5 bound to the core peptide composed of residues 40-47. Peptide 32-56 effectively blocked the binding of mAbs A1 and A5 to rh[Ser17]IFN-beta and markedly inhibited their neutralizing activity. Biologic activity of the peptides was undetectable. Rabbit antisera raised against peptides 32-47 and 40-56 recognized rh[Ser17]IFN-beta but did not neutralize its antiviral activity. Thus, structure-function analysis by peptide mapping has permitted the identification of a linear epitope recognized by neutralizing antibody on a biologically active cytokine. We conclude that the region spanning residues 32-56 is of major importance in the expression of the biologic activity of human IFN-beta. Images PMID:1708891

  4. Investigation of purification process stresses on erythropoietin peptide mapping profile

    PubMed Central

    Sepahi, Mina; Kaghazian, Hooman; Hadadian, Shahin; Norouzian, Dariush

    2015-01-01

    Background: Full compliance of recombinant protein peptide mapping chromatogram with the standard reference material, is one of the most basic quality control tests of biopharmaceuticals. Changing a single amino acid substitution or side chain diversity for a given peptide changes protein hydrophobicity and causes peak shape or retention time alteration in a peptide mapping assay. In this work, the effect of different stresses during the recombinant erythropoietin (EPO) purification process, including pH 4, pH 5, and room temperature were checked on product peptide mapping results. Materials and Methods: Cell culture harvest was purified under stress by different chromatographic techniques consisting of gel filtration, anionic ion exchange, concentration by ultrafiltration, and high resolution size exclusion chromatography. To induce more pH stresses, the purified EPO was exposed to pH stress 4 and 5 by exchanging buffer by a 10 KDa dialysis sac overnight. The effects of temperature and partial deglycosylation (acid hydrolysis) on purified EPO were also studied by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and peptide mapping analysis. Removal of sialic acid by mild hydrolysis was performed by exposure to two molar acetic acid at 80°C for 3 h. Results: No significant effect was observed between intact and stressed erythropoietin peptide mapping profiles and SDS-PAGE results. To validate the sensibility of the technique, erythropoietin was partially acid hydrolyzed and significant changes in the chromatographic peptide map of the intact form and a reduction on its molecular weight were detected, which indicates some partial deglycosylation. Conclusions: Purification process does not alter the peptide mapping profile and purification process stresses are not the cause of peptide mapping noncompliance. PMID:26261816

  5. Epitope mapping by epitope excision, hydrogen/deuterium exchange, and peptide-panning techniques combined with in silico analysis.

    PubMed

    Clementi, Nicola; Mancini, Nicasio; Criscuolo, Elena; Cappelletti, Francesca; Clementi, Massimo; Burioni, Roberto

    2014-01-01

    The fine characterization of protective B cell epitopes plays a pivotal role in the development of novel vaccines. The development of epitope-based vaccines, in fact, cannot be possible without a clear definition of the antigenic regions involved in the binding between the protective antibody (Ab) and its molecular target. To achieve this result, different epitope-mapping approaches have been widely described (Clementi et al. Drug Discov Today 18(9-10):464-471, 2013). Nowadays, the best way to characterize an Ab bound region is still the resolution of Ab-antigen (Ag) co-crystal structure. Unfortunately, the crystallization approaches are not always feasible. However, different experimental strategies aimed to predict Ab-Ag interaction and followed by in silico analysis of the results may be good surrogate approaches to achieve this result. Here, we review few experimental techniques followed by the use of "basic" informatics tools for the analysis of the results. PMID:24515481

  6. Combinatorial peptide ligand libraries for the analysis of low-expression proteins: Validation for normal urine and definition of a first protein MAP.

    PubMed

    Santucci, Laura; Candiano, Giovanni; Bruschi, Maurizio; D'Ambrosio, Chiara; Petretto, Andrea; Scaloni, Andrea; Urbani, Andrea; Righetti, Pier G; Ghiggeri, Gian M

    2012-02-01

    In this review, we report the evolution on experimental conditions for the analysis of normal urine based on combinatorial peptide ligand library (CPLL) treatment and successive 2-DE and 2-DE/MS analysis. The main topics are (i) definition of the urine sample requirements, (ii) optimization of the urine/ligand ratio, (iii) essay conditions, (iv) en bloc elution. Overall, normal urine protein composition as studied by 2-DE includes over 2600 spots. Relevant data on inter and intraessay reproducibility obtained by the analysis of different normal urines repeated several times are also here presented. We found a 73% reproducibility upon analysis of the same sample and 68% correspondence of protein composition among different normal urine samples. Based on the above results, we are completing the characterization with LC-MS of 249 spots. The composition of normal urine proteins after CPLLs is finally shown with the indication of those spots which are currently under identification. This map will be completed in a near future; in the meantime this would represent the basic reference sample for newly developed studies on human diseases. PMID:22246922

  7. A simple contact mapping algorithm for identifying potential peptide mimetics in protein–protein interaction partners

    PubMed Central

    Krall, Alex; Brunn, Jonathan; Kankanala, Spandana; Peters, Michael H

    2014-01-01

    A simple, static contact mapping algorithm has been developed as a first step at identifying potential peptide biomimetics from protein interaction partner structure files. This rapid and simple mapping algorithm, “OpenContact” provides screened or parsed protein interaction files based on specified criteria for interatomic separation distances and interatomic potential interactions. The algorithm, which uses all-atom Amber03 force field models, was blindly tested on several unrelated cases from the literature where potential peptide mimetics have been experimentally developed to varying degrees of success. In all cases, the screening algorithm efficiently predicted proposed or potential peptide biomimetics, or close variations thereof, and provided complete atom-atom interaction data necessary for further detailed analysis and drug development. In addition, we used the static parsing/mapping method to develop a peptide mimetic to the cancer protein target, epidermal growth factor receptor. In this case, secondary, loop structure for the peptide was indicated from the intra-protein mapping, and the peptide was subsequently synthesized and shown to exhibit successful binding to the target protein. The case studies, which all involved experimental peptide drug advancement, illustrate many of the challenges associated with the development of peptide biomimetics, in general. Proteins 2014; 82:2253–2262. © 2014 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc. PMID:24756879

  8. Rat hepatic (Na/sup +/, K/sup +/)-ATPase:. cap alpha. =subunit isolation by immunoaffinity chromatography and structural analysis by peptide mapping

    SciTech Connect

    Hubert, J.J.; Schenk, D.B.; Skelly, H.; Leffert, H.L.

    1986-07-01

    The catalytic ..cap alpha..-subunit of rat hepatic (Na/sup +/, K/sup +/)-ATPase (EC 3.6.1.3) has been isolated by immunoaffinity chromatography from microsomes solubilized in n-dodecyl octaethylene glycol monoether. The procedure employs an anticatalytic mouse monoclonal antibody (9-A5) covalently linked to Sepharose 4B that specifically block phosphorylation of the sodium pump's ..cap alpha..-subunit from (..gamma..-/sup 32/P)ATP. The hepatic subunit is virtually identical with purified rat, dog, and human renal ..cap alpha..-subunits as judged by its apparent molecular weight after polyacrylamide gel electrophoresis in sodium dodecyl sulfate (M/sub r/ 92K) and its two-dimensional tryptic and chymotryptic peptide maps on cellulose-coated thin-layer plates. In contrast, the structures of authentic renal ..beta..-subunits from the three species differ significantly from each other as judged by their peptide maps; no detectable homologies are seen between their chymotryptic maps and those of putative hepatic ..beta..-subunits (M/sub r/ 50K and 55K) eluted from 9-A5-Spharose. Additional studies of ouabain-sensitive /sup 86/Rb/sup +/ uptake in primary cultures of adult rat hepatocytes reveal inhibition curves with single inflection points in the absence or presence of pump-stimulating peptides like insulin, glucagon, and epidermal growth factor. These findings indicate that rat hepatocytes express only one of two know structurally conserved forms of catalytic subunit (the renallike ..cap alpha.. form) and, if at all, structurally divergent forms of the sodium pump's ..beta..-subunit.

  9. Low-Cost Peptide Microarrays for Mapping Continuous Antibody Epitopes.

    PubMed

    McBride, Ryan; Head, Steven R; Ordoukhanian, Phillip; Law, Mansun

    2016-01-01

    With the increasing need for understanding antibody specificity in antibody and vaccine research, pepscan assays provide a rapid method for mapping and profiling antibody responses to continuous epitopes. We have developed a relatively low-cost method to generate peptide microarray slides for studying antibody binding. Using a setup of an IntavisAG MultiPep RS peptide synthesizer, a Digilab MicroGrid II 600 microarray printer robot, and an InnoScan 1100 AL scanner, the method allows the interrogation of up to 1536 overlapping, alanine-scanning, and mutant peptides derived from the target antigens. Each peptide is tagged with a polyethylene glycol aminooxy terminus to improve peptide solubility, orientation, and conjugation efficiency to the slide surface. PMID:26490468

  10. Data on the peptide mapping and MS identification for phosphorylated peptide.

    PubMed

    Wang, Hui; Tu, Zong-Cai; Liu, Guang-Xian; Zhang, Lu; Chen, Yuan

    2016-09-01

    This article contains peptides mapping, mass spectrometry and processed data related to the research "Identification and quantification of the phosphorylated ovalbumin by high resolution mass spectrometry under dry-heating treatment" [1]. Fourier transform ion cyclotron mass spectrometry (FTICR MS) was used to investigate the specific phosphorylation sites and the degree of phosphorylation (DSP) at each site. Specifically, phosphorylated peptides were monitored through mass shift on the FTICR MS spectrum. DSP was evaluated through the relative abundance levels of the FTICR MS spectrometry. From these data, the calculation method of DSP was exemplified. PMID:27274527

  11. Quantitative Evaluation of Peptide-Material Interactions by a Force Mapping Method: Guidelines for Surface Modification.

    PubMed

    Mochizuki, Masahito; Oguchi, Masahiro; Kim, Seong-Oh; Jackman, Joshua A; Ogawa, Tetsu; Lkhamsuren, Ganchimeg; Cho, Nam-Joon; Hayashi, Tomohiro

    2015-07-28

    Peptide coatings on material surfaces have demonstrated wide application across materials science and biotechnology, facilitating the development of nanobio interfaces through surface modification. A guiding motivation in the field is to engineer peptides with a high and selective binding affinity to target materials. Herein, we introduce a quantitative force mapping method in order to evaluate the binding affinity of peptides to various hydrophilic oxide materials by atomic force microscopy (AFM). Statistical analysis of adhesion forces and probabilities obtained on substrates with a materials contrast enabled us to simultaneously compare the peptide binding affinity to different materials. On the basis of the experimental results and corresponding theoretical analysis, we discuss the role of various interfacial forces in modulating the strength of peptide attachment to hydrophilic oxide solid supports as well as to gold. The results emphasize the precision and robustness of our approach to evaluating the adhesion strength of peptides to solid supports, thereby offering guidelines to improve the design and fabrication of peptide-coated materials. PMID:26125092

  12. Distinction between mouse DNA polymerases alpha and beta by tryptic peptide mapping.

    PubMed Central

    Planck, S R; Tanabe, K; Wilson, S H

    1980-01-01

    Results presented here and in a previous paper (Tanabe et al. (1979) Biochemistry 18, 3401--3406) indicate that mouse beta-polymerase is a single polypeptide with an apparent molecular weight of 40,000. This polypeptide has now been analyzed by tryptic peptide mapping. Comparison of the results with identical analysis of mouse alpha-polymerase reveals that the tryptic peptides derived from the two enzymes are different. These results indicate that beta-polymerase is neither a subunit of alpha-polymerase nor a proteolytic degradation product of alpha-polymerase. Images PMID:7433094

  13. [Peptide mapping of the major proteins in 2 strains of influenza virus].

    PubMed

    Savich, I M; Gerasimova, L M; Mertvetsov, N P

    1985-01-01

    The protein composition of two influenza A virus strains from different serological groups was studied. For preliminary separation of envelope and core proteins the virus was treated with nonionic detergent Triton X-100 solution followed by chromatography in ultragel AcA 34. After their separation by disk electrophoresis and treatment with trypsin they were labeled with tritium and peptide analysis was carried out. Differences in peptide maps between the appropriate light and heavy chains of hemagglutinins of the strains under study were demonstrated. Differences in the composition of nucleoprotein and matrix protein were insignificant. PMID:3922120

  14. Studies on the autophosphorylation of the insulin receptor from human placenta. Analysis of the sites phosphorylated by two-dimensional peptide mapping.

    PubMed Central

    Tavaré, J M; Denton, R M

    1988-01-01

    1. A partially purified preparation of human placental insulin receptors was incubated with [gamma-32P]ATP in the presence or absence of insulin. The 32P-labelled insulin-receptor beta-subunits were then isolated, cleaved with trypsin followed by protease V8 and the [32P]phosphopeptides generated were analysed by thin layer electrophoresis and chromatography. This approach revealed that insulin stimulates autophosphorylation of the insulin-receptor beta-subunit in vitro on at least seven tyrosine residues distributed among three distinct domains. 2. One domain (domain 2), containing tyrosine residues 1146, 1150 and 1151 was the most rapidly phosphorylated and could be recovered as mono-, di- and triphosphorylated peptides cleaved by trypsin at Arg-1143 and either Lys-1153 or Lys-1156. Multiple phosphorylation of this domain appears to partially inhibit the cleavage at Lys-1153 by trypsin. 3. In a second domain (domain 3) containing two phosphorylated tyrosine residues at positions 1316 and 1322 the tyrosines were phosphorylated more slowly than those in domain 2. This domain is close to the C-terminus of the beta-subunit polypeptide chain. 4. At least two further tyrosine residues appeared to be phosphorylated after those in domains 2 and 3. These residues probably residue within a domain lying in close proximity to the inner face of the plasma membrane containing tyrosines 953, 960 and 972, but conclusive evidence is still required. 5. The two-dimensional thin-layer analysis employed in this study to investigate insulin-receptor phosphorylation has several advantages over previous methods based on reverse-phase chromatography. It allows greater resolution of 32P-labelled tryptic peptides and, when coupled to radioautography, is considerably more sensitive. The approach can be readily adapted to study phosphorylation of the insulin receptor within intact cells. Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. PMID:3166375

  15. Mapping peptide thiol accessibility in membranes using a quaternary ammonium isotope-coded mass tag (ICMT)

    PubMed Central

    Su, Chiao-Yung; London, Erwin; Sampson, Nicole S.

    2013-01-01

    The plasma membrane contains a diverse array of proteins, including receptors, channels, and signaling complexes, that serve as decision-making centers. Investigation of membrane protein topology is important for understanding the function of these types of protein. Here, we report a method to determine protein topology in the membrane that utilizes labeling of cysteine with isotope-coded mass tags. The mass tags contain a thiol reactive moiety, linker, and a quaternary ammonium group to aid ionization in the mass spectrometer and were synthesizes as both light and heavy (deuterated) forms. The probes were found to be membrane impermeable when applied to lipid vesicles. To assess the utility of the probes for mapping peptide thiol topology, we employed a two-step labeling procedure. Vesicles containing α-helical transmembrane peptides were labeled with heavy (or light) probe, solubilized by detergent, and then labeled by an excess of the complementary probe. Peptide for which the cysteine was oriented in the center of the lipid bilayer was not labeled until the lipid vesicles were lysed with detergent, consistent with the membrane impermeability of the probes and reduced ionization of the thiol in the hydrophobic membrane. Peptide for which the cysteine was positioned in the head group zone of the lipid bilayer was labeled rapidly. Peptide for which the cysteine was positioned below the head group abutting the hydrocarbon region was labeled at a reduced rate compared to the fully accessible cysteine. Moreover, the effect of lipid bilayer structure on the kinetics of peptide and lipid flipping in the bilayer was readily measured with our two-step labeling method. The small sample size required, the ease and rapidity of sample preparation, and the amenability of MALDI-TOF mass spectral to analysis in the presence of lipids will enable future facile investigation of membrane proteins in a cellular context. PMID:23725486

  16. LC-MS/MS Peptide Mapping with Automated Data Processing for Routine Profiling of N-Glycans in Immunoglobulins

    NASA Astrophysics Data System (ADS)

    Shah, Bhavana; Jiang, Xinzhao Grace; Chen, Louise; Zhang, Zhongqi

    2014-06-01

    Protein N-Glycan analysis is traditionally performed by high pH anion exchange chromatography (HPAEC), reversed phase liquid chromatography (RPLC), or hydrophilic interaction liquid chromatography (HILIC) on fluorescence-labeled glycans enzymatically released from the glycoprotein. These methods require time-consuming sample preparations and do not provide site-specific glycosylation information. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) peptide mapping is frequently used for protein structural characterization and, as a bonus, can potentially provide glycan profile on each individual glycosylation site. In this work, a recently developed glycopeptide fragmentation model was used for automated identification, based on their MS/MS, of N-glycopeptides from proteolytic digestion of monoclonal antibodies (mAbs). Experimental conditions were optimized to achieve accurate profiling of glycoforms. Glycan profiles obtained from LC-MS/MS peptide mapping were compared with those obtained from HPAEC, RPLC, and HILIC analyses of released glycans for several mAb molecules. Accuracy, reproducibility, and linearity of the LC-MS/MS peptide mapping method for glycan profiling were evaluated. The LC-MS/MS peptide mapping method with fully automated data analysis requires less sample preparation, provides site-specific information, and may serve as an alternative method for routine profiling of N-glycans on immunoglobulins as well as other glycoproteins with simple N-glycans.

  17. Temporal mapping and analysis

    NASA Technical Reports Server (NTRS)

    O'Hara, Charles G. (Inventor); Shrestha, Bijay (Inventor); Vijayaraj, Veeraraghavan (Inventor); Mali, Preeti (Inventor)

    2011-01-01

    A compositing process for selecting spatial data collected over a period of time, creating temporal data cubes from the spatial data, and processing and/or analyzing the data using temporal mapping algebra functions. In some embodiments, the temporal data cube is creating a masked cube using the data cubes, and computing a composite from the masked cube by using temporal mapping algebra.

  18. Mapping the human proteome for non-redundant peptide islands.

    PubMed

    Capone, G; De Marinis, A; Simone, S; Kusalik, A; Kanduc, D

    2008-06-01

    We describe immune-proteome structures using libraries of protein fragments that define a structural immunological alphabet. We propose and validate such an alphabet as i) composed of letters of five consecutive amino acids, pentapeptide units being sufficient minimal antigenic determinants in a protein, and ii) characterized by low-similarity to human proteins, so representing structures unknown to the host and potentially able to evoke an immune response. In this context, we have thoroughly sifted through the entire human proteome searching for non-redundant protein motifs. Here, for the first time, a complete sequence redundancy dissection of the human proteome has been conducted. The non-redundant peptide islands in the human proteome have been quantified and catalogued according to the amino acid length. The library of uniquely occurring n-peptide sequences that was obtained is characterized by a logarithmic decrease of the number of non-redundant peptides as a function of the peptide length. This library represents a highly specific catalogue of molecular protein signatures, the possible use of which in cancer/autoimmunity research is discussed, with a major focus on non-redundant dodecamer sequences. PMID:17701099

  19. Mapping the Vif-A3G interaction using peptide arrays: a basis for anti-HIV lead peptides.

    PubMed

    Reingewertz, Tali H; Britan-Rosich, Elena; Rotem-Bamberger, Shahar; Viard, Mathias; Jacobs, Amy; Miller, Abigail; Lee, Ji Youn; Hwang, Jeeseong; Blumenthal, Robert; Kotler, Moshe; Friedler, Assaf

    2013-06-15

    Human apolipoprotein-B mRNA-editing catalytic polypeptide-like 3G (A3G) is a cytidine deaminase that restricts retroviruses, endogenous retro-elements and DNA viruses. A3G plays a key role in the anti-HIV-1 innate cellular immunity. The HIV-1 Vif protein counteracts A3G mainly by leading A3G towards the proteosomal machinery and by direct inhibition of its enzymatic activity. Both activities involve direct interaction between Vif and A3G. Disrupting the interaction between A3G and Vif may rescue A3G antiviral activity and inhibit HIV-1 propagation. Here, mapping the interaction sites between A3G and Vif by peptide array screening revealed distinct regions in Vif important for A3G binding, including the N-terminal domain (NTD), C-terminal domain (CTD) and residues 83-99. The Vif-binding sites in A3G included 12 different peptides that showed strong binding to either full-length Vif, Vif CTD or both. Sequence similarity was found between Vif-binding peptides from the A3G CTD and NTD. A3G peptides were synthesized and tested for their ability to counteract Vif action. A3G 211-225 inhibited HIV-1 replication in cell culture and impaired Vif dependent A3G degradation. In vivo co-localization of full-length Vif with A3G 211-225 was demonstrated by use of FRET. This peptide has the potential to serve as an anti-HIV-1 lead compound. Our results suggest a complex interaction between Vif and A3G that is mediated by discontinuous binding regions with different affinities. PMID:23545135

  20. Comparative conformational analysis of peptide T analogs

    NASA Astrophysics Data System (ADS)

    Akverdieva, Gulnare; Godjayev, Niftali; Akyuz, Sevim

    2009-01-01

    A series of peptide T analogs were investigated within the molecular mechanics framework. In order to determine the role of the aminoacid residues in spatial formation of peptide T the conformational peculiarities of the glycine-substituted analogs were investigated. The conformational profiles of some biologically tested analogs of this peptide were determined independently. The received data permit to assess the active form of this peptide. It is characterized by β-turn at the C-terminal physiologically active pentapeptide fragment of peptide molecule. The received results are important for the investigation of the structure-activity relationship and may be used at design of a rigid-molecule drug against HIV.

  1. Bioinformatic analysis of peptide precursor proteins.

    PubMed

    Baggerman, G; Liu, F; Wets, G; Schoofs, L

    2005-04-01

    Neuropeptides are among the most important signal molecules in animals. Traditional identification of peptide hormones through peptide purification is a tedious and time-consuming process. With the advent of the genome sequencing projects, putative peptide precursor can be mined from the genome. However, because bioactive peptides are usually quite short in length and because the active core of a peptide is often limited to only a few amino acids, using the BLAST search engine to identify neuropeptide precursors in the genome is difficult and sometimes impossible. To overcome these shortcomings, we subject the entire set of all known Drosophila melanogaster peptide precursor sequences to motif-finding algorithms in search of a motif that is common for all prepropeptides and that could be used in the search for new peptide precursors. PMID:15891006

  2. HPLC analysis and purification of peptides.

    PubMed

    Mant, Colin T; Chen, Yuxin; Yan, Zhe; Popa, Traian V; Kovacs, James M; Mills, Janine B; Tripet, Brian P; Hodges, Robert S

    2007-01-01

    High-performance liquid chromatography (HPLC) has proved extremely versatile over the past 25 yr for the isolation and purification of peptides varying widely in their sources, quantity and complexity. This article covers the major modes of HPLC utilized for peptides (size-exclusion, ion-exchange, and reversed-phase), as well as demonstrating the potential of a novel mixed-mode hydrophilic interaction/cation-exchange approach developed in this laboratory. In addition to the value of these HPLC modes for peptide separations, the value of various HPLC techniques for structural characterization of peptides and proteins will be addressed, e.g., assessment of oligomerization state of peptides/proteins by size-exclusion chromatography and monitoring the hydrophilicity/hydrophobicity of amphipathic alpha-helical peptides, a vital precursor for the development of novel antimicrobial peptides. The value of capillary electrophoresis for peptide separations is also demonstrated. Preparative reversed-phase chromatography purification protocols for sample loads of up to 200 mg on analytical columns and instrumentation are introduced for both peptides and recombinant proteins. PMID:18604941

  3. Mapping the HLA ligandome landscape of acute myeloid leukemia: a targeted approach toward peptide-based immunotherapy.

    PubMed

    Berlin, C; Kowalewski, D J; Schuster, H; Mirza, N; Walz, S; Handel, M; Schmid-Horch, B; Salih, H R; Kanz, L; Rammensee, H-G; Stevanović, S; Stickel, J S

    2015-03-01

    Identification of physiologically relevant peptide vaccine targets calls for the direct analysis of the entirety of naturally presented human leukocyte antigen (HLA) ligands, termed the HLA ligandome. In this study, we implemented this direct approach using immunoprecipitation and mass spectrometry to define acute myeloid leukemia (AML)-associated peptide vaccine targets. Mapping the HLA class I ligandomes of 15 AML patients and 35 healthy controls, more than 25 000 different naturally presented HLA ligands were identified. Target prioritization based on AML exclusivity and high presentation frequency in the AML cohort identified a panel of 132 LiTAAs (ligandome-derived tumor-associated antigens), and 341 corresponding HLA ligands (LiTAPs (ligandome-derived tumor-associated peptides)) represented subset independently in >20% of AML patients. Functional characterization of LiTAPs by interferon-γ ELISPOT (Enzyme-Linked ImmunoSpot) and intracellular cytokine staining confirmed AML-specific CD8(+) T-cell recognition. Of note, our platform identified HLA ligands representing several established AML-associated antigens (e.g. NPM1, MAGED1, PRTN3, MPO, WT1), but found 80% of them to be also represented in healthy control samples. Mapping of HLA class II ligandomes provided additional CD4(+) T-cell epitopes and potentially synergistic embedded HLA ligands, allowing for complementation of a multipeptide vaccine for the immunotherapy of AML. PMID:25092142

  4. MAP stability, design, and analysis

    NASA Technical Reports Server (NTRS)

    Ericsson-Jackson, A. J.; Andrews, S. F.; O'Donnell, J. R., Jr.; Markley, F. L.

    1998-01-01

    The Microwave Anisotropy Probe (MAP) is a follow-on to the Differential Microwave Radiometer (DMR) instrument on the Cosmic Background Explorer (COBE) spacecraft. The design and analysis of the MAP attitude control system (ACS) have been refined since work previously reported. The full spacecraft and instrument flexible model was developed in NASTRAN, and the resulting flexible modes were plotted and reduced with the Modal Significance Analysis Package (MSAP). The reduced-order model was used to perform the linear stability analysis for each control mode, the results of which are presented in this paper. Although MAP is going to a relatively disturbance-free Lissajous orbit around the Earth-Sun L(2) Lagrange point, a detailed disturbance-torque analysis is required because there are only a small number of opportunities for momentum unloading each year. Environmental torques, including solar pressure at L(2), aerodynamic and gravity gradient during phasing-loop orbits, were calculated and simulated. Thruster plume impingement torques that could affect the performance of the thruster modes were estimated and simulated, and a simple model of fuel slosh was derived to model its effect on the motion of the spacecraft. In addition, a thruster mode linear impulse controller was developed to meet the accuracy requirements of the phasing loop burns. A dynamic attitude error limiter was added to improve the performance of the ACS during large attitude slews. The result of this analysis is a stable ACS subsystem that meets all of the mission's requirements.

  5. Structural and functional evaluation of the palindromic alanine-rich antimicrobial peptide Pa-MAP2.

    PubMed

    Migliolo, Ludovico; Felício, Mário R; Cardoso, Marlon H; Silva, Osmar N; Xavier, Mary-Ann E; Nolasco, Diego O; de Oliveira, Adeliana Silva; Roca-Subira, Ignasi; Vila Estape, Jordi; Teixeira, Leandro D; Freitas, Sonia M; Otero-Gonzalez, Anselmo J; Gonçalves, Sónia; Santos, Nuno C; Franco, Octavio L

    2016-07-01

    Recently, several peptides have been studied regarding the defence process against pathogenic microorganisms, which are able to act against different targets, with the purpose of developing novel bioactive compounds. The present work focuses on the structural and functional evaluation of the palindromic antimicrobial peptide Pa-MAP2, designed based on the peptide Pa-MAP from Pleuronectes americanus. For a better structural understanding, molecular modelling analyses were carried out, together with molecular dynamics and circular dichroism, in different media. Antibacterial activity against Gram-negative and positive bacteria was evaluated, as well as cytotoxicity against human erythrocytes, RAW 264.7, Vero and L6 cells. In silico docking experiments, lipid vesicle studies, and atomic force microscopy (AFM) imaging were carried out to explore the activity of the peptide. In vivo studies on infected mice were also done. The palindromic primary sequence favoured an α-helix structure that was pH dependent, only present on alkaline environment, with dynamic N- and C-terminals that are stabilized in anionic media. Pa-MAP2 only showed activity against Gram-negative bacteria, with a MIC of 3.2 μM, and without any cytotoxic effect. In silico, lipid vesicles and AFM studies confirm the preference for anionic lipids (POPG, POPS, DPPE, DPPG and LPS), with the positively charged lysine residues being essential for the initial electrostatic interaction. In vivo studies showed that Pa-MAP2 increases to 100% the survival rate of mice infected with Escherichia coli. Data here reported indicated that palindromic Pa-MAP2 could be an alternative candidate for use in therapeutics against Gram-negative bacterial infections. PMID:27063608

  6. Time-Frequency Analysis of Peptide Microarray Data: Application to Brain Cancer Immunosignatures.

    PubMed

    O'Donnell, Brian; Maurer, Alexander; Papandreou-Suppappola, Antonia; Stafford, Phillip

    2015-01-01

    One of the gravest dangers facing cancer patients is an extended symptom-free lull between tumor initiation and the first diagnosis. Detection of tumors is critical for effective intervention. Using the body's immune system to detect and amplify tumor-specific signals may enable detection of cancer using an inexpensive immunoassay. Immunosignatures are one such assay: they provide a map of antibody interactions with random-sequence peptides. They enable detection of disease-specific patterns using classic train/test methods. However, to date, very little effort has gone into extracting information from the sequence of peptides that interact with disease-specific antibodies. Because it is difficult to represent all possible antigen peptides in a microarray format, we chose to synthesize only 330,000 peptides on a single immunosignature microarray. The 330,000 random-sequence peptides on the microarray represent 83% of all tetramers and 27% of all pentamers, creating an unbiased but substantial gap in the coverage of total sequence space. We therefore chose to examine many relatively short motifs from these random-sequence peptides. Time-variant analysis of recurrent subsequences provided a means to dissect amino acid sequences from the peptides while simultaneously retaining the antibody-peptide binding intensities. We first used a simple experiment in which monoclonal antibodies with known linear epitopes were exposed to these random-sequence peptides, and their binding intensities were used to create our algorithm. We then demonstrated the performance of the proposed algorithm by examining immunosignatures from patients with Glioblastoma multiformae (GBM), an aggressive form of brain cancer. Eight different frameshift targets were identified from the random-sequence peptides using this technique. If immune-reactive antigens can be identified using a relatively simple immune assay, it might enable a diagnostic test with sufficient sensitivity to detect tumors in a

  7. Towards High-throughput Immunomics for Infectious Diseases: Use of Next-generation Peptide Microarrays for Rapid Discovery and Mapping of Antigenic Determinants*

    PubMed Central

    Carmona, Santiago J.; Nielsen, Morten; Schafer-Nielsen, Claus; Mucci, Juan; Altcheh, Jaime; Balouz, Virginia; Tekiel, Valeria; Frasch, Alberto C.; Campetella, Oscar; Buscaglia, Carlos A.; Agüero, Fernán

    2015-01-01

    Complete characterization of antibody specificities associated to natural infections is expected to provide a rich source of serologic biomarkers with potential applications in molecular diagnosis, follow-up of chemotherapeutic treatments, and prioritization of targets for vaccine development. Here, we developed a highly-multiplexed platform based on next-generation high-density peptide microarrays to map these specificities in Chagas Disease, an exemplar of a human infectious disease caused by the protozoan Trypanosoma cruzi. We designed a high-density peptide microarray containing more than 175,000 overlapping 15mer peptides derived from T. cruzi proteins. Peptides were synthesized in situ on microarray slides, spanning the complete length of 457 parasite proteins with fully overlapped 15mers (1 residue shift). Screening of these slides with antibodies purified from infected patients and healthy donors demonstrated both a high technical reproducibility as well as epitope mapping consistency when compared with earlier low-throughput technologies. Using a conservative signal threshold to classify positive (reactive) peptides we identified 2,031 disease-specific peptides and 97 novel parasite antigens, effectively doubling the number of known antigens and providing a 10-fold increase in the number of fine mapped antigenic determinants for this disease. Finally, further analysis of the chip data showed that optimizing the amount of sequence overlap of displayed peptides can increase the protein space covered in a single chip by at least ∼threefold without sacrificing sensitivity. In conclusion, we show the power of high-density peptide chips for the discovery of pathogen-specific linear B-cell epitopes from clinical samples, thus setting the stage for high-throughput biomarker discovery screenings and proteome-wide studies of immune responses against pathogens. PMID:25922409

  8. Matched Peptides: Tuning Matched Molecular Pair Analysis for Biopharmaceutical Applications

    PubMed Central

    2015-01-01

    Biopharmaceuticals hold great promise for the future of drug discovery. Nevertheless, rational drug design strategies are mainly focused on the discovery of small synthetic molecules. Herein we present matched peptides, an innovative analysis technique for biological data related to peptide and protein sequences. It represents an extension of matched molecular pair analysis toward macromolecular sequence data and allows quantitative predictions of the effect of single amino acid substitutions on the basis of statistical data on known transformations. We demonstrate the application of matched peptides to a data set of major histocompatibility complex class II peptide ligands and discuss the trends captured with respect to classical quantitative structure–activity relationship approaches as well as structural aspects of the investigated protein–peptide interface. We expect our novel readily interpretable tool at the interface of cheminformatics and bioinformatics to support the rational design of biopharmaceuticals and give directions for further development of the presented methodology. PMID:26501781

  9. Improved Methods for the Enrichment and Analysis of Glycated Peptides

    SciTech Connect

    Zhang, Qibin; Schepmoes, Athena A; Brock, Jonathan W; Wu, Si; Moore, Ronald J; Purvine, Samuel O; Baynes, John; Smith, Richard D; Metz, Thomas O

    2008-12-15

    Non-enzymatic glycation of tissue proteins has important implications in the development of complications of diabetes mellitus. Herein we report improved methods for the enrichment and analysis of glycated peptides using boronate affinity chromatography and electron transfer dissociation mass spectrometry, respectively. The enrichment of glycated peptides was improved by replacing an off-line desalting step with an on-line wash of column-bound glycated peptides using 50 mM ammonium acetate. The analysis of glycated peptides by MS/MS was improved by considering only higher charged (≥3) precursor-ions during data-dependent acquisition, which increased the number of glycated peptide identifications. Similarly, the use of supplemental collisional activation after electron transfer (ETcaD) resulted in more glycated peptide identifications when the MS survey scan was acquired with enhanced resolution. In general, acquiring ETD-MS/MS data at a normal MS survey scan rate, in conjunction with the rejection of both 1+ and 2+ precursor-ions, increased the number of identified glycated peptides relative to ETcaD or the enhanced MS survey scan rate. Finally, an evaluation of trypsin, Arg-C, and Lys-C showed that tryptic digestion of glycated proteins was comparable to digestion with Lys-C and that both were better than Arg-C in terms of the number glycated peptides identified by LC-MS/MS.

  10. Limited proteolysis and peptide mapping for comparability of biopharmaceuticals: An evaluation of repeatability, intra-assay precision and capability to detect structural change.

    PubMed

    Perrin, Camille; Burkitt, Will; Perraud, Xavier; O'Hara, John; Jone, Carl

    2016-05-10

    The use of limited proteolysis followed by peptide mapping for the comparability of the higher-order structure of biopharmaceuticals was investigated. In this approach the proteolysis is performed under non-reducing and non-denaturing conditions, and the resulting peptide map is determined by the samples primary and higher order structures. This allows comparability of biopharmaceuticals to be made in terms of their higher order structure, using a method that is relatively simple to implement. The digestion of a monoclonal antibody under non-denaturing conditions was analyzed using peptide mapping, circular dichroism (CD) and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). This allowed an optimal digestion time to be chosen. This method was then assessed for its ability to detect structural change using a monoclonal antibody, which had been subjected to a range of stresses; deglycosylation, mild denaturation and a batch that had failed specifications due to in-process reduction. The repeatability and inter-assay precision were assessed. It was demonstrated that the limited proteolysis peptide maps of the three stressed samples were significantly different to control samples and that the differences observed were consistent between the occasions when the assays were run. A combination of limited proteolysis and CD or SDS-PAGE analysis was shown to enhance the capacity of these techniques to detect structural change, which otherwise would not have been observed. PMID:26918895

  11. Protein surface topology-probing by selective chemical modification and mass spectrometric peptide mapping.

    PubMed Central

    Suckau, D; Mak, M; Przybylski, M

    1992-01-01

    Aminoacetylation of lysine residues and the modification of arginine by 1,2-cyclohexanedione to N7,N8-(dihydroxy-1,2-cyclohexylidene)arginine were used for probing the surface topology of hen-eggwhite lysozyme as a model protein. The molecular identification of lysine and arginine modification sites was provided by molecular weight determinations of modified and unmodified tryptic peptide mixtures (peptide mapping) using 252Cf plasma desorption mass spectrometry. At conditions of limited chemical modification, mass-spectrometric peptide-mapping analyses of lysozyme derivatives enabled the direct assignment of relative reactivities of lysine and arginine residues at different reaction times and reagent concentrations. The relative reactivities of lysine residues showed a direct correlation with their surface accessibilities from x-ray structure data. For the reaction with 1,2-cyclohexanedione, a selective modification at Arg-5, -125, -112, and -73 was identified, and an inverse correlation of relative reactivities with the surface accessibility ratios of the N7- and the N8-guanidino functions was obtained. By examination of the x-ray structural data of lysozyme, this selective modification was attributed to intramolecular catalysis because of the presence of neighboring proton acceptor groups, such as the Asp-119 carboxylate group for Arg-125 and the Trp-123 and Arg-125 carbonyl groups for Arg-5. PMID:1608973

  12. Comparison of peptide mass mapping and electron capture dissociation as assays for histone posttranslational modifications

    NASA Astrophysics Data System (ADS)

    Zhang, Liwen; Freitas, Michael A.

    2004-05-01

    Posttranslational modifications of core histones play a critical role in the structure of chromatin and the regulation of gene activities. Improved techniques for determining these modification sites may lead to a better understanding of histone regulation at the molecular level. LC-MS peptide mass mapping was performed on pepsin, trypsin and Glu-C digests of bovine thymus H4 using a QqTOF instrument. The well established modification sites of H4 (acetylation of K8, 12, 16 and methylation of K20) were observed in addition to several recently discovered modifications including: methylation of K31, 44, 59 and acetylation of K20, 77, 79. For comparison, electron capture dissociation (ECD) was performed on intact H4 along with several peptides from enzymatic digestion. The results from the ECD experiments of histone H4 indicated the acetylation of K5, 12, 16, 31, 91 and the methylation of K20 and 59 in good agreement with the result from peptide mapping. The work is dedicated to Alan G. Marshall on his 60th birthday. His endeavors in the advancement of FT-ICR facilitated experiments reported herein.

  13. Global Analysis of Human Nonreceptor Tyrosine Kinase Specificity Using High-Density Peptide Microarrays

    PubMed Central

    2015-01-01

    Protein kinases phosphorylate substrates in the context of specific phosphorylation site sequence motifs. The knowledge of the specific sequences that are recognized by kinases is useful for mapping sites of phosphorylation in protein substrates and facilitates the generation of model substrates to monitor kinase activity. Here, we have adapted a positional scanning peptide library method to a microarray format that is suitable for the rapid determination of phosphorylation site motifs for tyrosine kinases. Peptide mixtures were immobilized on glass slides through a layer of a tyrosine-free Y33F mutant avidin to facilitate the analysis of phosphorylation by radiolabel assay. A microarray analysis provided qualitatively similar results in comparison with the solution phase peptide library “macroarray” method. However, much smaller quantities of kinases were required to phosphorylate peptides on the microarrays, which thus enabled a proteome scale analysis of kinase specificity. We illustrated this capability by microarray profiling more than 80% of the human nonreceptor tyrosine kinases (NRTKs). Microarray results were used to generate a universal NRTK substrate set of 11 consensus peptides for in vitro kinase assays. Several substrates were highly specific for their cognate kinases, which should facilitate their incorporation into kinase-selective biosensors. PMID:25164267

  14. Immobilized Pepsin Microreactor for Rapid Peptide Mapping with Nanoelectrospray Ionization Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Long, Ying; Wood, Troy D.

    2015-01-01

    Most enzymatic microreactors for protein digestion are based on trypsin, but proteins with hydrophobic segments may be difficult to digest because of the paucity of Arg and Lys residues. Microreactors based on pepsin, which is less specific than trypsin, can overcome this challenge. Here, an integrated immobilized pepsin microreactor (IPMR)/nanoelectrospray emitter is examined for its potential for peptide mapping. For myoglobin, equivalent sequence coverage is obtained in a thousandth the time of solution digestion with better sequence coverage. While sequence coverage of cytochrome c is lesser than solution in this short duration, more highly-charged peptic peptides are produced and a number of peaks are unidentified at low-resolution, suggesting that high-resolution mass spectrometry is needed to take full advantage of integrated IPMR/nanoelectrospray devices.

  15. Mapping protein-protein interactions with phage-displayed combinatorial peptide libraries.

    SciTech Connect

    Kay, B. K.; Castagnoli, L.; Biosciences Division; Univ. of Rome

    2003-01-01

    This unit describes the process and analysis of affinity selecting bacteriophage M13 from libraries displaying combinatorial peptides fused to either a minor or major capsid protein. Direct affinity selection uses target protein bound to a microtiter plate followed by purification of selected phage by ELISA. Alternatively, there is a bead-based affinity selection method. These methods allow one to readily isolate peptide ligands that bind to a protein target of interest and use the consensus sequence to search proteomic databases for putative interacting proteins.

  16. Screening Method for the Discovery of Potential Bioactive Cysteine-Containing Peptides Using 3D Mass Mapping

    NASA Astrophysics Data System (ADS)

    van Oosten, Luuk N.; Pieterse, Mervin; Pinkse, Martijn W. H.; Verhaert, Peter D. E. M.

    2015-12-01

    Animal venoms and toxins are a valuable source of bioactive peptides with pharmacologic relevance as potential drug leads. A large subset of biologically active peptides discovered up till now contain disulfide bridges that enhance stability and activity. To discover new members of this class of peptides, we developed a workflow screening specifically for those peptides that contain inter- and intra-molecular disulfide bonds by means of three-dimensional (3D) mass mapping. Two intrinsic properties of the sulfur atom, (1) its relatively large negative mass defect, and (2) its isotopic composition, allow for differentiation between cysteine-containing peptides and peptides lacking sulfur. High sulfur content in a peptide decreases the normalized nominal mass defect (NMD) and increases the normalized isotopic shift (NIS). Hence in a 3D plot of mass, NIS, and NMD, peptides with sulfur appear in this plot with a distinct spatial localization compared with peptides that lack sulfur. In this study we investigated the skin secretion of two frog species; Odorrana schmackeri and Bombina variegata. Peptides from the crude skin secretions were separated by nanoflow LC, and of all eluting peptides high resolution zoom scans were acquired in order to accurately determine both monoisotopic mass and average mass. Both the NMD and the NIS were calculated from the experimental data using an in-house developed MATLAB script. Candidate peptides exhibiting a low NMD and high NIS values were selected for targeted de novo sequencing, and this resulted in the identification of several novel inter- and intra-molecular disulfide bond containing peptides.

  17. A conventional procedure to reduce Asn deamidation artifacts during trypsin peptide mapping.

    PubMed

    Kori, Yekaterina; Patel, Rekha; Neill, Alyssa; Liu, Hongcheng

    2016-01-15

    Asn deamidation is a common post-translational modification of proteins with significant biological consequences. Asn deamidation can cause changes in structure, stability and function of proteins. LC-MS peptide mapping is the most widely used method to detect and quantify Asn deamidation. However, a significant amount of deamidation can occur during sample preparation for peptide mapping, making it challenging to accurately determine the original level of deamidation. Although several protocols to reduce procedure-induced deamidation have been reported, they either require special procedural steps or are not optimal for maintaining trypsin activity. In the current study, several commonly used buffers that are optimal for trypsin activity were evaluated. The results demonstrated that much lower levels of Asn deamidation artifacts were observed when Tris buffer was used, especially at lower concentrations. The addition of 10% acetonitrile further reduced the levels of Asn deamidation artifacts. The utility of the optimized procedure was demonstrated by the digestion of a recombinant monoclonal antibody. The proposed procedure can be readily applied to any laboratory settings as it does not require any special reagents or procedures. PMID:26720699

  18. Structural and Functional Analysis of Horse Cathelicidin Peptides

    PubMed Central

    Skerlavaj, Barbara; Scocchi, Marco; Gennaro, Renato; Risso, Angela; Zanetti, Margherita

    2001-01-01

    Cathelicidin-derived antimicrobial peptides are a component of the peptide-based host defense of neutrophils and epithelia, with a widespread distribution in mammals. We recently reported the cDNA sequences of three putative horse myeloid cathelicidins, named eCATH-1, -2, and -3. A Western analysis was performed to investigate their presence in neutrophils and processing to mature peptides. eCATH-2 and eCATH-3, but not eCATH-1, were found to be present in uncleaved forms in horse neutrophils. The corresponding mature peptides were detected in inflammatory sites, suggesting that processing of the propeptides takes place upon neutrophil activation. A functional characterization was then performed with synthetic eCATH peptides. Circular dichroism measurements indicated an amphipathic α-helical conformation of these peptides in an anisotropic environment, and in vitro assays revealed a potent activity and a broad spectrum of antimicrobial activity for eCATH-1 and a somewhat more restricted spectrum of activity for eCATH-2. Conversely, a strong dependence on salt concentration was observed when the activity of eCATH-3 was tested. This peptide efficiently killed bacteria and some fungal species, i.e., Cryptococcus neoformans and Rhodotorula rubra, in low-ionic-strength media, but the activity was inhibited in the presence of physiological salt medium. This behavior could be modified by modulating the amphipathicity of the molecule. In fact, the synthetic analogue LLK-eCATH-3, with a slightly modified sequence that increases the hydrophobic moment of the peptide, displayed a potent activity in physiological salt medium against the strains resistant to eCATH-3 under these conditions. PMID:11181349

  19. Fine-Mapping of Immunodominant Linear B-Cell Epitopes of the Staphylococcus Aureus SEB Antigen Using Short Overlapping Peptides

    PubMed Central

    Zhao, Zhuo; Li, Bin; Sun, He-Qiang; Zhang, Jin-Yong; Wang, Yi-Lin; Chen, Li; Hu, Jian; He, Ya-Fei; Zeng, Hao; Zou, Quan-Ming; Wu, Chao

    2014-01-01

    Staphylococcal enterotoxin B (SEB) is one of the most potent Staphylococcus aureus exotoxins (SEs). Due to its conserved sequence and stable structure, SEB might be a good candidate antigen for MRSA vaccines. Although cellular immune responses to SEB are well-characterized, much less is known regarding SEB-specific humoral immune responses, particularly regarding detailed epitope mapping. In this study, we utilized a recombinant nontoxic mutant of SEB (rSEB) and an AlPO4 adjuvant to immunize BALB/c mice and confirmed that rSEB can induce a high antibody level and effective immune protection against MRSA infection. Next, the antisera of immunized mice were collected, and linear B cell epitopes within SEB were finely mapped using a series of overlapping synthetic peptides. Three immunodominant B cell epitopes of SEB were screened by ELISA, including a novel epitope, SEB205-222, and two known epitopes, SEB97–114 and SEB247-261. Using truncated peptides, an ELISA was performed with peptide-KLH antisera, and the core sequence of the three immunodominant B cell epitopes were verified as SEB97-112, SEB207-222, and SEB247-257. In vitro, all of the immunodominant epitope-specific antisera (anti-SEB97-112, anti-SEB207-222 and anti-SEB247-257) were observed to inhibit SEB-induced T cell mitogenesis and cytokine production from splenic lymphocytes of BALB/c mice. The homology analysis indicated that SEB97–112 and SEB207-222 were well-conserved among different Staphylococcus aureus strains. The 3D crystal structure of SEB indicated that SEB97–112 was in the loop region inside SEB, whereas SEB207-222 and SEB247-257 were in the β-slice region outside SEB. In summary, the fine-mapping of linear B-cell epitopes of the SEB antigen in this study will be useful to understand anti-SEB immunity against MRSA infection further and will be helpful to optimize MRSA vaccine designs that are based on the SEB antigen. PMID:24599257

  20. UNIT 11.10 N-Terminal Sequence Analysis of Proteins and Peptides

    PubMed Central

    Speicher, Kaye D.; Gorman, Nicole; Speicher, David W.

    2009-01-01

    Automated N-terminal sequence analysis involves a series of chemical reactions that derivatize and remove one amino acid at a time from the N-terminal of purified peptides or intact proteins. At least several pmoles of a purified protein or 10 to 20 pmoles of a purified peptide with an unmodified N-terminal is required in order to obtain useful sequence information. In recent years the demand for N-terminal sequencing has decreased substantially as some applications for protein identification and characterization can now be more effectively performed using mass spectrometry. However, N-terminal sequencing remains the method of choice for verifying the N-terminal boundary of recombinant proteins, determining the N-terminal of protease-resistant domains, identifying proteins isolated from species where most of the genome has not yet been sequenced, and mapping modified or crosslinked sites in proteins that prove to be refractory to analysis by mass spectrometry. PMID:18429102

  1. Micropreparative separation, fractionation, and peptide mapping of beta-lactoglobulin A and B variants by capillary electrophoresis.

    PubMed

    Olguin-Arredondo, Hector Armando; Vallejo-Cordoba, Belinda; González-Córdova, Aarón Fernando

    2005-01-01

    The methodological aspects for the separation, fractionation, and peptide mapping by free zone capillary electrophoresis (CZE) of beta-lactoglobulin (beta-Lg) variants A and B were established. First, beta-Lg variants A or B were separated and fractionated by CZE. Then, the collected protein fraction was subjected to off-line tryptic digestion. Second, peptide mapping of the tryptic hydrolysates and peptide fraction collection were carried out by CZE. beta-Lg variants were separated and collected using an uncoated capillary (72 cm x 75 microm i.d.) in 0.05 M borate buffer containing 0.1% Tween 20 at pH 8.0 by applying 20 kV. By subjecting the capillary under pressure after a delay time of 15%, the protein was collected in a microvial containing digestion buffer. The most suitable conditions for the tryptic digestion of beta-Lg were established by monitoring the reaction products with CZE. A tryptic hydrolysis with an enzyme-to-substrate ratio (E/S) of 1/20 and incubation for 20 hr at 37 degrees C was found to result in the most suitable conditions. Peptides were separated and collected using an uncoated capillary (120 cm x 75 microm i.d.) in 0.15 M formic acid at pH 2.3 by applying 28 kV. Peptide maps were highly reproducible as shown by coefficients of variation of less than 0.89 and 5.42% for migration times and peak areas, respectively. Moreover, very good resolution of the peptide maps revealed the region in which the aberrant peptides of the beta-Lg variants may be located. PMID:16042127

  2. Monomeric Aβ1–40 and Aβ1–42 Peptides in Solution Adopt Very Similar Ramachandran Map Distributions That Closely Resemble Random Coil

    PubMed Central

    2016-01-01

    The pathogenesis of Alzheimer’s disease is characterized by the aggregation and fibrillation of amyloid peptides Aβ1–40 and Aβ1–42 into amyloid plaques. Despite strong potential therapeutic interest, the structural pathways associated with the conversion of monomeric Aβ peptides into oligomeric species remain largely unknown. In particular, the higher aggregation propensity and associated toxicity of Aβ1–42 compared to that of Aβ1–40 are poorly understood. To explore in detail the structural propensity of the monomeric Aβ1–40 and Aβ1–42 peptides in solution, we recorded a large set of nuclear magnetic resonance (NMR) parameters, including chemical shifts, nuclear Overhauser effects (NOEs), and J couplings. Systematic comparisons show that at neutral pH the Aβ1–40 and Aβ1–42 peptides populate almost indistinguishable coil-like conformations. Nuclear Overhauser effect spectra collected at very high resolution remove assignment ambiguities and show no long-range NOE contacts. Six sets of backbone J couplings (3JHNHα, 3JC′C′, 3JC′Hα, 1JHαCα, 2JNCα, and 1JNCα) recorded for Aβ1–40 were used as input for the recently developed MERA Ramachandran map analysis, yielding residue-specific backbone ϕ/ψ torsion angle distributions that closely resemble random coil distributions, the absence of a significantly elevated propensity for β-conformations in the C-terminal region of the peptide, and a small but distinct propensity for αL at K28. Our results suggest that the self-association of Aβ peptides into toxic oligomers is not driven by elevated propensities of the monomeric species to adopt β-strand-like conformations. Instead, the accelerated disappearance of Aβ NMR signals in D2O over H2O, particularly pronounced for Aβ1–42, suggests that intermolecular interactions between the hydrophobic regions of the peptide dominate the aggregation process. PMID:26780756

  3. How to unveil self-quenched fluorophores and subsequently map the subcellular distribution of exogenous peptides

    PubMed Central

    Swiecicki, Jean-Marie; Thiebaut, Frédéric; Di Pisa, Margherita; Gourdin -Bertin, Simon; Tailhades, Julien; Mansuy, Christelle; Burlina, Fabienne; Chwetzoff, Serge; Trugnan, Germain; Chassaing, Gérard; Lavielle, Solange

    2016-01-01

    Confocal laser scanning microscopy (CLSM) is the most popular technique for mapping the subcellular distribution of a fluorescent molecule and is widely used to investigate the penetration properties of exogenous macromolecules, such as cell-penetrating peptides (CPPs), within cells. Despite the membrane-association propensity of all these CPPs, the signal of the fluorescently labeled CPPs did not colocalize with the plasma membrane. We studied the origin of this fluorescence extinction and the overall consequence on the interpretation of intracellular localizations from CLSM pictures. We demonstrated that this discrepancy originated from fluorescence self-quenching. The fluorescence was unveiled by a “dilution” protocol, i.e. by varying the ratio fluorescent/non-fluorescent CPP. This strategy allowed us to rank with confidence the subcellular distribution of several CPPs, contributing to the elucidation of the penetration mechanism. More generally, this study proposes a broadly applicable and reliable method to study the subcellular distribution of any fluorescently labeled molecules. PMID:26839211

  4. Automated carboxy-terminal sequence analysis of peptides.

    PubMed Central

    Bailey, J. M.; Shenoy, N. R.; Ronk, M.; Shively, J. E.

    1992-01-01

    current limitations, the methodology should be a valuable new tool for the C-terminal sequence analysis of peptides. PMID:1304884

  5. Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data

    SciTech Connect

    Ting, Ying S.; Egertson, Jarrett D.; Payne, Samuel H.; Kim, Sangtae; MacLean, Brendan; Kall, Lukas; Aebersold, Ruedi; Smith, Richard D.; Noble, William; MacCoss, Michael

    2015-09-01

    In mass spectrometry-based bottom-up proteomics, data-independent acquisition (DIA) is an emerging technique due to its comprehensive and unbiased sampling of precursor ions. However, current DIA methods use wide precursor isolation windows, resulting in co- fragmentation and complex mixture spectra. Thus, conventional database searching tools that identify peptides by interpreting individual MS/MS spectra are inherently limited in analyzing DIA data. Here we discuss an alternative approach, peptide-centric analysis, which tests directly for the presence and absence of query peptides. We discuss how peptide-centric analysis resolves some limitations of traditional spectrum-centric analysis, and we outline the benefits of peptide-centric analysis in general.

  6. MALDI imaging mass spectrometry and analysis of endogenous peptides.

    PubMed

    Chatterji, Bijon; Pich, Andreas

    2013-08-01

    In recent years, MALDI imaging mass spectrometry (MALDI-IMS) has developed as a promising tool to investigate the spatial distribution of biomolecules in intact tissue specimens. Ion densities of various molecules can be displayed as heat maps while preserving anatomical structures. In this short review, an overview of different biomolecules that can be analyzed by MALDI-IMS is given. Many reviews have covered imaging of lipids, small metabolites, whole proteins and enzymatically digested proteins in the past. However, little is known about imaging of endogenous peptides, for example, in the rat brain, and this will therefore be highlighted in this review. Furthermore, sample preparation of frozen or formalin-fixed, paraffin-embedded (FFPE) tissue is crucial for imaging experiments. Therefore, some aspects of sample preparation will be addressed, including washing and desalting, the choice of MALDI matrix and its deposition. Apart from mapping endogenous peptides, their reliable identification in situ still remains challenging and will be discussed as well. PMID:23992420

  7. Genetic and biochemical analysis of peptide transport in Escherichia coli

    SciTech Connect

    Andrews, J.C.

    1986-01-01

    E. coli peptide transport mutants have been isolated based on their resistance to toxic tripeptides. These genetic defects were found to map in two distinct chromosomal locations. The transport systems which require expression of the trp-linked opp genes and the oppE gene(s) for activity were shown to have different substrate preferences. Growth of E. coli in medium containing leucine results in increased entry of exogenously supplied tripeptides into the bacterial cell. This leucine-mediated elevation of peptide transport required expression of the trp-linked opp operon and was accompanied by increased sensitivity to toxic tripeptides, by an enhanced capacity to utilize nutritional peptides, and by an increase in both the velocity and apparent steady-state level of L-(U-/sup 14/C)alanyl-L-alanyl-L-alanine accumulation for E. coli grown in leucine-containing medium relative to these parameters of peptide transport measured with bacteria grown in media lacking leucine. Direct measurement of opp operon expression by pulse-labeling experiments demonstrated that growth of E. coli in the presence of leucine resulted in increased synthesis of the oppA-encoded periplasmic binding protein. The transcriptional regulation of the trp-linked opp operon of E. coli was investigated using lambda placMu51-generated lac operon fusions. Synthesis of ..beta..-galactosidase by strains harboring oppA-lac, oppB-lac, and oppD-lac fusions occurred at a basal level when the fusion-containing strains were grown in minimal medium.

  8. Serial concept maps: tools for concept analysis.

    PubMed

    All, Anita C; Huycke, LaRae I

    2007-05-01

    Nursing theory challenges students to think abstractly and is often a difficult introduction to graduate study. Traditionally, concept analysis is useful in facilitating this abstract thinking. Concept maps are a way to visualize an individual's knowledge about a specific topic. Serial concept maps express the sequential evolution of a student's perceptions of a selected concept. Maps reveal individual differences in learning and perceptions, as well as progress in understanding the concept. Relationships are assessed and suggestions are made during serial mapping, which actively engages the students and faculty in dialogue that leads to increased understanding of the link between nursing theory and practice. Serial concept mapping lends itself well to both online and traditional classroom environments. PMID:17547345

  9. Recombinant expression and purification of a MAP30-cell penetrating peptide fusion protein with higher anti-tumor bioactivity.

    PubMed

    Lv, Qiang; Yang, Xu-Zhong; Fu, Long-Yun; Lu, Yv-Ting; Lu, Yan-Hua; Zhao, Jian; Wang, Fu-Jun

    2015-07-01

    MAP30 (Momordica Antiviral Protein 30 Kd), a single-stranded type-I ribosome inactivating protein, possesses versatile biological activities including anti-tumor abilities. However, the low efficiency penetrating into tumor cells hampers the tumoricidal effect of MAP30. This paper describes MAP30 fused with a human-derived cell penetrating peptide HBD which overcome the low uptake efficiency by tumor cells and exhibits higher anti-tumor bioactivity. MAP30 gene was cloned from the genomic DNA of Momordica charantia and the recombinant plasmid pET28b-MAP30-HBD was established and transferred into Escherichia coli BL21 (DE3). The recombinant MAP30-HBD protein (rMAP30-HBD) was expressed in a soluble form after being induced by 0.5mM IPTG for 14h at 15°C. The recombinant protein was purified to greater than 95% purity with Ni-NTA affinity chromatography. The rMAP30-HBD protein not only has topological inactivation and protein translation inhibition activity but also showed significant improvements in cytotoxic activity compared to that of the rMAP30 protein without HBD in the tested tumor cell lines, and induced higher apoptosis rates in HeLa cells analyzed by Annexin V-FITC with FACS. This paper demonstrated a new method for improving MAP30 protein anti-tumor activity and might have potential applications in cancer therapy area. PMID:25797209

  10. Structure of the gene for porcine peptide antibiotic PR-39, a cathelin gene family member: comparative mapping of the locus for the human peptide antibiotic FALL-39.

    PubMed Central

    Gudmundsson, G H; Magnusson, K P; Chowdhary, B P; Johansson, M; Andersson, L; Boman, H G

    1995-01-01

    PR-39 is a porcine 39-aa peptide antibiotic composed of 49% proline and 24% arginine, with an activity against Gram-negative bacteria comparable to that of tetracycline. In Escherichia coli, it inhibits DNA and protein synthesis. PR-39 was originally isolated from pig small intestine, but subsequent cDNA cloning showed that the gene is expressed in the bone marrow. The open reading frame of the clone showed that PR-39 is made as 173-aa precursor whose proregion belongs to the cathelin family. The PR39 gene, which is rather compact and spans only 1784 bp has now been sequenced. The coding information is split into four exons. The first exon contains the signal sequence of 29 residues and the first 37 residues of the cathelin propart. Exons 2 and 3 contain only cathelin information, while exon 4 codes for the four C-terminal cathelin residues and the mature PR-39 peptide extended by three residues. The sequenced upstream region (1183 bp) contains four potential recognition sites for NF-IL6 and three for APRF, transcription factors known to regulate genes for both cytokines and acute phase response factors. Genomic hybridizations revealed a fairly high level of restriction fragment length polymorphism and indicated that there are at least two copies of the PR39 gene in the pig genome. PR39 was mapped to pig chromosome 13 by linkage and in situ hybridization mapping. The gene for the human peptide antibiotic FALL-39 (also a member of the cathelin family) was mapped to human chromosome 3, which is homologous to pig chromosome 13. Images Fig. 2 Fig. 3 PMID:7624374

  11. Mask Analysis Program (MAP) reference manual

    NASA Technical Reports Server (NTRS)

    Mitchell, C. L.

    1976-01-01

    A document intended to serve as a User's Manual and a Programmer's Manual for the Mask Analysis Program is presented. The first portion of the document is devoted to the user. It contains all of the information required to execute MAP. The remainder of the document describes the details of MAP software logic. Although the information in this portion is not required to run the program, it is recommended that every user review it to gain an appreciation for the program functions.

  12. Rapid sequencing and disulfide mapping of peptides containing disulfide bonds by using 1,5-diaminonaphthalene as a reductive matrix.

    PubMed

    Fukuyama, Yuko; Iwamoto, Shinichi; Tanaka, Koichi

    2006-02-01

    MS/MS is indispensable for the amino acid sequencing of peptides. However, its use is limited for peptides containing disulfide bonds. We have applied the reducing properties of 1,5-diaminonaphthalene (1,5-DAN) as a MALDI matrix to amino acid sequencing and disulfide bond mapping of human urotensin II possessing one disulfide bond, and human guanylin possessing two disulfide bonds. 1,5-DAN was used in the same manner as the usual MALDI matrices without any pre-treatment of the peptide, and MS/MS was performed using a matrix-assisted laser desorption/ionization quadrupole ion trap time-of-flight mass spectrometer (MALDI QIT TOFMS). The results demonstrated that MS/MS of the molecular ions reduced by 1,5-DAN provided a series of significant b-/y-product ions. All 11 amino acid residues of urotensin II were identified using 1,5-DAN, while only 5 out of 11 residues were identified using 2,5-dihydroxybenzoic acid (DHB); similarly 11 out of 15 amino acid residues of guanylin were identified using 1,5-DAN, while only three were identified using DHB. In addition, comparison of the theoretical and measured values of the mass differences between corresponding MS/MS product ions using 1,5-DAN and DHB narrowed down the possible disulfide bond arrangement candidates. Consequently, 1,5-DAN as a reductive matrix facilitates rapid amino acid sequencing and disulfide mapping for peptides containing disulfide bonds. PMID:16382486

  13. MapReduce Implementation of a Hybrid Spectral Library-Database Search Method for Large-Scale Peptide Identification

    SciTech Connect

    Kalyanaraman, Anantharaman; Cannon, William R.; Latt, Benjamin K.; Baxter, Douglas J.

    2011-11-01

    A MapReduce-based implementation called MR- MSPolygraph for parallelizing peptide identification from mass spectrometry data is presented. The underlying serial method, MSPolygraph, uses a novel hybrid approach to match an experimental spectrum against a combination of a protein sequence database and a spectral library. Our MapReduce implementation can run on any Hadoop cluster environment. Experimental results demonstrate that, relative to the serial version, MR-MSPolygraph reduces the time to solution from weeks to hours, for processing tens of thousands of experimental spectra. Speedup and other related performance studies are also reported on a 400-core Hadoop cluster using spectral datasets from environmental microbial communities as inputs.

  14. Characterization of desmoglein-3 epitope region peptides as synthetic antigens: analysis of their in vitro T cell stimulating efficacy, cytotoxicity, stability, and their conformational features.

    PubMed

    Szabados, Hajnalka; Uray, Katalin; Majer, Zsuzsa; Silló, Pálma; Kárpáti, Sarolta; Hudecz, Ferenc; Bősze, Szilvia

    2015-09-01

    Desmoglein-3 (Dsg3) adhesion protein is the main target of autoantibodies and autoreactive T cells in Pemphigus vulgaris (PV) autoimmune skin disorder. Several mapping studies of Dsg3 T cell epitope regions were performed, and based on those data, we designed and synthesized four peptide series corresponding to Dsg3 T cell epitope regions. Each peptide series consists of a 17mer full-length peptide (Dsg3/189-205, Dsg3/206-222, Dsg3/342-358, and Dsg3/761-777) and its N-terminally truncated derivatives, resulting in 15 peptides altogether. The peptides were prepared on solid phase and were chemically characterized. In order to establish a structure-activity relationship, the solution conformation of the synthetic peptides has been investigated using electronic circular dichroism spectroscopy. The in vitro T cell stimulating efficacy of the peptides has been determined on peripheral blood mononuclear cells isolated from whole blood of PV patients and also from healthy donors. After 20 h of stimulation, the interferon (IFN)-γ content of the supernatants was measured by enzyme-linked immunosorbent assay. In the in vitro conditions, peptides were stable and non-cytotoxic. The in vitro IFN-γ production profile of healthy donors and PV patients, induced by peptides as synthetic antigens, was markedly different. The most unambiguous differences were observed after stimulation with 17mer peptide Dsg3/342-358, and three truncated derivatives from two other peptide series, namely, peptides Dsg3/192-205, Dsg3/763-777, and Dsg3/764-777. Comparative analysis of in vitro activity and the capability of oligopeptides to form ordered or unordered secondary structure showed that peptides bearing high solvent sensibility and backbone flexibility were the most capable to distinguish between healthy and PV donors. PMID:26250896

  15. Liquid MALDI MS Analysis of Complex Peptide and Proteome Samples.

    PubMed

    Wiangnon, Kanjana; Cramer, Rainer

    2016-09-01

    Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) is well-known to be a powerful technique for the analysis of biological samples. By using glycerol-based liquid support matrices (LSMs) instead of conventional MALDI matrices the power of this technique can be extended further. In this study, we exploited LSMs for the identification of complex samples, that is, the Lactobacillus proteome and a bovine serum albumin (BSA) digest. Liquid and solid MALDI samples were manually and robotically prepared by coupling a nanoflow high-performance liquid chromatography (nanoHPLC) system to an automated MALDI sample spotting device. MS and MS/MS data were successfully acquired at the femtomole level using TOF/TOF as well as Q-TOF instrumentation and used for protein identification searching sequence databases. For the BSA digest analysis, liquid MALDI samples resulted in peptide mass fingerprints, which led to a higher confidence in protein identification compared with solid (crystalline) MALDI samples; however, postsource decay (PSD) MS/MS analysis of both the proteome of Lactobacillus plantarum WCFS1 cells and BSA digest showed that further optimization of the formation and detection of peptide fragment ions is still needed for liquid MALDI samples, as the MS/MS ion search score was lower than that for the solid MALDI samples, reflecting the poorer quality of the liquid MALDI-PSD spectra, which can be attributed to the differences in PSD parameters and their optimization that is currently achievable. PMID:27418427

  16. Mapping protein-protein interactions with phage-displayed combinatorial peptide libraries and alanine scanning.

    PubMed

    Kokoszka, Malgorzata E; Kay, Brian K

    2015-01-01

    One avenue for inferring the function of a protein is to learn what proteins it may bind to in the cell. Among the various methodologies, one way for doing so is to affinity select peptide ligands from a phage-displayed combinatorial peptide library and then to examine if the proteins that carry such peptide sequences interact with the target protein in the cell. With the protocols described in this chapter, a laboratory with skills in microbiology, molecular biology, and protein biochemistry can readily identify peptides in the library that bind selectively, and with micromolar affinity, to a given target protein on the time scale of 2 months. To illustrate this approach, we use a library of bacteriophage M13 particles, which display 12-mer combinatorial peptides, to affinity select different peptide ligands for two different targets, the SH3 domain of the human Lyn protein tyrosine kinase and a segment of the yeast serine/threonine protein kinase Cbk1. The binding properties of the selected peptide ligands are then dissected by sequence alignment, Kunkel mutagenesis, and alanine scanning. Finally, the peptide ligands can be used to predict cellular interacting proteins and serve as the starting point for drug discovery. PMID:25616333

  17. Identification and mapping of linear antibody epitopes in human serum albumin using high-density Peptide arrays.

    PubMed

    Hansen, Lajla Bruntse; Buus, Soren; Schafer-Nielsen, Claus

    2013-01-01

    We have recently developed a high-density photolithographic, peptide array technology with a theoretical upper limit of 2 million different peptides per array of 2 cm(2). Here, we have used this to perform complete and exhaustive analyses of linear B cell epitopes of a medium sized protein target using human serum albumin (HSA) as an example. All possible overlapping 15-mers from HSA were synthesized and probed with a commercially available polyclonal rabbit anti-HSA antibody preparation. To allow for identification of even the weakest epitopes and at the same time perform a detailed characterization of key residues involved in antibody binding, the array also included complete single substitution scans (i.e. including each of the 20 common amino acids) at each position of each 15-mer peptide. As specificity controls, all possible 15-mer peptides from bovine serum albumin (BSA) and from rabbit serum albumin (RSA) were included as well. The resulting layout contained more than 200.000 peptide fields and could be synthesized in a single array on a microscope slide. More than 20 linear epitope candidates were identified and characterized at high resolution i.e. identifying which amino acids in which positions were needed, or not needed, for antibody interaction. As expected, moderate cross-reaction with some peptides in BSA was identified whereas no cross-reaction was observed with peptides from RSA. We conclude that high-density peptide microarrays are a very powerful methodology to identify and characterize linear antibody epitopes, and should advance detailed description of individual specificities at the single antibody level as well as serologic analysis at the proteome-wide level. PMID:23894373

  18. Specific degradation of the mucus adhesion-promoting protein (MapA) of Lactobacillus reuteri to an antimicrobial peptide.

    PubMed

    Bøhle, Liv Anette; Brede, Dag Anders; Diep, Dzung B; Holo, Helge; Nes, Ingolf F

    2010-11-01

    The intestinal flora of mammals contains lactic acid bacteria (LAB) that may provide positive health effects for the host. Such bacteria are referred to as probiotic bacteria. From a pig, we have isolated a Lactobacillus reuteri strain that produces an antimicrobial peptide (AMP). The peptide was purified and characterized, and it was unequivocally shown that the AMP was a well-defined degradation product obtained from the mucus adhesion-promoting protein (MapA); it was therefore termed AP48-MapA. This finding demonstrates how large proteins might inherit unexpected pleiotropic functions by conferring antimicrobial capacities on the producer. The MapA/AP48-MapA system is the first example where a large protein of an intestinal LAB is shown to give rise to such an AMP. It is also of particular interest that the protein that provides this AMP is associated with the binding of the bacterium producing it to the surface/lining of the gut. This finding gives us new perspective on how some probiotic bacteria may successfully compete in this environment and thereby contribute to a healthy microbiota. PMID:20833791

  19. Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

    SciTech Connect

    Nedialkova, Lilia V.; Amat, Miguel A.; Kevrekidis, Ioannis G. E-mail: gerhard.hummer@biophys.mpg.de; Hummer, Gerhard E-mail: gerhard.hummer@biophys.mpg.de

    2014-09-21

    Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlap with clusters obtained previously by using the backbone dihedral angles as input, with small—but nontrivial—differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space.

  20. Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions.

    PubMed

    Nedialkova, Lilia V; Amat, Miguel A; Kevrekidis, Ioannis G; Hummer, Gerhard

    2014-09-21

    Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlap with clusters obtained previously by using the backbone dihedral angles as input, with small--but nontrivial--differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space. PMID:25240340

  1. Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

    NASA Astrophysics Data System (ADS)

    Nedialkova, Lilia V.; Amat, Miguel A.; Kevrekidis, Ioannis G.; Hummer, Gerhard

    2014-09-01

    Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlap with clusters obtained previously by using the backbone dihedral angles as input, with small—but nontrivial—differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space.

  2. Proteomic analysis of peptides tagged with dimedone and related probes.

    PubMed

    Martínez-Acedo, Pablo; Gupta, Vinayak; Carroll, Kate S

    2014-04-01

    Owing to its labile nature, a new role for cysteine sulfenic acid (-SOH) modification has emerged. This oxidative modification modulates protein function by acting as a redox switch during cellular signaling. The identification of proteins that undergo this modification represents a methodological challenge, and its resolution remains a matter of current interest. The development of strategies to chemically modify cysteinyl-containing peptides for liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis has increased significantly within the past decade. The method of choice to selectively label sulfenic acid is based on the use of dimedone or its derivatives. For these chemical probes to be effective on a proteome-wide level, their reactivity toward -SOH must be high to ensure reaction completion. In addition, the presence of an adduct should not interfere with electrospray ionization, the efficiency of induced dissociation in MS/MS experiments or with the identification of Cys-modified peptides by automated database searching algorithms. Herein, we employ a targeted proteomics approach to study the electrospray ionization and fragmentation effects of different -SOH specific probes and compared them to commonly used alkylating agents. We then extend our study to a whole proteome extract using shotgun proteomic approaches. These experiments enable us to demonstrate that dimedone adducts do not interfere with electrospray by suppressing the ionization nor impede product ion assignment by automated search engines, which detect a + 138 Da increase from unmodified peptides. Collectively, these results suggest that dimedone can be a powerful tool to identify sulfenic acid modifications by high-throughput shotgun proteomics of a whole proteome. PMID:24719340

  3. Identification of peptide-specific TCR genes by in vitro peptide stimulation and CDR3 length polymorphism analysis.

    PubMed

    Shao, Hongwei; Lin, Yanmei; Wang, Teng; Ou, Yusheng; Shen, Han; Tao, Changli; Wu, Fenglin; Zhang, Wenfeng; Bo, Huaben; Wang, Hui; Huang, Shulin

    2015-07-10

    Identification of TCR genes specific for tumor-associated antigens (TAAs) is necessary for TCR gene modification of T cells, which is applied in anti-tumor adoptive T cell therapy (ACT). The usual identification methods are based on isolating single peptide-responding T cells and cloning the TCR gene by in vitro expansion or by single-cell RT-PCR. However, the long and exacting in vitro culture period and demanding operational requirements restrict the application of these methods. Immunoscope is an effective tool that profiles a repertoire of TCRs and identifies significantly expanded clones through CDR3 length analysis. In this study, a survivin-derived mutant peptide optimized for HLA-A2 binding was selected to load DCs and activate T cells. The monoclonal expansion of TCRA and TCRB genes was separately identified by Immunoscope analysis and following sequence identification, the properly paired TCR genes were transferred into T cells. Peptide recognition and cytotoxicity assays indicated that TCR-modified PBMCs could respond to both the mutant and wild type peptides and lyse target cells. These results show that combining Immunoscope with in vitro peptide stimulation provides an alternative and superior method for identifying specific TCR genes, which represents a significant advance for the application of TCR gene-modified T cells. PMID:25890221

  4. Parallel map analysis on 2-D grids

    SciTech Connect

    Berry, M.; Comiskey, J.; Minser, K.

    1993-12-31

    In landscape ecology, computer modeling is used to assess habitat fragmentation and its ecological iMPLications. Specifically, maps (2-D grids) of habitat clusters must be analyzed to determine number, sizes and geometry of clusters. Models prior to this study relied upon sequential Fortran-77 programs which limited the sizes of maps and densities of clusters which could be analyzed. In this paper, we present more efficient computer models which can exploit recursion or parallelism. Significant improvements over the original Fortran-77 programs have been achieved using both recursive and nonrecursive C implementations on a variety of workstations such as the Sun Sparc 2, IBM RS/6000-350, and HP 9000-750. Parallel implementations on a 4096-processor MasPar MP-1 and a 32-processor CM-5 are also studied. Preliminary experiments suggest that speed improvements for the parallel model on the MasPar MP-1 (written in MPL) and on the CM-5 (written in C using CMMD) can be as much as 39 and 34 times faster, respectively, than the most efficient sequential C program on a Sun Sparc 2 for a 512 map. An important goal in this research effort is to produce a scalable map analysis algorithm for the identification and characterization of clusters for relatively large maps on massively-parallel computers.

  5. Inhibition of inflammation by a p38 MAP kinase targeted cell permeable peptide.

    PubMed

    Fu, Jing; Meng, Xianmei; He, Junyun; Gu, Jun

    2008-11-01

    p38 MAPK has been the key therapeutic target for multiple inflammation diseases. However, the clinical applications of p38 inhibitors, most of which target on the ATP binding groove in the kinase, have been held back, largely because of their limited specificity and severe side-effects. An alternative strategy to generate highly selective p38 inhibitor is to block the specific interaction in the p38 signal pathway. Based on the hypothesis that specific binding peptides targeting on the docking groove would interfere the intrinsic interaction between p38 and its partners, we have designed a fusion peptide containing 12aa p38 docking sequence derived from MKK3b and 11aa HIV-TAT transmembrane sequence to form a cell permeable peptide. The peptide specifically binds to p38, and aborts its interaction with upstream kinase as well as downstream substrates, and thus to inhibit p38 phosphorylation and its signaling. Furthermore, the induction and secretion of TNFalpha and other inflammatory factors by LPS are blocked in peptide treated cells and mice. Finally the peptide has been shown to significantly inhibit ear oedema in mice. Therefore, the peptide holds great potential as an anti-inflammation agent for the treatment of inflammation and its related diseases. PMID:18991745

  6. Wavelet analysis of electron-density maps.

    PubMed

    Main, P; Wilson, J

    2000-05-01

    The wavelet transform is a powerful technique in signal processing and image analysis and it is shown here that wavelet analysis of low-resolution electron-density maps has the potential to increase their resolution. Like Fourier analysis, wavelet analysis expresses the image (electron density) in terms of a set of orthogonal functions. In the case of the Fourier transform, these functions are sines and cosines and each one contributes to the whole of the image. In contrast, the wavelet functions (simply called wavelets) can be quite localized and may only contribute to a small part of the image. This gives control over the amount of detail added to the map as the resolution increases. The mathematical details are outlined and an algorithm which achieves a resolution increase from 10 to 7 A using a knowledge of the wavelet-coefficient histograms, electron-density histogram and the observed structure amplitudes is described. These histograms are calculated from the electron density of known structures, but it seems likely that the histograms can be predicted, just as electron-density histograms are at high resolution. The results show that the wavelet coefficients contain the information necessary to increase the resolution of electron-density maps. PMID:10771431

  7. Meteorological analysis of MAPS first shuttle flight

    NASA Technical Reports Server (NTRS)

    Doherty, M.; Newell, R. E.

    1983-01-01

    The data from the MAPS radiometer launched on board the first shuttle flight was analyzed. The meteorological data relevant to the MAPS measurements was also analyzed so that the in situ calibration measurements and any anomalous features within the data set can be evaluated in the context of the atmospheric circulation during the period of observation. The three dimensioned isentropic analysis scheme was used as the main analytical tool. A graphical output of the N and delta channel signals, black body reference temperatures, reduced CO concentrations and ground tracks for orbits 15 and 16 were provided. The insentropic trajectory methods was emphasized because it is a basic requirement that the analysis be extended to incorporate daily data within the tropics.

  8. MAP Attitude Control System Design and Analysis

    NASA Technical Reports Server (NTRS)

    Andrews, S. F.; Campbell, C. E.; Ericsson-Jackson, A. J.; Markley, F. L.; ODonnell, J. R., Jr.

    1997-01-01

    The Microwave Anisotropy Probe (MAP) is a follow-on to the Differential Microwave Radiometer (DMR) instrument on the Cosmic Background Explorer (COBE) spacecraft. The MAP spacecraft will perform its mission in a Lissajous orbit around the Earth-Sun L(sub 2) Lagrange point to suppress potential instrument disturbances. To make a full-sky map of cosmic microwave background fluctuations, a combination fast spin and slow precession motion will be used. MAP requires a propulsion system to reach L(sub 2), to unload system momentum, and to perform stationkeeping maneuvers once at L(sub 2). A minimum hardware, power and thermal safe control mode must also be provided. Sufficient attitude knowledge must be provided to yield instrument pointing to a standard deviation of 1.8 arc-minutes. The short development time and tight budgets require a new way of designing, simulating, and analyzing the Attitude Control System (ACS). This paper presents the design and analysis of the control system to meet these requirements.

  9. Quality Analysis of Open Street Map Data

    NASA Astrophysics Data System (ADS)

    Wang, M.; Li, Q.; Hu, Q.; Zhou, M.

    2013-05-01

    Crowd sourcing geographic data is an opensource geographic data which is contributed by lots of non-professionals and provided to the public. The typical crowd sourcing geographic data contains GPS track data like OpenStreetMap, collaborative map data like Wikimapia, social websites like Twitter and Facebook, POI signed by Jiepang user and so on. These data will provide canonical geographic information for pubic after treatment. As compared with conventional geographic data collection and update method, the crowd sourcing geographic data from the non-professional has characteristics or advantages of large data volume, high currency, abundance information and low cost and becomes a research hotspot of international geographic information science in the recent years. Large volume crowd sourcing geographic data with high currency provides a new solution for geospatial database updating while it need to solve the quality problem of crowd sourcing geographic data obtained from the non-professionals. In this paper, a quality analysis model for OpenStreetMap crowd sourcing geographic data is proposed. Firstly, a quality analysis framework is designed based on data characteristic analysis of OSM data. Secondly, a quality assessment model for OSM data by three different quality elements: completeness, thematic accuracy and positional accuracy is presented. Finally, take the OSM data of Wuhan for instance, the paper analyses and assesses the quality of OSM data with 2011 version of navigation map for reference. The result shows that the high-level roads and urban traffic network of OSM data has a high positional accuracy and completeness so that these OSM data can be used for updating of urban road network database.

  10. Analysis of illegal peptide biopharmaceuticals frequently encountered by controlling agencies.

    PubMed

    Vanhee, Celine; Janvier, Steven; Desmedt, Bart; Moens, Goedele; Deconinck, Eric; De Beer, Jacques O; Courselle, Patricia

    2015-09-01

    Recent advances in genomics, recombinant expression technologies and peptide synthesis have led to an increased development of protein and peptide therapeutics. Unfortunately this goes hand in hand with a growing market of counterfeit and illegal biopharmaceuticals, including substances that are still under pre-clinical and clinical development. These counterfeit and illegal protein and peptide substances could imply severe health threats as has been demonstrated by numerous case reports. The Belgian Federal Agency for Medicines and Health Products (FAMHP) and customs are striving, together with their global counterparts, to curtail the trafficking and distributions of these substances. At their request, suspected protein and peptide preparations are analysed in our Official Medicines Control Laboratory (OMCL). It stands to reason that a general screening method would be beneficiary in the battle against counterfeit and illegal peptide drugs. In this paper we present such general screening method employing liquid chromatography-tandem mass spectrometry (LC-MS/MS) for the identification of counterfeit and illegal injectable peptide preparations, extended with a subsequent quantification method using ultra-high performance liquid chromatography with diode array detection (UHPLC-DAD). The screening method, taking only 30 min, is able to selectively detect 25 different peptides and incorporates the proposed minimum of five identification points (IP) as has been recommended for sports drug testing applications. The group of peptides represent substances which have already been detected in illegal and counterfeit products seized by different European countries as well as some biopharmaceutical peptides which have not been confiscated yet by the controlling agencies, but are already being used according to the many internet users forums. Additionally, we also show that when applying the same LC gradient, it is also possible to quantify these peptides without the need for

  11. Likelihood Analysis for Mega Pixel Maps

    NASA Technical Reports Server (NTRS)

    Kogut, Alan J.

    1999-01-01

    The derivation of cosmological parameters from astrophysical data sets routinely involves operations counts which scale as O(N(exp 3) where N is the number of data points. Currently planned missions, including MAP and Planck, will generate sky maps with N(sub d) = 10(exp 6) or more pixels. Simple "brute force" analysis, applied to such mega-pixel data, would require years of computing even on the fastest computers. We describe an algorithm which allows estimation of the likelihood function in the direct pixel basis. The algorithm uses a conjugate gradient approach to evaluate X2 and a geometric approximation to evaluate the determinant. Monte Carlo simulations provide a correction to the determinant, yielding an unbiased estimate of the likelihood surface in an arbitrary region surrounding the likelihood peak. The algorithm requires O(N(sub d)(exp 3/2) operations and O(Nd) storage for each likelihood evaluation, and allows for significant parallel computation.

  12. Chaotic map clustering algorithm for EEG analysis

    NASA Astrophysics Data System (ADS)

    Bellotti, R.; De Carlo, F.; Stramaglia, S.

    2004-03-01

    The non-parametric chaotic map clustering algorithm has been applied to the analysis of electroencephalographic signals, in order to recognize the Huntington's disease, one of the most dangerous pathologies of the central nervous system. The performance of the method has been compared with those obtained through parametric algorithms, as K-means and deterministic annealing, and supervised multi-layer perceptron. While supervised neural networks need a training phase, performed by means of data tagged by the genetic test, and the parametric methods require a prior choice of the number of classes to find, the chaotic map clustering gives a natural evidence of the pathological class, without any training or supervision, thus providing a new efficient methodology for the recognition of patterns affected by the Huntington's disease.

  13. Sequence analysis by iterated maps, a review.

    PubMed

    Almeida, Jonas S

    2014-05-01

    Among alignment-free methods, Iterated Maps (IMs) are on a particular extreme: they are also scale free (order free). The use of IMs for sequence analysis is also distinct from other alignment-free methodologies in being rooted in statistical mechanics instead of computational linguistics. Both of these roots go back over two decades to the use of fractal geometry in the characterization of phase-space representations. The time series analysis origin of the field is betrayed by the title of the manuscript that started this alignment-free subdomain in 1990, 'Chaos Game Representation'. The clash between the analysis of sequences as continuous series and the better established use of Markovian approaches to discrete series was almost immediate, with a defining critique published in same journal 2 years later. The rest of that decade would go by before the scale-free nature of the IM space was uncovered. The ensuing decade saw this scalability generalized for non-genomic alphabets as well as an interest in its use for graphic representation of biological sequences. Finally, in the past couple of years, in step with the emergence of BigData and MapReduce as a new computational paradigm, there is a surprising third act in the IM story. Multiple reports have described gains in computational efficiency of multiple orders of magnitude over more conventional sequence analysis methodologies. The stage appears to be now set for a recasting of IMs with a central role in processing nextgen sequencing results. PMID:24162172

  14. Antisera preparation and epitope mapping of a recombinant protein comprising three peptide fragments of the cystic fibrosis transmembrane conductance regulator.

    PubMed

    Li, Kun; Tang, Haiping; Xu, Wanxiang; Chen, Aijun; Shi, Qixian; Sun, Zhida; Wang, Liyan; Ni, Ya

    2015-10-01

    Antibodies targeting a single epitope of the cystic fibrosis transmembrane conductance regulator (CFTR) have been reported to influence the validity of immunological analyses; however, autoimmune mechanisms associated with CFTR epitopes are not well understood. In this study, antiserum raised against a multi-epitope recombinant protein composed of three peptide fragments of CFTR (r-CFTR-3P) was prepared and B cell epitope mapping of the protein was carried out using biosynthetic peptides. The r-CFTR-3P gene was cloned into the pSY621 expression plasmid and the protein was expressed in the BL21 strain of Escherichia coli. The rabbit r-CFTR-3P antiserum recognized the native CFTR antigen extracted from human sperm and the GST188 fusion peptides CFTR(25-36), CFTR(103-117), and CFTR(1387-1480) spanning different regions of CFTR. Four novel r-CFTR-3P B cell epitopes were identified: (29)RQRLEL(34), (104)RIIASY(109), (111)PDN(113), and (1447)VKLF(1450) of CFTR. Other proteins from various species shared sequence homology with the identified epitopes based on NCBI BLAST alignment. This study provides new tools for detecting CFTR protein and insight into the characteristics of minimal B cell epitopes of CFTR and associated immunological mechanisms. PMID:26087025

  15. Combining Ultracentrifugation and Peptide Termini Group-specific Immunoprecipitation for Multiplex Plasma Protein Analysis

    PubMed Central

    Volk, Sonja; Schreiber, Thomas D.; Eisen, David; Wiese, Calvin; Planatscher, Hannes; Pynn, Christopher J.; Stoll, Dieter; Templin, Markus F.; Joos, Thomas O.; Pötz, Oliver

    2012-01-01

    Blood plasma is a valuable source of potential biomarkers. However, its complexity and the huge dynamic concentration range of its constituents complicate its analysis. To tackle this problem, an immunoprecipitation strategy was employed using antibodies directed against short terminal epitope tags (triple X proteomics antibodies), which allow the enrichment of groups of signature peptides derived from trypsin-digested plasma. Isolated signature peptides are subsequently detected using MALDI-TOF/TOF mass spectrometry. Sensitivity of the immunoaffinity approach was, however, compromised by the presence of contaminant peaks derived from the peptides of nontargeted high abundant proteins. A closer analysis of the enrichment strategy revealed nonspecific peptide binding to the solid phase affinity matrix as the major source of the contaminating peptides. We therefore implemented a sucrose density gradient ultracentrifugation separation step into the procedure. This yielded a 99% depletion of contaminating peptides from a sucrose fraction containing 70% of the peptide-antibody complexes and enabled the detection of the previously undetected low abundance protein filamin-A. Assessment of this novel approach using 15 different triple X proteomics antibodies demonstrated a more consistent detection of a greater number of targeted peptides and a significant reduction in the intensity of nonspecific peptides. Ultracentrifugation coupled with immunoaffinity MS approaches presents a powerful tool for multiplexed plasma protein analysis without the requirement for demanding liquid chromatography separation techniques. PMID:22527512

  16. Molecular Evolutionary Analysis of β-Defensin Peptides in Vertebrates

    PubMed Central

    Tu, Jianbo; Li, Diyan; Li, Qingqing; Zhang, Long; Zhu, Qing; Gaur, Uma; Fan, Xiaolan; Xu, Huailiang; Yao, Yongfang; Zhao, Xiaoling; Yang, Mingyao

    2015-01-01

    Vertebrate β-defensins comprise an important family of antimicrobial peptides that protect organisms from a diverse spectrum of bacteria, viruses, fungi, and protozoan parasites. Previous studies have shown a marked variation in the number of β-defensins among species, but the underlying reason is unclear. To address this question, we performed comprehensive computational searches to study the intact β-defensin genes from 29 vertebrates. Phylogenetic analysis of the β-defensin genes in vertebrates identified frequent changes in the number of β-defensin genes and multiple species-specific gene gains and losses that have been occurring throughout the evolution of vertebrates. The number of intact β-defensin genes varied from 1 in the western clawed frog to 20 in cattle, with numerous expansions and contractions of the gene family throughout vertebrates, especially among tetrapods. The β-defensin gene number in a species is relevant to the ever-changing microbial challenges from the environment that they inhabit. Selection pressure analysis shows there exist three amino acid sites under significant positive selection. Protein structural characteristics analysis suggests that structural diversity determines the diverse functions of β-defensins. Our study provides a new perspective on the relationships among vertebrate β-defensin gene repertoires and different survival circumstances, which helps explain how β-defensins have evolved. PMID:26056425

  17. Molecular Evolutionary Analysis of β-Defensin Peptides in Vertebrates.

    PubMed

    Tu, Jianbo; Li, Diyan; Li, Qingqing; Zhang, Long; Zhu, Qing; Gaur, Uma; Fan, Xiaolan; Xu, Huailiang; Yao, Yongfang; Zhao, Xiaoling; Yang, Mingyao

    2015-01-01

    Vertebrate β-defensins comprise an important family of antimicrobial peptides that protect organisms from a diverse spectrum of bacteria, viruses, fungi, and protozoan parasites. Previous studies have shown a marked variation in the number of β-defensins among species, but the underlying reason is unclear. To address this question, we performed comprehensive computational searches to study the intact β-defensin genes from 29 vertebrates. Phylogenetic analysis of the β-defensin genes in vertebrates identified frequent changes in the number of β-defensin genes and multiple species-specific gene gains and losses that have been occurring throughout the evolution of vertebrates. The number of intact β-defensin genes varied from 1 in the western clawed frog to 20 in cattle, with numerous expansions and contractions of the gene family throughout vertebrates, especially among tetrapods. The β-defensin gene number in a species is relevant to the ever-changing microbial challenges from the environment that they inhabit. Selection pressure analysis shows there exist three amino acid sites under significant positive selection. Protein structural characteristics analysis suggests that structural diversity determines the diverse functions of β-defensins. Our study provides a new perspective on the relationships among vertebrate β-defensin gene repertoires and different survival circumstances, which helps explain how β-defensins have evolved. PMID:26056425

  18. [Amino acid composition and peptide maps of udder and serum albumins in lactating and nonlactating cows].

    PubMed

    Lagodiuk, P Z; Klos, Iu S; Charkin, V A; Kisil', I O

    1983-01-01

    Amino acids and peptides of albumin hydrolyzates from the mammary gland and blood serum were studied for lactating and nonlactating (dry, pregnant 1-4.5 and 4.5-9 months) black-and-white cows. Most pronounced difference between the content of certain amino acids of the mammary gland and blood serum albumins are established for lactating cows and least pronounced for nonlactating dry cows. Dactylography detected 55-57 fragments of products resulted from trypsin hydrolysis of the mammary gland and blood serum albumins of the animals under study. Differences are found in the content and mobility of certain peptides. PMID:6829076

  19. Identification of 2D-gel proteins : a comparison of MALDI/TOF peptide mass mapping to {mu} LC-ESI tandem mass spectrometry.

    SciTech Connect

    Lim, H.; Hays, L. G.; Eng, J.; Tollaksen, S. L.; Giometti, C. S.; Holden, J. F.; Adams, M. W. W.; Reich, C. I.; Olsen, G. J.; Yates, J. R.; Biosciences Division; The Scripps Research Inst.; Univ. of Georgia; Univ. of Illinois

    2003-09-01

    A comparative analysis of protein identification for a total of 162 protein spots separated by two-dimensional gel electrophoresis from two fully sequenced archaea, Methanococcus jannaschii and Pyrococcus furiosus, using MALDI-TOF peptide mass mapping (PMM) and mu LC-MS/MS is presented. 100% of the gel spots analyzed were successfully matched to the predicted proteins in the two corresponding open reading frame databases by mu LC-MS/MS while 97% of them were identified by MALDI-TOF PMM. The high success rate from the PMM resulted from sample desalting/concentrating with ZipTip(C18) and optimization of several PMM search parameters including a 25 ppm average mass tolerance and the application of two different protein molecular weight search windows. By using this strategy, low-molecular weight (<23 kDa) proteins could be identified unambiguously with less than 5 peptide matches. Nine percent of spots were identified as containing multiple proteins. By using mu LC-MS/MS, 50% of the spots analyzed were identified as containing multiple proteins. mu LC-MS/MS demonstrated better protein sequence coverage than MALDI-TOF PMM over the entire mass range of proteins identified. MALDI-TOF and PMM produced unique peptide molecular weight matches that were not identified by mu LC-MS/MS. By incorporating amino acid sequence modifications into database searches, combined sequence coverage obtained from these two complimentary ionization methods exceeded 50% for approximately 70% of the 162 spots analyzed. This improved sequence coverage in combination with enzymatic digestions of different specificity is proposed as a method for analysis of post-translational modification from 2D-gel separated proteins.

  20. Magnetic properties and energy-mapping analysis.

    PubMed

    Xiang, Hongjun; Lee, Changhoon; Koo, Hyun-Joo; Gong, Xingao; Whangbo, Myung-Hwan

    2013-01-28

    The magnetic energy levels of a given magnetic solid are closely packed in energy because the interactions between magnetic ions are weak. Thus, in describing its magnetic properties, one needs to generate its magnetic energy spectrum by employing an appropriate spin Hamiltonian. In this review article we discuss how to determine and specify a necessary spin Hamiltonian in terms of first principles electronic structure calculations on the basis of energy-mapping analysis and briefly survey important concepts and phenomena that one encounters in reading the current literature on magnetic solids. Our discussion is given on a qualitative level from the perspective of magnetic energy levels and electronic structures. The spin Hamiltonian appropriate for a magnetic system should be based on its spin lattice, i.e., the repeat pattern of its strong magnetic bonds (strong spin exchange paths), which requires one to evaluate its Heisenberg spin exchanges on the basis of energy-mapping analysis. Other weaker energy terms such as Dzyaloshinskii-Moriya (DM) spin exchange and magnetocrystalline anisotropy energies, which a spin Hamiltonian must include in certain cases, can also be evaluated by performing energy-mapping analysis. We show that the spin orientation of a transition-metal magnetic ion can be easily explained by considering its split d-block levels as unperturbed states with the spin-orbit coupling (SOC) as perturbation, that the DM exchange between adjacent spin sites can become comparable in strength to the Heisenberg spin exchange when the two spin sites are not chemically equivalent, and that the DM interaction between rare-earth and transition-metal cations is governed largely by the magnetic orbitals of the rare-earth cation. PMID:23128376

  1. Two dimensional mass mapping as a general method of data representation in comprehensive analysis of complex molecular mixtures.

    PubMed

    Artemenko, Konstantin A; Zubarev, Alexander R; Samgina, Tatiana Yu; Lebedev, Albert T; Savitski, Mikhail M; Zubarev, Roman A

    2009-05-15

    A recent proteomics-grade (95%+ sequence reliability) high-throughput de novo sequencing method utilizes the benefits of high resolution, high mass accuracy, and the use of two complementary fragmentation techniques collision-activated dissociation (CAD) and electron capture dissociation (ECD). With this high-fidelity sequencing approach, hundreds of peptides can be sequenced de novo in a single LC-MS/MS experiment. The high productivity of the new analysis technique has revealed a new bottleneck which occurs in data representation. Here we suggest a new method of data analysis and visualization that presents a comprehensive picture of the peptide content including relative abundances and grouping into families. The 2D mass mapping consists of putting the molecular masses onto a two-dimensional bubble plot, with the relative monoisotopic mass defect and isotopic shift being the axes and with the bubble area proportional to the peptide abundance. Peptides belonging to the same family form a compact group on such a plot, so that the family identity can in many cases be determined from the molecular mass alone. The performance of the method is demonstrated on the high-throughput analysis of skin secretion from three frogs, Rana ridibunda, Rana arvalis, and Rana temporaria. Two dimensional mass maps simplify the task of global comparison between the species and make obvious the similarities and differences in the peptide contents that are obscure in traditional data presentation methods. Even biological activity of the peptide can sometimes be inferred from its position on the plot. Two dimensional mass mapping is a general method applicable to any complex mixture, peptide and nonpeptide alike. PMID:19382811

  2. Peptide Arrays for Kinome Analysis of Livestock Species

    PubMed Central

    Daigle, Joanna; Van Wyk, Brenden; Trost, Brett; Scruten, Erin; Arsenault, Ryan; Kusalik, Anthony; Griebel, Philip John; Napper, Scott

    2014-01-01

    Reversible protein phosphorylation is a central mechanism for both the transfer of intracellular information and the initiation of cellular responses. Within human medicine, considerable emphasis is placed on understanding and controlling the enzymes (kinases) that are responsible for catalyzing these modifications. This is evident in the prominent use of kinase inhibitors as drugs as well as the trend to understand complex biology and identify biomarkers via characterizations of global kinase (kinome) activity. Despite the demonstrated value of focusing on kinome activity, the application of this perspective to livestock has been restricted by the absence of appropriate research tools. In this review, we discuss the development of software platforms that facilitate the development and application of species-specific peptide arrays for kinome analysis of livestock. Examples of the application of kinomic approaches to a number of priority species (cattle, pigs, and chickens) in a number of biological contexts (infections, biomarker discovery, and food quality) are presented as are emerging trends for kinome analysis of livestock. PMID:26664912

  3. Peptide Arrays for Kinome Analysis of Livestock Species.

    PubMed

    Daigle, Joanna; Van Wyk, Brenden; Trost, Brett; Scruten, Erin; Arsenault, Ryan; Kusalik, Anthony; Griebel, Philip John; Napper, Scott

    2014-01-01

    Reversible protein phosphorylation is a central mechanism for both the transfer of intracellular information and the initiation of cellular responses. Within human medicine, considerable emphasis is placed on understanding and controlling the enzymes (kinases) that are responsible for catalyzing these modifications. This is evident in the prominent use of kinase inhibitors as drugs as well as the trend to understand complex biology and identify biomarkers via characterizations of global kinase (kinome) activity. Despite the demonstrated value of focusing on kinome activity, the application of this perspective to livestock has been restricted by the absence of appropriate research tools. In this review, we discuss the development of software platforms that facilitate the development and application of species-specific peptide arrays for kinome analysis of livestock. Examples of the application of kinomic approaches to a number of priority species (cattle, pigs, and chickens) in a number of biological contexts (infections, biomarker discovery, and food quality) are presented as are emerging trends for kinome analysis of livestock. PMID:26664912

  4. Parametric Response Mapping of Apparent Diffusion Coefficient (ADC) as an Imaging Biomarker to Distinguish Pseudoprogression from True Tumor Progression In Peptide-Based Vaccine Therapy for Pediatric Diffuse Instrinsic Pontine Glioma

    PubMed Central

    Ceschin, Rafael; Kurland, Brenda F.; Abberbock, Shira R.; Ellingson, Benjamin M.; Okada, Hideho; Jakacki, Regina I.; Pollack, Ian F.; Panigrahy, Ashok

    2015-01-01

    Background and Purpose Immune response to cancer therapy may result in pseudoprogression, which can only be identified retrospectively and which may disrupt an effective therapy. This study assesses whether serial parametric response mapping (PRM, a voxel-by-voxel method of image analysis also known as functional diffusion mapping) analysis of ADC measurements following peptide-based vaccination may help prospectively distinguish progression from pseudoprogression in pediatric patients with diffuse intrinsic pontine gliomas. Materials and Methods From 2009–2012, 21 children age 4–18 with diffuse intrinsic pontine gliomas were enrolled in a serial peptide-based vaccination protocol following radiotherapy. DWI was acquired before immunotherapy and at six week intervals during vaccine treatment. Pseudoprogression was identified retrospectively based on clinical and radiographic findings, excluding DWI. Parametric response mapping was used to analyze 96 scans, comparing ADC measures at multiple time points (from first vaccine to up to 12 weeks after the vaccine was halted) to pre-vaccine baseline values. Log-transformed fractional increased ADC (fiADC), fractional decreased ADC (fdADC), and parametric response mapping ratio (fiADC/fdADC) were compared between patients with and without pseudoprogression, using generalized estimating equations with inverse weighting by cluster size. Results Median survival was 13.1 months from diagnosis (range 6.4–24.9 months). Four of 21 children (19%) were assessed as experiencing pseudoprogression. Patients with pseudoprogression had higher fitted average log-transformed parametric response mapping ratios (p=0.01) and fiADCs (p=0.0004), compared to patients without pseudoprogression. Conclusion Serial parametric response mapping of ADC, performed at multiple time points of therapy, may distinguish pseudoprogression from true progression in patients with diffuse intrinsic pontine gliomas treated with peptide-based vaccination

  5. A complete mass spectrometric map for the analysis of the yeast proteome and its application to quantitative trait analysis

    PubMed Central

    Picotti, Paola; Clement-Ziza, Mathieu; Lam, Henry; Campbell, David S.; Schmidt, Alexander; Deutsch, Eric W.; Röst, Hannes; Sun, Zhi; Rinner, Oliver; Reiter, Lukas; Shen, Qin; Michaelson, Jacob J.; Frei, Andreas; Alberti, Simon; Kusebauch, Ulrike; Wollscheid, Bernd; Moritz, Robert; Beyer, Andreas; Aebersold, Ruedi

    2013-01-01

    Complete reference maps or datasets, like the genomic map of an organism, are highly beneficial tools for biological and biomedical research. Attempts to generate such reference datasets for a proteome so far failed to reach complete proteome coverage, with saturation apparent at approximately two thirds of the proteomes tested, even for the most thoroughly characterized proteomes. Here, we used a strategy based on high-throughput peptide synthesis and mass spectrometry to generate a close to complete reference map (97% of the genome-predicted proteins) of the S. cerevisiae proteome. We generated two versions of this mass spectrometric map one supporting discovery- (shotgun) and the other hypothesis-driven (targeted) proteomic measurements. The two versions of the map, therefore, constitute a complete set of proteomic assays to support most studies performed with contemporary proteomic technologies. The reference libraries can be browsed via a web-based repository and associated navigation tools. To demonstrate the utility of the reference libraries we applied them to a protein quantitative trait locus (pQTL) analysis, which requires measurement of the same peptides over a large number of samples with high precision. Protein measurements over a set of 78 S. cerevisiae strains revealed a complex relationship between independent genetic loci, impacting on the levels of related proteins. Our results suggest that selective pressure favors the acquisition of sets of polymorphisms that maintain the stoichiometry of protein complexes and pathways. PMID:23334424

  6. Mapping and analysis of Martian landslides

    NASA Astrophysics Data System (ADS)

    Crosta, Giovanni B.; Frattini, Paolo; Valbuzzi, Elena; Russo, Valeria

    2013-04-01

    This work is part of a larger effort aimed to a more quantitative description of landslide phenomena on Mars and the understanding of rock mass properties and landslide mobility with respect to their Earth equivalents. Recently, large satellite imagery datasets have become available and they have been mosaicked in different suitable tools making mapping an easier job than before. Furthermore, the availability of other georeferenced database makes possible and easily feasible some spatially distributed analyses. We prepared a new landslide inventory to acquire information about: landslide size distribution and areal density, controls of geometrical condition along Martian slopes, landslide typology and mechanism, relationship with impact craters distribution, runout, volume estimates, characteristic features. We adopted Google Earth, Google, Inc. as a mapping tool using both visible and CTX images. Landslides have been mapped according to standard geomorphological criteria, by two landslide experts delineating both the landslide scar and accumulation limits, associating each scarp to a deposit. Multiple accumulations have been differentiated where possible to obtain a more sound dataset. We prevalently mapped landslides located along the Martian valleys and Chasma flanks with only minor attention to classical block and slump instabilities typical of crater rim failures. This because we were mainly interested in long runout landslides or complex failures which could allow to define some rock mass characteristics along these slopes, and to study landslide mobility with respect to Earth equivalent phenomena. So long runout landslides have been mapped also when recognized within crater rims. Topographic characteristics have been extracted by means of the available MOLA dataset. The inventory presently consists of 1232 landslides covering a total area of about 180,000 km2. Landslide size ranges from 0.15 km2 to a maximum of 12,000 km2. We examined area

  7. Monolithic capillary columns based on pentaerythritol tetraacrylate for peptide analysis

    NASA Astrophysics Data System (ADS)

    Kucherenko, E. V.; Melnik, D. M.; Korolev, A. A.; Kanateva, A. Yu.; Pirogov, A. V.; Kurganov, A. A.

    2015-09-01

    Monolythic medium-polar capillary columns based on pentaerythritol tetraacrylate were optimized for separation of peptides. The synthesis temperature and time, the fraction of monomer in the initial polymerization mixture, and the nature of alcohol contained in the complex porogen were chosen as optimization parameters. The highest efficiency was attained for columns obtained with 33 and 34% monomer at a polymerization time of 75 min and a temperature of 75°C. The columns with the optimum structure were effective in separation of a model mixture of five peptides. The sensitivity of the method was 200 ng of peptide per column.

  8. Sequence analysis by iterated maps, a review

    PubMed Central

    2014-01-01

    Among alignment-free methods, Iterated Maps (IMs) are on a particular extreme: they are also scale free (order free). The use of IMs for sequence analysis is also distinct from other alignment-free methodologies in being rooted in statistical mechanics instead of computational linguistics. Both of these roots go back over two decades to the use of fractal geometry in the characterization of phase-space representations. The time series analysis origin of the field is betrayed by the title of the manuscript that started this alignment-free subdomain in 1990, ‘Chaos Game Representation’. The clash between the analysis of sequences as continuous series and the better established use of Markovian approaches to discrete series was almost immediate, with a defining critique published in same journal 2 years later. The rest of that decade would go by before the scale-free nature of the IM space was uncovered. The ensuing decade saw this scalability generalized for non-genomic alphabets as well as an interest in its use for graphic representation of biological sequences. Finally, in the past couple of years, in step with the emergence of BigData and MapReduce as a new computational paradigm, there is a surprising third act in the IM story. Multiple reports have described gains in computational efficiency of multiple orders of magnitude over more conventional sequence analysis methodologies. The stage appears to be now set for a recasting of IMs with a central role in processing nextgen sequencing results. PMID:24162172

  9. Low-Energy Collision-Induced Dissociation Fragmentation Analysis of Cysteinyl-Modified Peptides

    SciTech Connect

    Borisov, Oleg V.; Goshe, Michael B. ); Conrads, Thomas P. ); Rakov, Vsevolod S. ); Veenstra, Timothy D. ); Smith, Richard D. )

    2002-05-15

    The development of methods to chemically modify and isolate cysteinyl-residue containing peptides (Cys-peptides) for LC-MS/MS analysis has generated considerable interest in the field of proteomics. Methods using isotope-coded affinity tags (ICAT) and (+)-biotinyl-iodoacetamidyl-3,6-dioxaoctanediamine (iodoacetyl-PEO-biotin) employ similar Cys-modifying reagents that contain a thiolate-specific biotin group to modify and isolate Cys-containing peptides in conjunction with immobilized avidin. For these strategies to be effective on a proteome-wide level, the presence of the ICAT or acetyl-PEO-biotin tag should not interfere with the efficiency of induced dissociation in MS/MS experiments or with the identification of the modified Cys-peptides by automated database searching algorithms. We have compared the collision-induced dissociation (CID) fragmentation patterns of peptides labeled with iodoacetyl-PEO-biotin and the ICAT reagent to those of the unmodified peptides. CID of Cys-peptides modified with either reagent resulted in the formation of ions attributed to the modified Cys-peptides as well as those unique to the labeling reagent. As demonstrated by analyzing acetyl-PEO-biotin labeled peptides from ribonuclease A and the ICAT-labeled proteome of D. radiodurans, the presence of these labeled-specific product ions provides a useful identifier to discern whether a peptide has been modified with the Cys-specific reagent, especially when a number of peptides analyzed using these methods do not contain a modified Cys-residue, and to differentiate identical Cys-peptides labeled with either ICAT-D0 or ICAT-D8.

  10. Development of the affinity materials for phosphorylated proteins/peptides enrichment in phosphoproteomics analysis.

    PubMed

    Wang, Zhi-Gang; Lv, Nan; Bi, Wen-Zhi; Zhang, Ji-Lin; Ni, Jia-Zuan

    2015-04-29

    Reversible protein phosphorylation is a key event in numerous biological processes. Mass spectrometry (MS) is the most powerful analysis tool in modern phosphoproteomics. However, the direct MS analysis of phosphorylated proteins/peptides is still a big challenge because of the low abundance and insufficient ionization of phosphorylated proteins/peptides as well as the suppression effects of nontargets. Enrichment of phosphorylated proteins/peptides by affinity materials from complex biosamples is the most widely used strategy to enhance the MS detection. The demand of efficiently enriching phosphorylated proteins/peptides has spawned diverse affinity materials based on different enrichment principles (e.g., electronic attraction, chelating). In this review, we summarize the recent development of various affinity materials for phosphorylated proteins/peptides enrichment. We will highlight the design and fabrication of these affinity materials, discuss the enrichment mechanisms involved in different affinity materials, and suggest the future challenges and research directions in this field. PMID:25845677

  11. Preparation of a verifiable peptide-protein immunogen: direction-controlled conjugation of a synthetic fragment of the monitor peptide with myoglobin and application for sequence analysis.

    PubMed

    Iwai, K; Fukuoka, S; Fushiki, T; Kido, K; Sengoku, Y; Semba, T

    1988-06-01

    A useful method for preparing a synthetic peptide-carrying protein for specific antibody production was established. The monitor peptide is a trypsin-sensitive cholecystokinin-releasing peptide purified from rat pancreatic juice on the basis of its stimulatory activity toward pancreatic enzyme secretion. The NH2-terminus fragment of the monitor peptide (residues 1-14) was synthesized by a solid phase method. Cysteine at the COOH terminus of the fragment was conjugated with amino groups of myoglobin using a hetero-bifunctional reagent. Sequence analysis of the fragment-myoglobin conjugate indicated that the peptide/myoglobin conjugation ratio was about 1/1 (mol/mol). Antiserum against the conjugate from a rabbit effectively abolished the stimulatory activity of the monitor peptide in the rat small intestine. PMID:3407924

  12. UAV for landslide mapping and deformation analysis

    NASA Astrophysics Data System (ADS)

    Shi, Beiqi; Liu, Chun

    2015-12-01

    Unmanned aerial vehicle (UAV) can be a flexible, cost-effective, and accurate method to monitor landslides with high resolution aerial images. Images acquired on 05 May 2013 and 13 December 2014 of the Xishan landslide, China, have been used to produce a high-resolution ortho-mosaic of the entire landslide and digital elevation model (DEM). The UAV capability for imaging detection and displacements on the landslide surface has been evaluated, and the subsequent image processing approaches for suitably georectifying the data have been assessed. Objects derived from the segmentation of a multispectral image were used as classifying units for landslide object-oriented analysis. Spectral information together with various morphometric characteristics was applied for recognizing landslides from false positives. Digital image correlation technique was evaluated to quantify and map terrain displacements. The magnitude and direction of the displacement vectors derived from correlating two temporal UAV images corresponded to a visual interpretation of landslide change. Therefore, the UAV can demonstrate its capability for producing valuable landslide mapping data and deformation information.

  13. Coupling protein complex analysis to peptide based proteomics.

    PubMed

    Gao, Qiang; Madian, Ashraf G; Liu, Xiuping; Adamec, Jiri; Regnier, Fred E

    2010-12-01

    Proteolysis is a central component of most proteomics methods. Unfortunately much of the information relating to the structural diversity of proteins is lost during digestion. This paper describes a method in which the native proteome of yeast was subjected to preliminary fractionation by size exclusion chromatography (SEC) prior to trypsin digestion of SEC fractions and reversed phase chromatography-mass spectral analysis to identify tryptic peptides thus generated. Through this approach proteins associated with other proteins in high molecular mass complexes were recognized and identified. A focus of this work was on the identification of Hub proteins that associate with multiple interaction partners. A critical component of this strategy is to choose methods and conditions that maximize retention of native structure during the various stages of analysis prior to proteolysis, especially during cell lysis. Maximum survival of protein complexes during lysis was obtained with the French press and bead-beater methods of cell disruption at approximately pH 8 with 200 mM NaCl in the lysis buffer. Structure retention was favored by higher ionic strength, suggesting that hydrophobic effects are important in maintaining the structure of protein complexes. Recovery of protein complexes declined substantially with storage at any temperature, but storage at -20°C was best when low temperature storage was necessary. Slightly lower recovery was obtained with storage at -80°C while lowest recovery was achieved at 4°C. It was concluded that initial fractionation of native proteins in cell lysates by SEC prior to RPC-MS/MS of tryptic digests can be used to recognize and identify proteins in complexes along with their interaction partners in known protein complexes. PMID:21036361

  14. Mapping protein-RNA interactions by RCAP, RNA-cross-linking and peptide fingerprinting.

    PubMed

    Vaughan, Robert C; Kao, C Cheng

    2015-01-01

    RNA nanotechnology often feature protein RNA complexes. The interaction between proteins and large RNAs are difficult to study using traditional structure-based methods like NMR or X-ray crystallography. RCAP, an approach that uses reversible-cross-linking affinity purification method coupled with mass spectrometry, has been developed to map regions within proteins that contact RNA. This chapter details how RCAP is applied to map protein-RNA contacts within virions. PMID:25896007

  15. Signature Peptide-Enabled Metagenomics (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    McMahon, Ben [LANL

    2013-01-25

    Ben McMahon of Los Alamos National Laboratory (LANL) presents "Signature Peptide-Enabled Metagenomics" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  16. Signature Peptide-Enabled Metagenomics (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    SciTech Connect

    McMahon, Ben

    2012-06-01

    Ben McMahon of Los Alamos National Laboratory (LANL) presents "Signature Peptide-Enabled Metagenomics" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  17. Interrelationships of the subgenera of Coryphaenoides (Teleostei: Gadiformes: Macrouridae): synthesis of allozyme, peptide mapping, and DNA sequence data.

    PubMed

    Wilson, Raymond R; Attia, Phoebe

    2003-05-01

    DNA sequences of the 12s rRNA mitochondrial gene from 12 species key to the question of the monophyly of the deep-sea fish genus Coryphaenoides (Macrouridae) were analyzed phylogenetically using maximum parsimony and maximum likelihood. The results were compared with those of three previous studies in which allozyme, peptide mapping, and DNA sequence data were similarly analyzed. The allozyme and DNA sequence data suggested that the largest subgenus (Coryphaenoides), which contained most of the species inhabiting continental slopes between approximately 600 and 2000m depth, is monophyletic. Two of the three subgenera containing the species inhabiting abyssal ocean basins below approximately 2000m together formed a sister group to subgenus Coryphaenoides. The macrourids of the abyssal basins and those of the continental slopes thus appear to have experienced separate radiations from a common ancestor. PMID:12695096

  18. Analysis of protective antigen peptide binding motifs using bacterial display technology

    NASA Astrophysics Data System (ADS)

    Sarkes, Deborah A.; Dorsey, Brandi L.; Stratis-Cullum, Dimitra N.

    2015-05-01

    In today's fast-paced world, a new biological threat could emerge at any time, necessitating a prompt, reliable, inexpensive detection reagent in each case. Combined with magnetic-activated cell sorting (MACS), bacterial display technology makes it possible to isolate selective, high affinity peptide reagents in days to weeks. Utilizing the eCPX display scaffold is also a rapid way to screen potential peptide reagents. Peptide affinity reagents for protective antigen (PA) of the biothreat Bacillus anthracis were previously discovered using bacterial display. Bioinformatics analysis resulted in the consensus sequence WXCFTC. Additionally, we have discovered PA binding peptides with a WW motif, one of which, YGLHPWWKNAPIGQR, can pull down PA from 1% human serum. The strength of these two motifs combined, to obtain a WWCFTC consensus, is assessed here using Fluorescence Activated Cell Sorting (FACS). While monitoring binding to PA, overall expression of the display scaffold was assessed using the YPet Mona expression control tag (YPet), and specificity was assessed by binding to Streptavidin R-Phycoerythrin (SAPE). The importance of high YPet binding is highlighted as many of the peptides in one of the three replicate experiments fell below our 80% binding threshold. We demonstrate that it is preferable to discard this experiment, due to questionable expression of the peptide itself, than to try to normalize for relative expression. The peptides containing the WWCFTC consensus were of higher affinity and greater specificity than the peptides containing the WW consensus alone, validating further investigation to optimize known PA binders.

  19. Coupling in silico and in vitro analysis of peptide-MHC binding: a bioinformatic approach enabling prediction of superbinding peptides and anchorless epitopes.

    PubMed

    Doytchinova, Irini A; Walshe, Valerie A; Jones, Nicola A; Gloster, Simone E; Borrow, Persephone; Flower, Darren R

    2004-06-15

    The ability to define and manipulate the interaction of peptides with MHC molecules has immense immunological utility, with applications in epitope identification, vaccine design, and immunomodulation. However, the methods currently available for prediction of peptide-MHC binding are far from ideal. We recently described the application of a bioinformatic prediction method based on quantitative structure-affinity relationship methods to peptide-MHC binding. In this study we demonstrate the predictivity and utility of this approach. We determined the binding affinities of a set of 90 nonamer peptides for the MHC class I allele HLA-A*0201 using an in-house, FACS-based, MHC stabilization assay, and from these data we derived an additive quantitative structure-affinity relationship model for peptide interaction with the HLA-A*0201 molecule. Using this model we then designed a series of high affinity HLA-A2-binding peptides. Experimental analysis revealed that all these peptides showed high binding affinities to the HLA-A*0201 molecule, significantly higher than the highest previously recorded. In addition, by the use of systematic substitution at principal anchor positions 2 and 9, we showed that high binding peptides are tolerant to a wide range of nonpreferred amino acids. Our results support a model in which the affinity of peptide binding to MHC is determined by the interactions of amino acids at multiple positions with the MHC molecule and may be enhanced by enthalpic cooperativity between these component interactions. PMID:15187128

  20. Chemical cross-linking with thiol-cleavable reagents combined with differential mass spectrometric peptide mapping--a novel approach to assess intermolecular protein contacts.

    PubMed Central

    Bennett, K. L.; Kussmann, M.; Björk, P.; Godzwon, M.; Mikkelsen, M.; Sørensen, P.; Roepstorff, P.

    2000-01-01

    The intermolecular contact regions between monomers of the homodimeric DNA binding protein ParR and the interaction between the glycoproteins CD28 and CD80 were investigated using a strategy that combined chemical cross-linking with differential MALDI-MS analyses. ParR dimers were modified in vitro with the thiol-cleavable cross-linker 3,3'-dithio-bis(succinimidylproprionate) (DTSSP), proteolytically digested with trypsin and analyzed by MALDI-MS peptide mapping. Comparison of the peptide maps obtained from digested cross-linked ParR dimers in the presence and absence of a thiol reagent strongly supported a "head-to-tail" arrangement of the monomers in the dimeric complex. Glycoprotein fusion constructs CD28-IgG and CD80-Fab were cross-linked in vitro by DTSSP, characterized by nonreducing SDS-PAGE, digested in situ with trypsin and analyzed by MALDI-MS peptide mapping (+/- thiol reagent). The data revealed the presence of an intermolecular cross-link between the receptor regions of the glycoprotein constructs, as well as a number of unexpected but nonetheless specific interactions between the fusion domains of CD28-IgG and the receptor domain of CD80-Fab. The strategy of chemical cross-linking combined with differential MALDI-MS peptide mapping (+ thiol reagent) enabled localization of the interface region(s) of the complexes studied and clearly demonstrates the utility of such an approach to obtain structural information on interacting noncovalent complexes. PMID:10975572

  1. High throughput comparative proteome analysis using a quantitative cysteinyl-peptide enrichment technology

    SciTech Connect

    Liu, Tao; Qian, Weijun; Strittmatter, Eric F.; Camp, David G.; Anderson, Gordon A.; Thrall, Brian D.; Smith, Richard D.

    2004-09-15

    A new quantitative cysteinyl-peptide enrichment technology (QCET) was developed to achieve higher efficiency, greater dynamic range, and higher throughput in quantitative proteomics that use stable-isotope labeling techniques combined with high resolution liquid chromatography (LC)-mass spectrometry (MS). This approach involves {sup 18}O labeling of tryptic peptides, high efficiency enrichment of cysteine-containing peptides, and confident protein identification and quantification using the accurate mass and time tag strategy. Proteome profiling of naive and in vitro-differentiated human mammary epithelial cells using QCET resulted in the identification and quantification of 603 proteins in a single LC-Fourier transform ion cyclotron resonance MS analysis. Advantages of this technology include: (1) a simple, highly efficient method for enriching cysteinyl-peptides; (2) a high throughput strategy suitable for extensive proteome analysis; and (3) improved labeling efficiency for better quantitative measurements. This technology enhances both the functional analysis of biological systems and the detection of potential clinical biomarkers.

  2. Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas

    PubMed Central

    King, Nichole L; Deutsch, Eric W; Ranish, Jeffrey A; Nesvizhskii, Alexey I; Eddes, James S; Mallick, Parag; Eng, Jimmy; Desiere, Frank; Flory, Mark; Martin, Daniel B; Kim, Bong; Lee, Hookeun; Raught, Brian; Aebersold, Ruedi

    2006-01-01

    We present the Saccharomyces cerevisiae PeptideAtlas composed from 47 diverse experiments and 4.9 million tandem mass spectra. The observed peptides align to 61% of Saccharomyces Genome Database (SGD) open reading frames (ORFs), 49% of the uncharacterized SGD ORFs, 54% of S. cerevisiae ORFs with a Gene Ontology annotation of 'molecular function unknown', and 76% of ORFs with Gene names. We highlight the use of this resource for data mining, construction of high quality lists for targeted proteomics, validation of proteins, and software development. PMID:17101051

  3. A peptide N-terminal protection strategy for comprehensive glycoproteome analysis using hydrazide chemistry based method

    PubMed Central

    Huang, Junfeng; Qin, Hongqiang; Sun, Zhen; Huang, Guang; Mao, Jiawei; Cheng, Kai; Zhang, Zhang; Wan, Hao; Yao, Yating; Dong, Jing; Zhu, Jun; Wang, Fangjun; Ye, Mingliang; Zou, Hanfa

    2015-01-01

    Enrichment of glycopeptides by hydrazide chemistry (HC) is a popular method for glycoproteomics analysis. However, possible side reactions of peptide backbones during the glycan oxidation in this method have not been comprehensively studied. Here, we developed a proteomics approach to locate such side reactions and found several types of the side reactions that could seriously compromise the performance of glycoproteomics analysis. Particularly, the HC method failed to identify N-terminal Ser/Thr glycopeptides because the oxidation of vicinal amino alcohol on these peptides generates aldehyde groups and after they are covalently coupled to HC beads, these peptides cannot be released by PNGase F for identification. To overcome this drawback, we apply a peptide N-terminal protection strategy in which primary amine groups on peptides are chemically blocked via dimethyl labeling, thus the vicinal amino alcohols on peptide N-termini are eliminated. Our results showed that this strategy successfully prevented the oxidation of peptide N-termini and significantly improved the coverage of glycoproteome. PMID:25959593

  4. AMYLOID-β PEPTIDE BINDS TO MICROTUBULE-ASSOCIATED PROTEIN 1B (MAP1B)

    PubMed Central

    Gevorkian, Goar; Gonzalez-Noriega, Alfonso; Acero, Gonzalo; Ordoñez, Jorge; Michalak, Colette; Munguia, Maria Elena; Govezensky, Tzipe; Cribbs, David H.; Manoutcharian, Karen

    2008-01-01

    Extracellular and intraneuronal formation of amyloid-beta aggregates have been demonstrated to be involved in the pathogenesis of Alzheimer’s disease. However, the precise mechanism of amyloid-beta neurotoxicity is not completely understood. Previous studies suggest that binding of amyloid-beta to a number of targets have deleterious effects on cellular functions. In the present study we have shown for the first time that amyloid-beta 1-42 bound to a peptide comprising the microtubule binding domain of the heavy chain of microtubule-associated protein 1B by the screening of a human brain cDNA library expressed on M13 phage. This interaction may explain, in part, the loss of neuronal cytoskeletal integrity, impairment of microtubule-dependent transport and synaptic dysfunction observed previously in Alzheimer’s disease. PMID:18079022

  5. Amyloid-beta peptide binds to microtubule-associated protein 1B (MAP1B).

    PubMed

    Gevorkian, Goar; Gonzalez-Noriega, Alfonso; Acero, Gonzalo; Ordoñez, Jorge; Michalak, Colette; Munguia, Maria Elena; Govezensky, Tzipe; Cribbs, David H; Manoutcharian, Karen

    2008-05-01

    Extracellular and intraneuronal formation of amyloid-beta aggregates have been demonstrated to be involved in the pathogenesis of Alzheimer's disease. However, the precise mechanism of amyloid-beta neurotoxicity is not completely understood. Previous studies suggest that binding of amyloid-beta to a number of targets have deleterious effects on cellular functions. In the present study we have shown for the first time that amyloid-beta 1-42 bound to a peptide comprising the microtubule binding domain of the heavy chain of microtubule-associated protein 1B by the screening of a human brain cDNA library expressed on M13 phage. This interaction may explain, in part, the loss of neuronal cytoskeletal integrity, impairment of microtubule-dependent transport and synaptic dysfunction observed previously in Alzheimer's disease. PMID:18079022

  6. Gardony Map Drawing Analyzer: Software for quantitative analysis of sketch maps.

    PubMed

    Gardony, Aaron L; Taylor, Holly A; Brunyé, Tad T

    2016-03-01

    Sketch maps are effective tools for assessing spatial memory. However, despite their widespread use in cognitive science research, sketch map analysis techniques remain unstandardized and carry limitations. In the present article, we present the Gardony Map Drawing Analyzer (GMDA), an open-source software package for sketch map analysis. GMDA combines novel and established analysis techniques into a graphical user interface that permits rapid computational sketch map analysis. GMDA calculates GMDA-unique measures based on pairwise comparisons between landmarks, as well as bidimensional regression parameters (Friedman & Kohler, 2003), which together reflect sketch map quality at two levels: configural and individual landmark. The configural measures assess the overall landmark configuration and provide a whole-map analysis. Individual landmark measures, introduced in GMDA, assess individual landmark placement and indicate how individual landmarks contribute to the configural scores. Together, these measures provide a more complete psychometric picture of sketch map analysis, allowing for comparisons between sketch maps and between landmarks. The calculated measures reflect specific and cognitively relevant aspects of interlandmark spatial relationships, including distance and angular representation. GMDA supports complex environments (up to 48 landmarks) and two software modes that capture aspects of maps not addressed by existing techniques, such as landmark size and shape variation and interlandmark containment relationships. We describe the software and its operation and present a formal specification of calculation procedures for its unique measures. We then validate the software by demonstrating the capabilities and reliability of its measures using simulation and experimental data. The most recent version of GMDA is available at www.aarongardony.com/tools/map-drawing-analyzer. PMID:25673320

  7. Peptide motif analysis predicts alphaviruses as triggers for rheumatoid arthritis.

    PubMed

    Hogeboom, Charissa

    2015-12-01

    Rheumatoid arthritis (RA) develops in response to both genetic and environmental factors. The strongest genetic determinant is HLA-DR, where polymorphisms within the P4 and P6 binding pockets confer elevated risk. However, low disease concordance across monozygotic twin pairs underscores the importance of an environmental factor, probably infectious. The goal of this investigation was to predict the microorganism most likely to interact with HLA-DR to trigger RA under the molecular mimicry hypothesis. A set of 185 structural proteins from viruses or intracellular bacteria was scanned for regions of sequence homology with a collagen peptide that binds preferentially to DR4; candidates were then evaluated against a motif required for T cell cross-reactivity. The plausibility of the predicted agent was evaluated by comparison of microbial prevalence patterns to epidemiological characteristics of RA. Peptides from alphavirus capsid proteins provided the closest fit. Variations in the P6 position suggest that the HLA binding preference may vary by species, with Ross River virus, Chikungunya virus, and Mayaro virus peptides binding preferentially to DR4, and peptides from Sindbis/Ockelbo virus showing stronger affinity to DR1. The predicted HLA preference is supported by epidemiological studies of post-infection chronic arthralgia. Parallels between the cytokine profiles of RA and chronic alphavirus infection are discussed. PMID:26476978

  8. Global Proteomics and Pathway Analysis of Pressure-overload Induced Heart Failure and Its Attenuation by Mitochondrial Targeted Peptides

    PubMed Central

    Dai, Dao-Fu; Hsieh, Edward J.; Chen, Tony; Menendez, Lorena G.; Basisty, Nathan B.; Tsai, Lauren; Beyer, Richard P.; Crispin, David A.; Shulman, Nicholas J.; Szeto, Hazel H.; Tian, Rong; MacCoss, Michael J.; Rabinovitch, Peter S.

    2013-01-01

    Background We investigated the protective effects of mitochondrial-targeted antioxidant and protective peptides, SS31 and SS20, on cardiac function, proteomic remodeling and signaling pathways. Methods and Results We applied an improved label-free shotgun proteomics approach to evaluate the global proteomics changes in transverse aortic constriction (TAC) induced heart failure, and the associated signaling pathway changes using Ingenuity Pathway Analysis (IPA). We found 538 proteins significantly changed after TAC, which mapped to 53 pathways. The top pathways were in the categories of actin cytoskeleton, mitochondrial function, intermediate metabolism, glycolysis / gluconeogenesis and citrate cycle. Concomitant treatment with SS31 ameliorated the congestive heart failure phenotypes and mitochondrial damage induced by TAC, in parallel with global attenuation of mitochondrial proteome changes, with an average of 84% protection of mitochondrial and 69% of non-mitochondrial protein changes. This included significant amelioration of All the IPA pathways noted above. SS20 had only modest effects on heart failure and this tracked with only partial attenuation of global proteomics changes; furthermore, while actin cytoskeleton pathways were significantly protected in SS20, mitochondrial and metabolic pathways essentially were not. Conclusions This study elucidates the signaling pathways significantly changed in pressure-overload induced heart failure. The global attenuation of TAC-induced proteomic alterations by the mitochondrial targeted peptide SS-31 suggests that perturbed mitochondrial function may be an upstream signal to many of pathway alterations in TAC and supports the potential clinical application of mitochondrial-targeted peptide drugs for the treatment heart failure. PMID:23935006

  9. Cloning, characterization, and embryonic expression analysis of the Drosophila melanogaster gene encoding insulin/relaxin-like peptide.

    PubMed

    Nasonkin, Igor O; Alikasifoglu, Ayfer; Barrette, Terry; Cheng, Michael M; Thomas, Pamela M; Nikitin, Alexey G

    2002-07-12

    Insulin is one of the key peptide hormones that regulates growth and metabolism in vertebrates. Evolutionary conservation of many elements of the insulin/IGF signaling network makes it possible to study the basic genetic function of this pathway in lower metazoan models such as Drosophila. Here we report the cloning and characterization of the gene for Drosophila insulin/relaxin-like peptide (DIRLP). The predicted protein structure of DIRLP greatly resembles typical insulin structure and contains features that differentiate it from the Drosophila juvenile hormone, another member of the insulin family. The Dirlp gene is represented as a single copy in the Drosophila melanogaster genome (compared to multiple copies for Drosophila juvenile hormone) and shows evolutionary conservation of genetic structure. The gene was mapped to the Drosophila chromosome 3, region 67D2. In situ hybridization of whole-mount Drosophila embryos with Dirlp antisense RNA probe reveals early embryonic mesodermal/ventral furrow expression pattern, consistent with earlier observation of the insulin protein immunoreactivity in Drosophila embryos. The in situ hybridization pattern was found to be identical to that obtained during immunohistochemistry analysis of the Drosophila embryos using various insulin monoclonal and polyclonal antibodies that do not recognize Drosophila juvenile hormone, supporting the idea that Dirlp is a possible Drosophila insulin ortholog. Identification of the gene for DIRLP provides a new approach for study of the regulatory pathway of the insulin family of peptides. PMID:12150949

  10. Assessment of amide I spectroscopic maps for a gas-phase peptide using IR-UV double-resonance spectroscopy and density functional theory calculations

    NASA Astrophysics Data System (ADS)

    Carr, J. K.; Zabuga, A. V.; Roy, S.; Rizzo, T. R.; Skinner, J. L.

    2014-06-01

    The spectroscopy of amide I vibrations has become a powerful tool for exploring protein structure and dynamics. To help with spectral interpretation, it is often useful to perform molecular dynamics (MD) simulations. To connect spectroscopic experiments to simulations in an efficient manner, several researchers have proposed "maps," which relate observables in classical MD simulations to quantum spectroscopic variables. It can be difficult to discern whether errors in the theoretical results (compared to experiment) arise from inaccuracies in the MD trajectories or in the maps themselves. In this work, we evaluate spectroscopic maps independently from MD simulations by comparing experimental and theoretical spectra for a single conformation of the α-helical model peptide Ac-Phe-(Ala)5-Lys-H+ in the gas phase. Conformation-specific experimental spectra are obtained for the unlabeled peptide and for several singly and doubly 13C-labeled variants using infrared-ultraviolet double-resonance spectroscopy, and these spectra are found to be well-modeled by density functional theory (DFT) calculations at the B3LYP/6-31G** level. We then compare DFT results for the deuterated and 13C18O-labeled peptide with those from spectroscopic maps developed and used previously by the Skinner group. We find that the maps are typically accurate to within a few cm-1 for both frequencies and couplings, having larger errors only for the frequencies of terminal amides.

  11. Assessment of amide I spectroscopic maps for a gas-phase peptide using IR-UV double-resonance spectroscopy and density functional theory calculations

    SciTech Connect

    Carr, J. K.; Roy, S.; Skinner, J. L.; Zabuga, A. V.; Rizzo, T. R.

    2014-06-14

    The spectroscopy of amide I vibrations has become a powerful tool for exploring protein structure and dynamics. To help with spectral interpretation, it is often useful to perform molecular dynamics (MD) simulations. To connect spectroscopic experiments to simulations in an efficient manner, several researchers have proposed “maps,” which relate observables in classical MD simulations to quantum spectroscopic variables. It can be difficult to discern whether errors in the theoretical results (compared to experiment) arise from inaccuracies in the MD trajectories or in the maps themselves. In this work, we evaluate spectroscopic maps independently from MD simulations by comparing experimental and theoretical spectra for a single conformation of the α-helical model peptide Ac-Phe-(Ala){sub 5}-Lys-H{sup +} in the gas phase. Conformation-specific experimental spectra are obtained for the unlabeled peptide and for several singly and doubly {sup 13}C-labeled variants using infrared-ultraviolet double-resonance spectroscopy, and these spectra are found to be well-modeled by density functional theory (DFT) calculations at the B3LYP/6-31G** level. We then compare DFT results for the deuterated and {sup 13}C{sup 18}O-labeled peptide with those from spectroscopic maps developed and used previously by the Skinner group. We find that the maps are typically accurate to within a few cm{sup −1} for both frequencies and couplings, having larger errors only for the frequencies of terminal amides.

  12. Assessment of amide I spectroscopic maps for a gas-phase peptide using IR-UV double-resonance spectroscopy and density functional theory calculations

    PubMed Central

    Carr, J. K.; Zabuga, A. V.; Roy, S.; Rizzo, T. R.; Skinner, J. L.

    2014-01-01

    The spectroscopy of amide I vibrations has become a powerful tool for exploring protein structure and dynamics. To help with spectral interpretation, it is often useful to perform molecular dynamics (MD) simulations. To connect spectroscopic experiments to simulations in an efficient manner, several researchers have proposed “maps,” which relate observables in classical MD simulations to quantum spectroscopic variables. It can be difficult to discern whether errors in the theoretical results (compared to experiment) arise from inaccuracies in the MD trajectories or in the maps themselves. In this work, we evaluate spectroscopic maps independently from MD simulations by comparing experimental and theoretical spectra for a single conformation of the α-helical model peptide Ac-Phe-(Ala)5-Lys-H+ in the gas phase. Conformation-specific experimental spectra are obtained for the unlabeled peptide and for several singly and doubly 13C-labeled variants using infrared-ultraviolet double-resonance spectroscopy, and these spectra are found to be well-modeled by density functional theory (DFT) calculations at the B3LYP/6-31G** level. We then compare DFT results for the deuterated and 13C18O-labeled peptide with those from spectroscopic maps developed and used previously by the Skinner group. We find that the maps are typically accurate to within a few cm−1 for both frequencies and couplings, having larger errors only for the frequencies of terminal amides. PMID:24929378

  13. Disulfide structures of highly bridged peptides: a new strategy for analysis.

    PubMed Central

    Gray, W. R.

    1993-01-01

    A new approach is described for analyzing disulfide linkage patterns in peptides containing tightly clustered cystines. Such peptides are very difficult to analyze with traditional strategies, which require that the peptide chain be split between close or adjacent Cys residues. The water-soluble tris-(2-carboxyethyl)-phosphine (TCEP) reduced disulfides at pH 3, and partially reduced peptides were purified by high performance liquid chromatography with minimal thiol-disulfide exchange. Alkylation of free thiols, followed by sequencer analysis, provided explicit assignment of disulfides that had been reduced. Thiol-disulfide exchange occurred during alkylation of some peptides, but correct deductions were still possible. Alkylation competed best with exchange when peptide solution was added with rapid mixing to 2.2 M iodoacetamide. Variants were developed in which up to three alkylating agents were used to label different pairs of thiols, allowing a full assignment in one sequencer analysis. Model peptides used included insulin (three bridges, intra- and interchain disulfides; -Cys.Cys- pair), endothelin and apamin (two disulfides; -Cys.x.Cys- pair), conotoxin GI and isomers (two disulfides; -Cys.Cys- pair), and bacterial enterotoxin (three bridges within 13 residues; two -Cys.Cys- pairs). With insulin, all intermediates in the reduction pathway were identified; with conotoxin GI, analysis was carried out successfully for all three disulfide isomers. In addition to these known structures, the method has been applied successfully to the analysis of several previously unsolved structures of similar complexity. Rates of reduction of disulfide bonds varied widely, but most peptides did not show a strongly preferred route for reduction. PMID:8251945

  14. Mapping of the Signal Peptide-Binding Domain of Escherichia coli SecA Using Förster Resonance Energy Transfer†

    PubMed Central

    Auclair, Sarah M.; Moses, Julia P.; Musial-Siwek, Monika; Kendall, Debra A.; Oliver, Donald B.; Mukerji, Ishita

    2010-01-01

    Identification of the signal peptide-binding domain within SecA ATPase is an important goal for understanding the molecular basis of SecA preprotein recognition as well as elucidating the chemo-mechanical cycle of this nanomotor during protein translocation. In this study, Förster resonance energy transfer methodology was employed to map the location of the SecA signal peptide-binding domain using a collection of functional monocysteine SecA mutants and alkaline phosphatase signal peptides labeled with appropriate donor–acceptor fluorophores. Fluorescence anisotropy measurements yielded an equilibrium binding constant of 1.4 or 10.7 μM for the alkaline phosphatase signal peptide labeled at residue 22 or 2, respectively, with SecA, and a binding stoichiometry of one signal peptide bound per SecA monomer. Binding affinity measurements performed with a monomer-biased mutant indicate that the signal peptide binds equally well to SecA monomer or dimer. Distance measurements determined for 13 SecA mutants show that the SecA signal peptide-binding domain encompasses a portion of the preprotein cross-linking domain but also includes regions of nucleotide-binding domain 1 and particularly the helical scaffold domain. The identified region lies at a multidomain interface within the heart of SecA, surrounded by and potentially responsive to domains important for binding nucleotide, mature portions of the preprotein, and the SecYEG channel. Our FRET-mapped binding domain, in contrast to the domain identified by NMR spectroscopy, includes the two-helix finger that has been shown to interact with the preprotein during translocation and lies at the entrance to the protein-conducting channel in the recently determined SecA–SecYEG structure. PMID:20025247

  15. C-peptide as a Therapy for Kidney Disease: A Systematic Review and Meta-Analysis.

    PubMed

    Shaw, James A; Shetty, Partha; Burns, Kevin D; Fergusson, Dean; Knoll, Greg A

    2015-01-01

    C-peptide has intrinsic biological activity and may be renoprotective. We conducted a systematic review to determine whether C-peptide had a beneficial effect on renal outcomes. MEDLINE, EMBASE, and the Cochrane Central Databases were searched for human and animal studies in which C-peptide was administered and renal endpoints were subsequently measured. We identified 4 human trials involving 74 patients as well as 18 animal studies involving 35 separate experiments with a total of 641 animals. In humans, the renal effects of exogenously delivered C-peptide were only studied in type 1 diabetics with either normal renal function or incipient nephropathy. Pooled analysis showed no difference in GFR (mean difference, -1.36 mL/min/1.73 m2, p = 0.72) in patients receiving C-peptide compared to a control group, but two studies reported a reduction in glomerular hyperfiltration (p<0.05). Reduction in albuminuria was also reported in the C-peptide group (p<0.05). In diabetic rodent models, C-peptide led to a reduction in GFR (mean difference, -0.62 mL/min, p<0.00001) reflecting a partial reduction in glomerular hyperfiltration. C-peptide also reduced proteinuria (mean difference, -186.25 mg/day, p = 0.05), glomerular volume (p<0.00001), and mesangial matrix area (p<0.00001) in diabetic animals without affecting blood pressure or plasma glucose. Most studies were relatively short-term in duration, ranging from 1 hour to 3 months. Human studies of sufficient sample size and duration are needed to determine if the beneficial effects of C-peptide seen in animal models translate into improved long-term clinical outcomes for patients with chronic kidney disease. (PROSPERO CRD42014007472). PMID:25993479

  16. C-peptide as a Therapy for Kidney Disease: A Systematic Review and Meta-Analysis

    PubMed Central

    Shaw, James A.; Shetty, Partha; Burns, Kevin D.; Fergusson, Dean; Knoll, Greg A.

    2015-01-01

    C-peptide has intrinsic biological activity and may be renoprotective. We conducted a systematic review to determine whether C-peptide had a beneficial effect on renal outcomes. MEDLINE, EMBASE, and the Cochrane Central Databases were searched for human and animal studies in which C-peptide was administered and renal endpoints were subsequently measured. We identified 4 human trials involving 74 patients as well as 18 animal studies involving 35 separate experiments with a total of 641 animals. In humans, the renal effects of exogenously delivered C-peptide were only studied in type 1 diabetics with either normal renal function or incipient nephropathy. Pooled analysis showed no difference in GFR (mean difference, -1.36 mL/min/1.73 m2, p = 0.72) in patients receiving C-peptide compared to a control group, but two studies reported a reduction in glomerular hyperfiltration (p<0.05). Reduction in albuminuria was also reported in the C-peptide group (p<0.05). In diabetic rodent models, C-peptide led to a reduction in GFR (mean difference, -0.62 mL/min, p<0.00001) reflecting a partial reduction in glomerular hyperfiltration. C-peptide also reduced proteinuria (mean difference, -186.25 mg/day, p = 0.05), glomerular volume (p<0.00001), and mesangial matrix area (p<0.00001) in diabetic animals without affecting blood pressure or plasma glucose. Most studies were relatively short-term in duration, ranging from 1 hour to 3 months. Human studies of sufficient sample size and duration are needed to determine if the beneficial effects of C-peptide seen in animal models translate into improved long-term clinical outcomes for patients with chronic kidney disease. (PROSPERO CRD42014007472) PMID:25993479

  17. Landform Mapping Using Multiscale Topographic Analysis

    NASA Astrophysics Data System (ADS)

    Bliss, N. B.

    2008-12-01

    Many ecological and agricultural processes depend on topographic relationships. Topography strongly influences microclimate, the types and productivity of plants, biomass, evapotranspiration rates, carbon storage rates, and fire fuel accumulation. These factors in turn influence the water cycle, stream flow, water quality, and soil formation. Most previous topographic analysis methods have focused on the elevation of a given grid cell (pixel) and very localized measures of slope and aspect (e.g., computed from elevation in a 3x3 window). Some measures have moved beyond a strictly local relationship, such as the compound topographic index, which can be used as a soil wetness index. I introduce a new method of multiscale topographic analysis which can be applied to digital elevation model (DEM) data of any resolution. The method calculates slope and curvature (change of slope) of the land not only in relation to adjacent grid cells but also for much larger distances downstream. The algorithm uses a flow direction grid to create a synthetic stream network as a set of connected line segments (a vector dataset). The multiscale measures are stored on a node attribute table, where the nodes are the endpoints of line segments connecting the original DEM grid cells. A pointer is computed for directly accessing data for nodes at selected distances down the stream network. Baseline distances are selected by counting cells down the flow path by each power of two (1, 2, 4, 8, ... cells downstream). Slope and curvature measures are defined for each of these baselines and are queried to distinguish multiscale topographic characteristics. Several applications of these methods have been tested. A floodplain measure identifies areas that are relatively low on the landscape, even as elevation changes while moving from plains into hills or mountains (study area: South Dakota). The landscape may be partitioned to provide zones for ecological analysis, including selection of field

  18. Analysis of thematic map classification error matrices.

    USGS Publications Warehouse

    Rosenfield, G.H.

    1986-01-01

    The classification error matrix expresses the counts of agreement and disagreement between the classified categories and their verification. Thematic mapping experiments compare variables such as multiple photointerpretation or scales of mapping, and produce one or more classification error matrices. This paper presents a tutorial to implement a typical problem of a remotely sensed data experiment for solution by the linear model method.-from Author

  19. Characterization of the Mouse Brain Proteome Using Global Proteomic Analysis Complemented with Cysteinyl-Peptide Enrichment

    SciTech Connect

    Wang, Haixing H.; Qian, Weijun; Chin, Mark H.; Petyuk, Vladislav A.; Barry, Richard C.; Liu, Tao; Gritsenko, Marina A.; Mottaz, Heather M.; Moore, Ronald J.; Camp, David G.; Khan, Arshad H.; Smith, Desmond; Smith, Richard D.

    2006-02-01

    Given the growing interest in applying genomic and proteomic approaches for studying the mammalian brain using mouse models, we hereby present for the first time a comprehensive characterization of the mouse brain proteome. Preparation of the whole brain sample incorporated a highly efficient cysteinyl-peptide enrichment (CPE) technique to complement a global enzymatic digestion method. Both the global and the cysteinyl-enriched peptide samples were analyzed by SCX fractionation coupled with reversed phase LC-MS/MS analysis. A total of 48,328 different peptides were confidently identified (>98% confidence level), covering 7792 non-redundant proteins (~34% of the predicted mouse proteome). 1564 and 1859 proteins were identified exclusively from the cysteinyl-peptide and the global peptide samples, respectively, corresponding to 25% and 31% improvements in proteome coverage compared to analysis of only the global peptide or cysteinyl-peptide samples. The identified proteins provide a broad representation of the mouse proteome with little bias evident due to protein pI, molecular weight, and/or cellular localization. Approximately 26% of the identified proteins with gene ontology (GO) annotations were membrane proteins, with 1447 proteins predicted to have transmembrane domains, and many of the membrane proteins were found to be involved in transport and cell signaling. The MS/MS spectrum count information for the identified proteins was used to provide a measure of relative protein abundances. The mouse brain peptide/protein database generated from this study represents the most comprehensive proteome coverage for the mammalian brain to date, and the basis for future quantitative brain proteomic studies using mouse models.

  20. A Method for Selective Enrichment and Analysis of Nitrotyrosine-Containing Peptides in Complex Proteome Samples

    SciTech Connect

    Zhang, Qibin; Qian, Weijun; Knyushko, Tanya V.; Clauss, Therese RW; Purvine, Samuel O.; Moore, Ronald J.; Sacksteder, Colette A.; Chin, Mark H.; Smith, Desmond J.; Camp, David G.; Bigelow, Diana J.; Smith, Richard D.

    2007-06-01

    Elevated levels of protein tyrosine nitration have been found in various neurodegenerative diseases and aging related pathologies; however, the lack of an efficient enrichment method has prevented the analysis of this important low level protein modification. We have developed an efficient method for specific enrichment of nitrotyrosine containing peptides that permits nitrotyrosine peptides and specific nitration sites to be unambiguously identified with LC-MS/MS. The method is based on the derivatization of nitrotyrosine into free sulfhydryl groups followed by high efficiency enrichment of sulfhydryl-containing peptides with thiopropyl sepharose beads. The derivatization process starts with acetylation with acetic anhydride to block all primary amines, followed by reduction of nitrotyrosine to aminotyrosine, then derivatization of aminotyrosine with N-Succinimidyl S-Acetylthioacetate (SATA), and finally deprotecting of S-acetyl on SATA to form free sulfhydryl groups. This method was evaluated using nitrotyrosine containing peptides, in-vitro nitrated human histone 1.2, and bovine serum albumin (BSA). 91% and 62% of the identified peptides from enriched histone and BSA samples were nitrotyrosine derivatized peptides, respectively, suggesting relative high specificity of the enrichment method. The application of this method to in-vitro nitrated mouse brain homogenate resulted in 35% of identified peptides containing nitrotyrosine (compared to only 5.9% observed from the global analysis of unenriched sample), and a total of 150 unique nitrated peptides covering 102 proteins were identified with a false discovery rate estimated at 3.3% from duplicate LC-MS/MS analyses of a single enriched sample.

  1. Gas-phase Ion Isomer Analysis Reveals the Mechanism of Peptide Sequence Scrambling

    PubMed Central

    Jia, Chenxi; Wu, Zhe; Lietz, Christopher B.; Liang, Zhidan; Cui, Qiang; Li, Lingjun

    2014-01-01

    Peptide sequence scrambling during mass spectrometry-based gas-phase fragmentation analysis causes misidentification of peptides and proteins. Thus, there is a need to develop an efficient approach to probing the gas-phase fragment ion isomers related to sequence scrambling and the underlying fragmentation mechanism, which will facilitate the development of bioinformatics algorithm for proteomics research. Herein, we report on the first use of electron transfer dissociation (ETD)-produced diagnostic fragment ions to probe the components of gas-phase peptide fragment ion isomers. In combination with ion mobility spectrometry (IMS) and formaldehyde labeling, this novel strategy enables qualitative and quantitative analysis of b-type fragment ion isomers. ETD fragmentation produced diagnostic fragment ions indicative of the precursor ion isomer components, and subsequent IMS analysis of b ion isomers provided their quantitative and structural information. The isomer components of three representative b ions (b9, b10, and b33 from three different peptides) were accurately profiled by this method. IMS analysis of the b9 ion isomers exhibited dynamic conversion among these structures. Furthermore, molecular dynamics simulation predicted theoretical drift time values which were in good agreement with experimentally measured values. Our results strongly support the mechanism of peptide sequence scrambling via b ion cyclization, and provide the first experimental evidence to support that the conversion from molecular precursor ion to cyclic b ion (M→cb) pathway is less energetically (or kinetically) favored. PMID:24313304

  2. Mapping of neutralizing epitopes on Renibacterium salmoninarum p57 by use of transposon mutagenesis and synthetic peptides.

    PubMed

    Wiens, Gregory D; Owen, Jennifer

    2005-06-01

    Renibacterium salmoninarum is a gram-positive bacterium that causes bacterial kidney disease in salmonid fish. The virulence mechanisms of R. salmoninarum are not well understood. Production of a 57-kDa protein (p57) has been associated with isolate virulence and is a diagnostic marker for R. salmoninarum infection. Biological activities of p57 include binding to eukaryotic cells and immunosuppression. We previously isolated three monoclonal antibodies (4D3, 4C11, and 4H8) that neutralize p57 activity. These monoclonal antibodies (MAbs) bind to the amino-terminal region of p57 between amino acids 32 though 243; however, the precise locations of the neutralizing epitopes were not determined. Here, we use transposon mutagenesis to map the 4D3, 4C11, and 4H8 epitopes. Forty-five transposon mutants were generated and overexpressed in Escherichia coli BL21(DE3). The ability of MAbs 4D3, 4H8, and 4C11 to bind each mutant protein was assessed by immunoblotting. Transposons inserting between amino acids 51 and 112 disrupted the 4H8 epitope. Insertions between residues 78 and 210 disrupted the 4C11 epitope, while insertions between amino acids 158 and 234 disrupted the 4D3 epitope. The three MAbs failed to bind overlapping, 15-mer peptides spanning these regions, suggesting that the epitopes are discontinuous in conformation. We conclude that recognition of secondary structure on the amino terminus of p57 is important for neutralization. The epitope mapping studies suggest directions for improvement of MAb-based immunoassays for detection of R. salmoninarum-infected fish. PMID:15932983

  3. Mapping of Neutralizing Epitopes on Renibacterium salmoninarum p57 by Use of Transposon Mutagenesis and Synthetic Peptides

    PubMed Central

    Wiens, Gregory D.; Owen, Jennifer

    2005-01-01

    Renibacterium salmoninarum is a gram-positive bacterium that causes bacterial kidney disease in salmonid fish. The virulence mechanisms of R. salmoninarum are not well understood. Production of a 57-kDa protein (p57) has been associated with isolate virulence and is a diagnostic marker for R. salmoninarum infection. Biological activities of p57 include binding to eukaryotic cells and immunosuppression. We previously isolated three monoclonal antibodies (4D3, 4C11, and 4H8) that neutralize p57 activity. These monoclonal antibodies (MAbs) bind to the amino-terminal region of p57 between amino acids 32 though 243; however, the precise locations of the neutralizing epitopes were not determined. Here, we use transposon mutagenesis to map the 4D3, 4C11, and 4H8 epitopes. Forty-five transposon mutants were generated and overexpressed in Escherichia coli BL21(DE3). The ability of MAbs 4D3, 4H8, and 4C11 to bind each mutant protein was assessed by immunoblotting. Transposons inserting between amino acids 51 and 112 disrupted the 4H8 epitope. Insertions between residues 78 and 210 disrupted the 4C11 epitope, while insertions between amino acids 158 and 234 disrupted the 4D3 epitope. The three MAbs failed to bind overlapping, 15-mer peptides spanning these regions, suggesting that the epitopes are discontinuous in conformation. We conclude that recognition of secondary structure on the amino terminus of p57 is important for neutralization. The epitope mapping studies suggest directions for improvement of MAb-based immunoassays for detection of R. salmoninarum-infected fish. PMID:15932983

  4. High-sensitivity HLA class I peptidome analysis enables a precise definition of peptide motifs and the identification of peptides from cell lines and patients' sera.

    PubMed

    Ritz, Danilo; Gloger, Andreas; Weide, Benjamin; Garbe, Claus; Neri, Dario; Fugmann, Tim

    2016-05-01

    The characterization of peptides bound to human leukocyte antigen (HLA) class I is of fundamental importance for understanding CD8+ T cell-driven immunological processes and for the development of immunomodulatory therapeutic strategies. However, until now, the mass spectrometric analysis of HLA-bound peptides has typically required billions of cells, still resulting in relatively few high-confidence peptide identifications. Capitalizing on the recent developments in mass spectrometry and bioinformatics, we have implemented a methodology for the efficient recovery of acid-eluted HLA peptides after purification with the pan-reactive antibody W6/32 and have identified a total of 27 862 unique peptides with high confidence (1% false discovery rate) from five human cancer cell lines. More than 93% of the identified peptides were eight to 11 amino acids in length and contained signatures that were in excellent agreement with published HLA binding motifs. Furthermore, by purifying soluble HLA class I complexes (sHLA) from sera of melanoma patients, up to 972 high-confidence peptides could be identified, including melanoma-associated antigens already described in the literature. Knowledge of the HLA class I peptidome should facilitate multiplex tetramer technology-based characterization of T cells, and allow the development of patient selection, stratification and immunomodulatory therapeutic strategies. PMID:26992070

  5. Mapping the Interactions between the Alzheimer’s Aβ-Peptide and Human Serum Albumin beyond Domain Resolution

    PubMed Central

    Algamal, Moustafa; Milojevic, Julijana; Jafari, Naeimeh; Zhang, William; Melacini, Giuseppe

    2013-01-01

    Human serum albumin (HSA) is a potent inhibitor of Aβ self-association and this novel, to our knowledge, function of HSA is of potential therapeutic interest for the treatment of Alzheimer’s disease. It is known that HSA interacts with Aβ oligomers through binding sites evenly partitioned across the three albumin domains and with comparable affinities. However, as of this writing, no information is available on the HSA-Aβ interactions beyond domain resolution. Here, we map the HSA-Aβ interactions at subdomain and peptide resolution. We show that each separate subdomain of HSA domain 3 inhibits Aβ self-association. We also show that fatty acids (FAs) compete with Aβ oligomers for binding to domain 3, but the determinant of the HSA/Aβ oligomer interactions are markedly distinct from those of FAs. Although salt bridges with the FA carboxylate determine the FA binding affinities, hydrophobic contacts are pivotal for Aβ oligomer recognition. Specifically, we identified a site of Aβ oligomer recognition that spans the HSA (494–515) region and aligns with the central hydrophobic core of Aβ. The HSA (495–515) segment includes residues affected by FA binding and this segment is prone to self-associate into β-amyloids, suggesting that sites involved in fibrilization may provide a lead to develop inhibitors of Aβ self-association. PMID:24094411

  6. StructMap: Elastic Distance Analysis of Electron Microscopy Maps for Studying Conformational Changes.

    PubMed

    Sanchez Sorzano, Carlos Oscar; Alvarez-Cabrera, Ana Lucia; Kazemi, Mohsen; Carazo, Jose María; Jonić, Slavica

    2016-04-26

    Single-particle electron microscopy (EM) has been shown to be very powerful for studying structures and associated conformational changes of macromolecular complexes. In the context of analyzing conformational changes of complexes, distinct EM density maps obtained by image analysis and three-dimensional (3D) reconstruction are usually analyzed in 3D for interpretation of structural differences. However, graphic visualization of these differences based on a quantitative analysis of elastic transformations (deformations) among density maps has not been done yet due to a lack of appropriate methods. Here, we present an approach that allows such visualization. This approach is based on statistical analysis of distances among elastically aligned pairs of EM maps (one map is deformed to fit the other map), and results in visualizing EM maps as points in a lower-dimensional distance space. The distances among points in the new space can be analyzed in terms of clusters or trajectories of points related to potential conformational changes. The results of the method are shown with synthetic and experimental EM maps at different resolutions. PMID:27119636

  7. De Novo Transcriptome Analysis and Detection of Antimicrobial Peptides of the American Cockroach Periplaneta americana (Linnaeus).

    PubMed

    Kim, In-Woo; Lee, Joon Ha; Subramaniyam, Sathiyamoorthy; Yun, Eun-Young; Kim, Iksoo; Park, Junhyung; Hwang, Jae Sam

    2016-01-01

    Cockroaches are surrogate hosts for microbes that cause many human diseases. In spite of their generally destructive nature, cockroaches have recently been found to harbor potentially beneficial and medically useful substances such as drugs and allergens. However, genomic information for the American cockroach (Periplaneta americana) is currently unavailable; therefore, transcriptome and gene expression profiling is needed as an important resource to better understand the fundamental biological mechanisms of this species, which would be particularly useful for the selection of novel antimicrobial peptides. Thus, we performed de novo transcriptome analysis of P. americana that were or were not immunized with Escherichia coli. Using an Illumina HiSeq sequencer, we generated a total of 9.5 Gb of sequences, which were assembled into 85,984 contigs and functionally annotated using Basic Local Alignment Search Tool (BLAST), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) database terms. Finally, using an in silico antimicrobial peptide prediction method, 86 antimicrobial peptide candidates were predicted from the transcriptome, and 21 of these peptides were experimentally validated for their antimicrobial activity against yeast and gram positive and -negative bacteria by a radial diffusion assay. Notably, 11 peptides showed strong antimicrobial activities against these organisms and displayed little or no cytotoxic effects in the hemolysis and cell viability assay. This work provides prerequisite baseline data for the identification and development of novel antimicrobial peptides, which is expected to provide a better understanding of the phenomenon of innate immunity in similar species. PMID:27167617

  8. De Novo Transcriptome Analysis and Detection of Antimicrobial Peptides of the American Cockroach Periplaneta americana (Linnaeus)

    PubMed Central

    Subramaniyam, Sathiyamoorthy; Yun, Eun-Young; Kim, Iksoo; Park, Junhyung; Hwang, Jae Sam

    2016-01-01

    Cockroaches are surrogate hosts for microbes that cause many human diseases. In spite of their generally destructive nature, cockroaches have recently been found to harbor potentially beneficial and medically useful substances such as drugs and allergens. However, genomic information for the American cockroach (Periplaneta americana) is currently unavailable; therefore, transcriptome and gene expression profiling is needed as an important resource to better understand the fundamental biological mechanisms of this species, which would be particularly useful for the selection of novel antimicrobial peptides. Thus, we performed de novo transcriptome analysis of P. americana that were or were not immunized with Escherichia coli. Using an Illumina HiSeq sequencer, we generated a total of 9.5 Gb of sequences, which were assembled into 85,984 contigs and functionally annotated using Basic Local Alignment Search Tool (BLAST), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) database terms. Finally, using an in silico antimicrobial peptide prediction method, 86 antimicrobial peptide candidates were predicted from the transcriptome, and 21 of these peptides were experimentally validated for their antimicrobial activity against yeast and gram positive and -negative bacteria by a radial diffusion assay. Notably, 11 peptides showed strong antimicrobial activities against these organisms and displayed little or no cytotoxic effects in the hemolysis and cell viability assay. This work provides prerequisite baseline data for the identification and development of novel antimicrobial peptides, which is expected to provide a better understanding of the phenomenon of innate immunity in similar species. PMID:27167617

  9. Expression analysis and identification of antimicrobial peptide transcripts from six North American frog species

    USGS Publications Warehouse

    Robertson, Laura S.; Fellers, Gary M.; Marranca, Jamie Marie; Kleeman, Patrick M.

    2013-01-01

    Frogs secrete antimicrobial peptides onto their skin. We describe an assay to preserve and analyze antimicrobial peptide transcripts from field-collected skin secretions that will complement existing methods for peptide analysis. We collected skin secretions from 4 North American species in the field in California and 2 species in the laboratory. Most frogs appeared healthy after release; however, Rana boylii in the Sierra Nevada foothills, but not the Coast Range, showed signs of morbidity and 2 died after handling. The amount of total RNA extracted from skin secretions was higher in R. boylii and R. sierrae compared to R. draytonii, and much higher compared to Pseudacris regilla. Interspecies variation in amount of RNA extracted was not explained by size, but for P. regilla it depended upon collection site and date. RNA extracted from skin secretions from frogs handled with bare hands had poor quality compared to frogs handled with gloves or plastic bags. Thirty-four putative antimicrobial peptide precursor transcripts were identified. This study demonstrates that RNA extracted from skin secretions collected in the field is of high quality suitable for use in sequencing or quantitative PCR (qPCR). However, some species do not secrete profusely, resulting in very little extracted RNA. The ability to measure transcript abundance of antimicrobial peptides in field-collected skin secretions complements proteomic analyses and may provide insight into transcriptional mechanisms that could affect peptide abundance.

  10. Structural Mass Spectrometry: Rapid Methods for Separation and Analysis of Peptide Natural Products

    PubMed Central

    Goodwin, Cody R.; Fenn, Larissa S.; Derewacz, Dagmara K.; Bachmann, Brian O.; McLean, John A.

    2012-01-01

    A significant challenge in natural product discovery is the initial discrimination of discrete secondary metabolites alongside functionally similar primary metabolic cellular components within complex biological samples. A property that has yet to be fully exploited for natural product identification and characterization is the gas phase collision cross section, or, more generally, the mobility-mass correlation. Peptide natural products possess many of the properties that distinguish natural products as they are frequently characterized by a high degree of intramolecular bonding, and possess extended and compact conformations among other structural modifications. This report describes a rapid structural mass spectrometry technique based on ion mobility-mass spectrometry for the comparison of peptide natural products to their primary metabolic congeners using mobility-mass correlation. This property is empirically determined using ion mobility-mass spectrometry, applied to the analysis of linear versus modified peptides, and used to discriminate peptide natural products in a crude microbial extract. Complementary computational approaches are utilized to understand the structural basis for the separation of primary metabolism derived linear peptides from secondary metabolite cyclic and modified cyclic species. These findings provide a platform for enhancing the identification of secondary metabolic peptides with distinct mobility-mass ratios within complex biological samples. PMID:22216918

  11. A Peptide-Based Method for 13C Metabolic Flux Analysis in Microbial Communities

    PubMed Central

    Ghosh, Amit; Nilmeier, Jerome; Weaver, Daniel; Adams, Paul D.; Keasling, Jay D.; Mukhopadhyay, Aindrila; Petzold, Christopher J.; Martín, Héctor García

    2014-01-01

    The study of intracellular metabolic fluxes and inter-species metabolite exchange for microbial communities is of crucial importance to understand and predict their behaviour. The most authoritative method of measuring intracellular fluxes, 13C Metabolic Flux Analysis (13C MFA), uses the labeling pattern obtained from metabolites (typically amino acids) during 13C labeling experiments to derive intracellular fluxes. However, these metabolite labeling patterns cannot easily be obtained for each of the members of the community. Here we propose a new type of 13C MFA that infers fluxes based on peptide labeling, instead of amino acid labeling. The advantage of this method resides in the fact that the peptide sequence can be used to identify the microbial species it originates from and, simultaneously, the peptide labeling can be used to infer intracellular metabolic fluxes. Peptide identity and labeling patterns can be obtained in a high-throughput manner from modern proteomics techniques. We show that, using this method, it is theoretically possible to recover intracellular metabolic fluxes in the same way as through the standard amino acid based 13C MFA, and quantify the amount of information lost as a consequence of using peptides instead of amino acids. We show that by using a relatively small number of peptides we can counter this information loss. We computationally tested this method with a well-characterized simple microbial community consisting of two species. PMID:25188426

  12. Short communication: peptide profiling in cheeses packed using different technologies.

    PubMed

    Sánchez-Rivera, Laura; Recio, Isidra; Ramos, Mercedes; Gómez-Ruiz, José Ángel

    2013-06-01

    Peptides released during the shelf life of cheeses packaged using 2 different technologies, vacuum packaging (VP) and modified-atmosphere packaging (MAP), were identified by on-line reverse phase-HPLC-tandem mass spectrometry. A total of 22 peptides from the N-terminal domain of αS1-casein (CN) and 26 from β-CN were identified, the latter more evenly distributed over the whole sequence. Peptides were monitored during the shelf life of these cheeses when stored at 4°C, revealing that the peptide profile changed significantly with the storage time. Qualitative differences between VP and MAP cheeses were only found for 3 αS1-CN peptides, which were absent in MAP cheeses. Semiquantitative analysis of peptides revealed some differences between cheeses packaged using different technologies. However, evolution of peptides during storage followed a common trend in both types of cheeses. In addition, the presence of certain peptides, which had been previously described because of their potential bioactivity, is illustrated. For instance, some of the identified peptides had been previously reported as antihypertensive peptides, such as peptide αS1-CN (1-9) or β-CN f(201-209). PMID:23548291

  13. Linkage Analysis and QTL Mapping Using SNP Dosage Data in a Tetraploid Potato Mapping Population

    PubMed Central

    Hackett, Christine A.; McLean, Karen; Bryan, Glenn J.

    2013-01-01

    New sequencing and genotyping technologies have enabled researchers to generate high density SNP genotype data for mapping populations. In polyploid species, SNP data usually contain a new type of information, the allele dosage, which is not used by current methodologies for linkage analysis and QTL mapping. Here we extend existing methodology to use dosage data on SNPs in an autotetraploid mapping population. The SNP dosages are inferred from allele intensity ratios using normal mixture models. The steps of the linkage analysis (testing for distorted segregation, clustering SNPs, calculation of recombination fractions and LOD scores, ordering of SNPs and inference of parental phase) are extended to use the dosage information. For QTL analysis, the probability of each possible offspring genotype is inferred at a grid of locations along the chromosome from the ordered parental genotypes and phases and the offspring dosages. A normal mixture model is then used to relate trait values to the offspring genotypes and to identify the most likely locations for QTLs. These methods are applied to analyse a tetraploid potato mapping population of parents and 190 offspring, genotyped using an Infinium 8300 Potato SNP Array. Linkage maps for each of the 12 chromosomes are constructed. The allele intensity ratios are mapped as quantitative traits to check that their position and phase agrees with that of the corresponding SNP. This analysis confirms most SNP positions, and eliminates some problem SNPs to give high-density maps for each chromosome, with between 74 and 152 SNPs mapped and between 100 and 300 further SNPs allocated to approximate bins. Low numbers of double reduction products were detected. Overall 3839 of the 5378 polymorphic SNPs can be assigned putative genetic locations. This methodology can be applied to construct high-density linkage maps in any autotetraploid species, and could also be extended to higher autopolyploids. PMID:23704960

  14. A Graphics System for Pole-Zero Map Analysis.

    ERIC Educational Resources Information Center

    Beyer, William Fred, III

    Computer scientists have developed an interactive, graphical display system for pole-zero map analysis. They designed it for use as an educational tool in teaching introductory courses in automatic control systems. The facilities allow the user to specify a control system and an input function in the form of a pole-zero map and then examine the…

  15. Recursive Frame Analysis: A Practitioner's Tool for Mapping Therapeutic Conversation

    ERIC Educational Resources Information Center

    Keeney, Hillary; Keeney, Bradford; Chenail, Ronald J.

    2012-01-01

    Recursive frame analysis (RFA), both a practical therapeutic tool and an advanced qualitative research method that maps the structure of therapeutic conversation, is introduced with a clinical case vignette. We present and illustrate a means of mapping metaphorical themes that contextualize the performance taking place in the room, recursively…

  16. UNCERTAINTY ANALYSIS OF RUNOFF ESTIMATES FROM A RUNOFF CONTOUR MAP

    EPA Science Inventory

    The US EPA in cooperation with the USGS conducted an analysis to quantify the uncertainty associated with interpolatinq runoff to specific sites using a runoff contour map. e interpolated runoff to 93 gaged watersheds from a runoff contour map using 1) hand interpolation to the w...

  17. Using Mind Maps To Teach Social Problems Analysis.

    ERIC Educational Resources Information Center

    Peterson, Anne R.; Snyder, Paula J.

    This paper identifies five difficulties in teaching the analysis of social problems, and proffers "mind maps," a concept that refers to the ways in which students create a visual representation of their thinking patterns, as a possible solution. In constructing mind maps, especially for a Social Problems course, the following four steps are…

  18. Conformations of rat brain hexokinase: studies with monoclonal antibodies and peptide mapping techniques

    SciTech Connect

    Smith, A.D.; Wilson, J.E.

    1987-05-01

    Brain hexokinase (HK) consists of a single polypeptide chain with M/sub r/ approx. 100,000. Limited proteolysis of native HK with trypsin yields three major fragments, thought to correspond to discrete structural domains, with molecular masses of approximately 10, 50, and 40 kDa, and derived from the N-terminal, central, and C-terminal regions, respectively. Additional tryptic cleavage sites become susceptible in conformations induced by binding of specific ligands. A library of monoclonal antibodies has been developed for use as probes in examining the structure and function of domains present in HK. Epitopes for several of these have been mapped to specific structural regions in HK. Immunoblotting experiments with these antibodies have been useful in defining the location of susceptible proteolytic cleavage sites in various ligand-induced conformations of HK. Effects of ligand binding on epitope recognition have indicated that several of the antibodies interact with epitopes perturbed by ligand-induced conformational changes. Effects of antibody binding on function have also provided a basis for establishing structure-function relationships. For example, several of the monoclonal antibodies inhibit binding of hexokinase to mitochondria and all recognize epitopes located in the 10 kDa N-terminal domain, consistent with other results indicating that this region is critical to the binding function of hexokinase.

  19. Modeling and Analysis of Information Product Maps

    ERIC Educational Resources Information Center

    Heien, Christopher Harris

    2012-01-01

    Information Product Maps are visual diagrams used to represent the inputs, processing, and outputs of data within an Information Manufacturing System. A data unit, drawn as an edge, symbolizes a grouping of raw data as it travels through this system. Processes, drawn as vertices, transform each data unit input into various forms prior to delivery…

  20. Mapping Peptide Hormone–Receptor Interactions Using a Disulfide-Trapping Approach†

    PubMed Central

    Monaghan, Paul; Thomas, Beena E.; Woznica, Iwona; Wittelsberger, Angela; Mierke, Dale F.; Rosenblatt, Michael

    2008-01-01

    Efforts to elucidate the nature of the bimolecular interaction of parathyroid hormone (PTH) with its cognate receptor, the PTH receptor type 1 (PTHR1), have relied heavily on benzoylphenylalanine- (Bpa-) based photoaffinity cross-linking. However, given the flexibility, size, and shape of Bpa, the resolution at the PTH–PTHR1 interface appears to be reaching the limit of this technique. Here we employ a disulfide-trapping approach developed by others primarily for use in screening compound libraries to identify novel ligands. In this method, cysteine substitutions are introduced into a specific site within the ligand and a region in the receptor predicted to interact with each other. Upon ligand binding, if these cysteines are in close proximity, they form a disulfide bond. Since the geometry governing disulfide bond formation is more constrained than Bpa cross-linking, this novel approach can be employed to generate a more refined molecular model of the PTH–PTHR1 complex. Using a PTH analogue containing a cysteine at position 1, we probed 24 sites and identified 4 in PTHR1 to which cross-linking occurred. Importantly, previous photoaffinity cross-linking studies using a PTH analogue with Bpa at position 1 only identified a single interaction site. The new sites identified by the disulfide-trapping procedure were used as constraints in molecular dynamics simulations to generate an updated model of the PTH–PTHR1 complex. Mapping by disulfide trapping extends and complements photoaffinity cross-linking. It is applicable to other peptide–receptor interfaces and should yield insights about yet unknown sites of ligand–receptor interactions, allowing for generation of more refined models. PMID:18459800

  1. Influence of analysis methods on interpretation of hazard maps.

    PubMed

    Koehler, Kirsten A; Peters, Thomas M

    2013-06-01

    Exposure or hazard mapping is becoming increasingly popular among industrial hygienists. Direct-reading instruments used for hazard mapping of data collection are steadily increasing in reliability and portability while decreasing in cost. Exposure measurements made with these instruments generally require no laboratory analysis although hazard mapping can be a time-consuming process. To inform decision making by industrial hygienists and management, it is crucial that the maps generated from mapping data are as accurate and representative as possible. Currently, it is unclear how many sampling locations are necessary to produce a representative hazard map. As such, researchers typically collect as many points as can be sampled in several hours and interpolation methods are used to produce higher resolution maps. We have reanalyzed hazard-mapping data sets from three industrial settings to determine which interpolation methods yield the most accurate results. The goal is to provide practicing industrial hygienists with some practical guidelines to generate accurate hazard maps with 'off-the-shelf' mapping software. Visually verifying the fit of the variogram model is crucial for accurate interpolation. Exponential and spherical variogram models performed better than Gaussian models. It was also necessary to diverge from some of the default interpolation parameters such as the number of bins used for the experimental variogram and whether or not to allow for a nugget effect to achieve reasonable accuracy of the interpolation for some data sets. PMID:23258453

  2. Use of a porous silicon-gold plasmonic nanostructure to enhance serum peptide signals in MALDI-TOF analysis.

    PubMed

    Li, Xiao; Tan, Jie; Yu, Jiekai; Feng, Jiandong; Pan, Aiwu; Zheng, Shu; Wu, Jianmin

    2014-11-01

    Small peptides in serum are potential biomarkers for the diagnosis of cancer and other diseases. The identification of peptide biomarkers in human plasma/serum has become an area of high interest in medical research. However, the direct analysis of peptides in serum samples using mass spectrometry is challenging due to the low concentration of peptides and the high abundance of high-molecular-weight proteins in serum, the latter of which causes severe signal suppression. Herein, we reported that porous semiconductor-noble metal hybrid nanostructures can both eliminate the interference from large proteins in serum samples and significantly enhance the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) yields of peptides captured on the nanostructure. Serum peptide fingerprints with high fidelity can be acquired rapidly, and successful discrimination of colorectal cancer patients based on peptide fingerprints is demonstrated. PMID:25300214

  3. Automated reduction and interpretation of multidimensional mass spectra for analysis of complex peptide mixtures

    NASA Astrophysics Data System (ADS)

    Gambin, Anna; Dutkowski, Janusz; Karczmarski, Jakub; Kluge, Boguslaw; Kowalczyk, Krzysztof; Ostrowski, Jerzy; Poznanski, Jaroslaw; Tiuryn, Jerzy; Bakun, Magda; Dadlez, Michal

    2007-01-01

    Here we develop a fully automated procedure for the analysis of liquid chromatography-mass spectrometry (LC-MS) datasets collected during the analysis of complex peptide mixtures. We present the underlying algorithm and outcomes of several experiments justifying its applicability. The novelty of our approach is to exploit the multidimensional character of the datasets. It is common knowledge that highly complex peptide mixtures can be analyzed by liquid chromatography coupled with mass spectrometry, but we are not aware of any existing automated MS spectra interpretation procedure designed to take into account the multidimensional character of the data. Our work fills this gap by providing an effective algorithm for this task, allowing for automated conversion of raw data to the list of masses of peptides.

  4. Nanopore analysis of the effect of metal ions on the folding of peptides and proteins.

    PubMed

    Lee, Jeremy S

    2014-03-01

    In this minireview, the nanopore analysis of peptides and proteins in the presence of divalent metal ions will be surveyed. In all cases the binding of the metal ions causes the peptide or protein to adopt a more compact conformation which can no longer enter the α-hemolysin pore. In the absence of Zn(II) the 30-amino acid Zn-finger peptide can readily translocate the pore; but upon addition of Zn(II) the peptide folds and only bumping events are observed. Similarly, the octapeptide repeat from the N-terminus of the prion protein binds Cu(II), which prevents it from translocating. The full-length prion protein also undergoes conformational changes upon binding Cu(II), which results in an increase in the proportion of bumping events. Myelin basic protein of 170 residues is intrinsically disordered and, perhaps surprisingly, for a basic protein of this size, can translocate against the electric field based on the observation that the event time increases with increasing voltage. It, too, folds into a more compact conformation upon binding Cu(II) and Zn(II), which prevents translocation. Finally even proteins such as maltose binding protein which does not contain a formal binding site for metal ions undergoes conformational changes in the presence of the metal chelator, EDTA. Thus, contamination of proteins with trace metal ions should be considered when studying proteins and peptides by nanopore analysis. PMID:24370255

  5. Recognition of ZnT8, Proinsulin, and Homologous MAP Peptides in Sardinian Children at Risk of T1D Precedes Detection of Classical Islet Antibodies

    PubMed Central

    Niegowska, Magdalena; Paccagnini, Daniela; Mannu, Carla; Targhetta, Clara; Songini, Marco; Sechi, Leonardo A.

    2016-01-01

    As numerous studies put in evidence the increasing incidence of type 1 diabetes (T1D) in children, an early diagnosis is of great importance to define correct treatment and diet. Currently, the identification of classical islet autoantibodies is the primary biomarker for diagnosis in subjects at risk, especially in pediatric patients. Recent studies suggest that detection of antibodies against ZnT8 protein in preclinical phase can predict the development of T1D. We previously demonstrated a significant association of Mycobacterium avium subspecies paratuberculosis (MAP) with T1D in adult Sardinian patients. To enforce this finding, we investigated the presence of antibodies against ZnT8 and proinsulin (PI) with respective homologous epitopes: MAP3865c133–141/ZnT8186–194, MAP3865c125–133/ZnT8178–186, MAP2404c70–85/PI46–61, and MAP1,4αgbp157–173/PI64–80, in 23 children at risk for T1D, formerly involved in the TRIGR study, and 22 healthy controls (HCs). Positivity to anti-MAP and homologous human peptides was detected in 48% of at-risk subjects compared to 5,85% HCs, preceding appearance of islet autoantibodies. Being MAP easily transmitted to humans with infected cow's milk and detected in retail infant formulas, MAP epitopes could be present in extensively hydrolyzed formula and act as antigens stimulating β-cell autoimmunity. PMID:26824044

  6. Mapping Rise Time Information with Down-Shift Analysis

    SciTech Connect

    Tunnell, T. W., Machorro, E. A., Diaz, A. B.

    2011-11-01

    These viewgraphs summarize the application of recent developments in digital down-shift (DDS) analysis of up converted PDV data to map out how well the PDV diagnostic would capture rise time information (mid point and rise time) in short rise time (<1 ns) shock events. The mapping supports a PDV vs VISAR challenge. The analysis concepts are new (~September FY 2011), simple, and run quickly, which makes them good tools to map out (with ~1 million Monte Carlo simulations) how well PDV captures rise time information as function of baseline velocity, rise time, velocity jump, and signal-to-noise ratios.

  7. Microfluidic enzymatic-reactors for peptide mapping: strategy, characterization, and performance.

    PubMed

    Wu, Huiling; Zhai, Jianjun; Tian, Yuping; Lu, Haojie; Wang, Xiaoyan; Jia, Weitao; Liu, Baohong; Yang, Pengyuang; Xu, Yunmin; Wang, Honghai

    2004-12-01

    The design and characterization of two kinds of poly(dimethylsiloxane)(PDMS) microfluidic enzymatic-reactors along with their analytical utility coupled to MALDI TOF and ESI MS were reported. Microfluidic devices integrated with microchannel and stainless steel tubing (SST) was fabricated using a PDMS casting technique, and was used for the preparation of the enzymatic-reactor. The chemical modification was performed by introducing carboxyl groups to PDMS surface based on ultraviolet graft polymerization of acrylic acid. The covalent and physical immobilization of trypsin was carried out with the use of the activation reagents 1-ethyl-3-(3-dimethyl aminopropyl)carbodiimide(EDC)/N-hydroxysuccinimide (NHS) and a coupling reagent poly(diallyldimethylammonium chloride)(PDDA), respectively. The properties and success of processes of trypsin immobilization were investigated by measuring contact angle, infrared absorption by attenuated total reflection spectra, AFM imaging and electropherograms. An innovative feature of the microfluidic enzymatic-reactors is the feasibility of performing on-line protein analysis by embedded SST electrode and replaceable tip. The lab-made devices provide an excellent extent of digestion of several model proteins even at the fast flow rate of 3.5 microL min(-1) for the EDC/NHS-made device and 0.8 microL min(-1) for the PDDA-made device, which afford very short residence times of 5 s and 20 s, respectively. In addition, the lab-made devices are less susceptive to memory effect and can be used for at least 50 runs in one week without noticeable loss of activity. Moreover, the degraded PDDA-made device can be regenerated by simple treatment of a HCl solution. These features are the most required for microfluidic devices used for protein analysis. PMID:15570370

  8. Unique diversity of the venom peptides from the scorpion Androctonus bicolor revealed by transcriptomic and proteomic analysis.

    PubMed

    Zhang, Lei; Shi, Wanxia; Zeng, Xian-Chun; Ge, Feng; Yang, Mingkun; Nie, Yao; Bao, Aorigele; Wu, Shifen; E, Guoji

    2015-10-14

    Androctonus bicolor is one of the most poisonous scorpion species in the world. However, little has been known about the venom composition of the scorpion. To better understand the molecular diversity and medical significance of the venom from the scorpion, we systematically analyzed the venom components by combining transcriptomic and proteomic surveys. Random sequencing of 1000 clones from a cDNA library prepared from the venom glands of the scorpion revealed that 70% of the total transcripts code for venom peptide precursors. Our efforts led to a discovery of 103 novel putative venom peptides. These peptides include NaTx-like, KTx-like and CaTx-like peptides, putative antimicrobial peptides, defensin-like peptides, BPP-like peptides, BmKa2-like peptides, Kunitz-type toxins and some new-type venom peptides without disulfide bridges, as well as many new-type venom peptides that are cross-linked with one, two, three, five or six disulfide bridges, respectively. We also identified three peptides that are identical to known toxins from scorpions. The venom was also analyzed using a proteomic technique. The presence of a total of 16 different venom peptides was confirmed by LC-MS/MS analysis. The discovery of a wide range of new and new-type venom peptides highlights the unique diversity of the venom peptides from A. bicolor. These data also provide a series of novel templates for the development of therapeutic drugs for treating ion channel-associated diseases and infections caused by antibiotic-resistant pathogens, and offer molecular probes for the exploration of structures and functions of various ion channels. PMID:26254009

  9. Meteorological Data Analysis Using MapReduce

    PubMed Central

    Fang, Wei; Sheng, V. S.; Wen, XueZhi; Pan, Wubin

    2014-01-01

    In the atmospheric science, the scale of meteorological data is massive and growing rapidly. K-means is a fast and available cluster algorithm which has been used in many fields. However, for the large-scale meteorological data, the traditional K-means algorithm is not capable enough to satisfy the actual application needs efficiently. This paper proposes an improved MK-means algorithm (MK-means) based on MapReduce according to characteristics of large meteorological datasets. The experimental results show that MK-means has more computing ability and scalability. PMID:24790576

  10. Using Infrared Spectroscopy of Cyanylated Cysteine to Map Membrane Binding Structure and Orientation of the Hybrid Antimicrobial Peptide CM15

    PubMed Central

    Alfieri, Katherine N.; Vienneau, Alice R.; Londergan, Casey H.

    2011-01-01

    The synthetic antimicrobial peptide CM15, a hybrid of N-terminal sequences from cecropin and melittin peptides, has been shown to be extremely potent. Its mechanism of action has been speculated to involve pore formation based on prior site-directed spin labeling studies. This study examines four single-site β-thiocyanatoalanine variants of CM15 in which the artificial amino acid side chain acts as a vibrational reporter of its local environment through the frequency and lineshape of the unique CN stretching band in the infrared spectrum. Circular dichroism experiments indicate that the placements of the artificial side chain have only small perturbative effects on the membrane-bound secondary structure of the CM15 peptide. All variant peptides were placed in buffer solution, in contact with dodecylphosphatidylcholine micelles, and in contact with vesicles formed from E. coli polar lipid extract. At each site, the CN stretching band reports a different behavior. Time-dependent attenuated total reflectance infrared spectra were also collected for each variant as it was allowed to remodel the E. coli lipid vesicles. These experiments agree with the previously proposed formation of toroidal pores, in which each peptide finds itself in an increasingly homogeneous and curved local environment without apparent peptide-peptide interactions. This work also demonstrates the excellent sensitivity of the SCN stretching vibration to small changes in peptide-lipid interfacial structure. PMID:22103476

  11. Superposition of an AC field improves the discrimination between peptides in nanopore analysis.

    PubMed

    Jakova, Elisabet; Lee, Jeremy S

    2015-07-21

    In standard nanopore analysis a constant DC voltage is used to electrophoretically drive small molecules and peptides towards a pore. Superposition of an AC voltage at particular frequencies causes molecules to oscillate as they approach the pore which can alter the event parameters, the blockade current (I) and blockade time (T). Four peptides with similar structures were studied. Alpha-helical peptides A10 (FmocDDA10KK), A14, A18 and retro-inverso A10. It was shown that the ratio of translocations to bumping events could be manipulated by a combination of AC voltages and frequencies. In particular, A10 could be studied without interference from retro-inverso A10. Similarly, a large, intrinsically disordered protein of 140 amino acids, α-synuclein, which translocates the pore readily in a DC field could be prevented from doing so by application of an AC field of 200 mV at 100 MHz. PMID:25699656

  12. Chemoselective synthesis and analysis of naturally occurring phosphorylated cysteine peptides.

    PubMed

    Bertran-Vicente, Jordi; Penkert, Martin; Nieto-Garcia, Olaia; Jeckelmann, Jean-Marc; Schmieder, Peter; Krause, Eberhard; Hackenberger, Christian P R

    2016-01-01

    In contrast to protein O-phosphorylation, studying the function of the less frequent N- and S-phosphorylation events have lagged behind because they have chemical features that prevent their manipulation through standard synthetic and analytical methods. Here we report on the development of a chemoselective synthetic method to phosphorylate Cys side-chains in unprotected peptides. This approach makes use of a reaction between nucleophilic phosphites and electrophilic disulfides accessible by standard methods. We achieve the stereochemically defined phosphorylation of a Cys residue and verify the modification using electron-transfer higher-energy dissociation (EThcD) mass spectrometry. To demonstrate the use of the approach in resolving biological questions, we identify an endogenous Cys phosphorylation site in IICB(Glc), which is known to be involved in the carbohydrate uptake from the bacterial phosphotransferase system (PTS). This new chemical and analytical approach finally allows further investigating the functions and significance of Cys phosphorylation in a wide range of crucial cellular processes. PMID:27586301

  13. Peptide Fragmentation and Surface Structural Analysis by Means of ToF-SIMS Using Large Cluster Ion Sources.

    PubMed

    Yokoyama, Yuta; Aoyagi, Satoka; Fujii, Makiko; Matsuo, Jiro; Fletcher, John S; Lockyer, Nicholas P; Vickerman, John C; Passarelli, Melissa K; Havelund, Rasmus; Seah, Martin P

    2016-04-01

    Peptide or protein structural analysis is crucial for the evaluation of biochips and biodevices, therefore an analytical technique with the ability to detect and identify protein and peptide species directly from surfaces with high lateral resolution is required. In this report, the efficacy of ToF-SIMS to analyze and identify proteins directly from surfaces is evaluated. Although the physics governing the SIMS bombardment process precludes the ability for researchers to detect intact protein or larger peptides of greater than a few thousand mass unit directly, it is possible to obtain information on the partial structures of peptides or proteins using low energy per atom argon cluster ion beams. Large cluster ion beams, such as Ar clusters and C60 ion beams, produce spectra similar to those generated by tandem MS. The SIMS bombardment process also produces peptide fragment ions not detected by conventional MS/MS techniques. In order to clarify appropriate measurement conditions for peptide structural analysis, peptide fragmentation dependency on the energy of a primary ion beam and ToF-SIMS specific fragment ions are evaluated. It was found that the energy range approximately 6 ≤ E/n ≤ 10 eV/atom is most effective for peptide analysis based on peptide fragments and [M + H] ions. We also observed the cleaving of side chain moieties at extremely low-energy E/n ≤ 4 eV/atom. PMID:26916620

  14. A quantitative analysis of IRAS maps of molecular clouds

    NASA Technical Reports Server (NTRS)

    Wiseman, Jennifer J.; Adams, Fred C.

    1994-01-01

    We present an analysis of IRAS maps of five molecular clouds: Orion, Ophiuchus, Perseus, Taurus, and Lupus. For the classification and description of these astrophysical maps, we use a newly developed technique which considers all maps of a given type to be elements of a pseudometric space. For each physical characteristic of interest, this formal system assigns a distance function (a pseudometric) to the space of all maps: this procedure allows us to measure quantitatively the difference between any two maps and to order the space of all maps. We thus obtain a quantitative classification scheme for molecular clouds. In this present study we use the IRAS continuum maps at 100 and 60 micrometer(s) to produce column density (or optical depth) maps for the five molecular cloud regions given above. For this sample of clouds, we compute the 'output' functions which measure the distribution of density, the distribution of topological components, the self-gravity, and the filamentary nature of the clouds. The results of this work provide a quantitative description of the structure in these molecular cloud regions. We then order the clouds according to the overall environmental 'complexity' of these star-forming regions. Finally, we compare our results with the observed populations of young stellar objects in these clouds and discuss the possible environmental effects on the star-formation process. Our results are consistent with the recently stated conjecture that more massive stars tend to form in more 'complex' environments.

  15. A quantitative analysis of IRAS maps of molecular clouds

    NASA Astrophysics Data System (ADS)

    Wiseman, Jennifer J.; Adams, Fred C.

    1994-11-01

    We present an analysis of IRAS maps of five molecular clouds: Orion, Ophiuchus, Perseus, Taurus, and Lupus. For the classification and description of these astrophysical maps, we use a newly developed technique which considers all maps of a given type to be elements of a pseudometric space. For each physical characteristic of interest, this formal system assigns a distance function (a pseudometric) to the space of all maps: this procedure allows us to measure quantitatively the difference between any two maps and to order the space of all maps. We thus obtain a quantitative classification scheme for molecular clouds. In this present study we use the IRAS continuum maps at 100 and 60 micrometer(s) to produce column density (or optical depth) maps for the five molecular cloud regions given above. For this sample of clouds, we compute the 'output' functions which measure the distribution of density, the distribution of topological components, the self-gravity, and the filamentary nature of the clouds. The results of this work provide a quantitative description of the structure in these molecular cloud regions. We then order the clouds according to the overall environmental 'complexity' of these star-forming regions. Finally, we compare our results with the observed populations of young stellar objects in these clouds and discuss the possible environmental effects on the star-formation process. Our results are consistent with the recently stated conjecture that more massive stars tend to form in more 'complex' environments.

  16. Diffusion maps and radar data analysis

    NASA Astrophysics Data System (ADS)

    Bhat, Y. S.; Arnold, Gregory

    2007-04-01

    Understanding and organizing data, in particular understanding the key modes of variation in the data, is a first step toward exploiting and evaluating sensor phenomenology. Spectral theory and manifold learning methods have been recently shown to offer sever powerful tools for many parts of the exploitation problem. We will describe the method of diffusion maps and give some examples with radar (backhoe data dome) data. The so-called diffusion coordinates are kernel based dimensionality reduction techniques that can, for example, organize random data and yield explicit insight into the type and relative importance of the data variation. We will provide sufficient background for others to adopt these tools and apply them to other aspects of exploitation and evaluation.

  17. On-Plate Desalting and SALDI-MS Analysis of Peptides with Hydrophobic Silicate Nanofilms on a Gold Substrate

    PubMed Central

    Duan, Jicheng; Wang, Hui; Cheng, Quan

    2010-01-01

    We report the use of silicate nanofilms for on-plate desalting and subsequently direct laser desorption/ionization-mass spectrometric (LDI-MS) analysis of peptides. A hydrophobic octadecyltrichlorosilane (OTS) monolayer is formed on a calcinated nanofilm on a gold substrate to facilitate sample deposition and interaction with the surface that allows effective removal of MS-incompatible contaminants such as salts and surfactants by simple on-plate washing while the peptides are retained on the spot. By eliminating interferences from matrix-related ions and contaminants, sensitivity of MS analysis has been enhanced over ca. 20 times, leading to improved detection of peptides at the low-fmol level. A high recovery rate of the peptides is obtained by using relatively rough nanofilms, which are prepared through a modified layer-by-layer (LbL)-deposition/calcination process. The performance of the films has been investigated with peptide samples in the presence of high salts (NaCl and sodium acetate) and urea. Compared to MALDI analysis with CHCA-matrix, LDI with on-plate desalting offers marked improvement for analysis of peptides due to low background ions and reduction of sample complexity. Additionally, selective capture of the hydrophobic components of a protein can be achieved, providing a highly useful strategy for specific peptide enrichment. LDI with on-plate desalting approach has also been successfully applied to peptide analysis from protein digests. PMID:20964322

  18. Linear Algebraic Method for Non-Linear Map Analysis

    SciTech Connect

    Yu,L.; Nash, B.

    2009-05-04

    We present a newly developed method to analyze some non-linear dynamics problems such as the Henon map using a matrix analysis method from linear algebra. Choosing the Henon map as an example, we analyze the spectral structure, the tune-amplitude dependence, the variation of tune and amplitude during the particle motion, etc., using the method of Jordan decomposition which is widely used in conventional linear algebra.

  19. Mapping the Future, Mapping Education: An Analysis of the 2011 State of the Union Address

    ERIC Educational Resources Information Center

    Collin, Ross

    2012-01-01

    This article presents a discourse analysis of President Barack Obama's 2011 State of the Union Address. Fredric Jameson's concepts of cognitive mapping, cultural revolution, and the unconscious are employed to examine the president's vision of educational and economic transformation. Ultimately, it is argued this vision evokes a world in which…

  20. Molecular Design, Structural Analysis and Antifungal Activity of Derivatives of Peptide CGA-N46.

    PubMed

    Li, Rui-Fang; Lu, Zhi-Fang; Sun, Ya-Nan; Chen, Shi-Hua; Yi, Yan-Jie; Zhang, Hui-Ru; Yang, Shuo-Ye; Yu, Guang-Hai; Huang, Liang; Li, Chao-Nan

    2016-09-01

    Chromogranin A (CGA)-N46, a derived peptide of human chromogranin A, has antifungal activity. To further research the active domain of CGA-N46, a series of derivatives were designed by successively deleting amino acid from both terminus of CGA-N46, and the amino acid sequence of each derivative was analyzed by bioinformatic software. Based on the predicted physicochemical properties of the peptides, including half-life time in mammalian reticulocytes (in vitro), yeast (in vivo) and E. coli (in vivo), instability index, aliphatic index and grand average of hydropathicity (GRAVY), the secondary structure, net charge, the distribution of hydrophobic residues and hydrophilic residues, the final derivatives CGA-N15, CGA-N16, CGA-N12 and CGA-N8 were synthesized by solid-phase peptide synthesis. The results of bioinformatic analysis showed that CGA-N46 and its derivatives were α-helix, neutral or weak positive charge, hydrophilic, and CGA-N12 and CGA-N8 were more stable than the other derivatives. The results of circular dichroism confirmed that CGA-N46 and its derived peptides displayed α-helical structure in an aqueous solution and 30 mM sodium dodecylsulfate, but α-helical contents decreased in hydrophobic lipid vesicles. CGA-N15, CGA-N16, CGA-N12 and CGA-N8 had higher antifungal activities than their mother peptide CGA-N46. Among of the derived peptides, CGA-N12 showed the least hemolytic activity. In conclusion, we have successfully identified the active domain of CGA-N46 with strong antifungal activity and weak hemolytic activity, which provides the possibility to develop a new class of antibiotics. PMID:27165480

  1. Large Improvements in MS/MS Based Peptide Identification Rates using a Hybrid Analysis

    SciTech Connect

    Cannon, William R.; Rawlins, Mitchell M.; Baxter, Douglas J.; Callister, Stephen J.; Lipton, Mary S.; Bryant, Donald A.

    2011-05-06

    We have developed a hybrid method for identifying peptides from global proteomics studies that significantly increases sensitivity and specificity in matching peptides to tandem mass spectra using database searches. The method increased the number of spectra that can be assigned to a peptide in a global proteomics study by 57-147% at an estimated false discovery rate of 5%, with clear room for even greater improvements. The approach combines the general utility of using consensus model spectra typical of database search methods1-3 with the accuracy of the intensity information contained in spectral libraries4-6. This hybrid approach is made possible by recent developments that elucidated the statistical framework common to both data analysis and statistical thermodynamics, resulting in a chemically inspired approach to incorporating fragment intensity information into both database searches and spectral library searches. We applied this approach to proteomics analysis of Synechococcus sp. PCC 7002, a cyanobacterium that is a model organism for studies of photosynthetic carbon fixation and biofuels development. The increased specificity and sensitivity of this approach allowed us to identify many more peptides involved in the processes important for photoautotrophic growth.

  2. Electron capture dissociation mass spectrometric analysis of lysine-phosphorylated peptides

    PubMed Central

    Kowalewska, Karolina; Stefanowicz, Piotr; Ruman, Tomasz; Frączyk, Tomasz; Rode, Wojciech; Szewczuk, Zbigniew

    2010-01-01

    Phosphorylation of proteins is an essential signalling mechanism in eukaryotic and prokaryotic cells. Although N-phosphorylation of basic amino acid is known for its importance in biological systems, it is still poorly explored in terms of products and mechanisms. In the present study, two MS fragmentation methods, ECD (electron-capture dissociation) and CID (collision-induced dissociation), were tested as tools for analysis of N-phosphorylation of three model peptides, RKRSRAE, RKRARKE and PLSRTLSVAAKK. The peptides were phosphorylated by reaction with monopotassium phosphoramidate. The results were confirmed by 1H NMR and 31P NMR studies. The ECD method was found useful for the localization of phosphorylation sites in unstable lysine-phosphorylated peptides. Its main advantage is a significant reduction of the neutral losses related to the phosphoramidate moiety. Moreover, the results indicate that the ECD–MS may be useful for analysis of regioselectivity of the N-phosphorylation reaction. Stabilities of the obtained lysine-phosphorylated peptides under various conditions were also tested. PMID:20144148

  3. Analysis of cardiac fibrillation using phase mapping.

    PubMed

    Clayton, Richard H; Nash, Martyn P

    2015-03-01

    The sequence of myocardial electrical activation during fibrillation is complex and changes with each cycle. Phase analysis represents the electrical activation-recovery process as an angle. Lines of equal phase converge at a phase singularity at the center of rotation of a reentrant wave, and the identification of reentry and tracking of reentrant wavefronts can be automated. We examine the basic ideas behind phase analysis. With the exciting prospect of using phase analysis of atrial electrograms to guide ablation in the human heart, we highlight several recent developments in preprocessing electrograms so that phase can be estimated reliably. PMID:25784022

  4. Data for comparative proteomics analysis of the antitumor effect of CIGB-552 peptide in HT-29 colon adenocarcinoma cells.

    PubMed

    Núñez de Villavicencio-Díaz, Teresa; Ramos Gómez, Yassel; Oliva Argüelles, Brizaida; Fernández Masso, Julio R; Rodríguez-Ulloa, Arielis; Cruz García, Yiliam; Guirola-Cruz, Osmany; Perez-Riverol, Yasset; Javier González, Luis; Tiscornia, Inés; Victoria, Sabina; Bollati-Fogolín, Mariela; Besada Pérez, Vladimir; Guerra Vallespi, Maribel

    2015-09-01

    CIGB-552 is a second generation antitumor peptide that displays potent cytotoxicity in lung and colon cancer cells. The nuclear subproteome of HT-29 colon adenocarcinoma cells treated with CIGB-552 peptide was identified and analyzed [1]. This data article provides supporting evidence for the above analysis. PMID:26306321

  5. An Approach to Conformational Analysis of Peptides and Proteins in Solution Based on a Combination of Nuclear Magnetic Resonance Spectroscopy and Conformational Energy Calculations

    PubMed Central

    Gibbons, W. A.; Némethy, George; Stern, Arnold; Craig, Lyman C.

    1970-01-01

    Simple criteria, based on the combined use of nmr spectral parameters and potential energy maps, are proposed for the conformational analysis of polypeptides and proteins. Experimentally determined coupling constants 3JNC for the N-Cα bond are consistent with the Karplus-Bystrov relationship. It is proposed therefore that 3JNC can be used to distinguish (a) between right-and left-handed α-helices, (b) between α-helical, β-pleated sheet, and randomly coiled forms of peptides. The average 3JNC for the random coil is predicted. The criteria proposed are valid for both L- and D-amino acids. Correlation between the Karplus-Bystrov relationship for 3JNC and the peptide conformational potential energy map limits the possible values of the N-Cα dihedral angle ϕ of each amino acid residue in a polypeptide and protein, and therefore presents a method of conformational analysis in solution superior to the use of either nmr or conformational maps alone. Nmr studies of hydrogen bonding or neighboring-group diamagnetic anisotropy reduce the number of possibilities consistent with the above criteria. A suggestion for evaluating the dihedral angle is presented. These criteria are useful provided the coupling constant is not obscured by line broadening. PMID:5272315

  6. Computational analysis of LDDMM for brain mapping

    PubMed Central

    Ceritoglu, Can; Tang, Xiaoying; Chow, Margaret; Hadjiabadi, Darian; Shah, Damish; Brown, Timothy; Burhanullah, Muhammad H.; Trinh, Huong; Hsu, John T.; Ament, Katarina A.; Crocetti, Deana; Mori, Susumu; Mostofsky, Stewart H.; Yantis, Steven; Miller, Michael I.; Ratnanather, J. Tilak

    2013-01-01

    One goal of computational anatomy (CA) is to develop tools to accurately segment brain structures in healthy and diseased subjects. In this paper, we examine the performance and complexity of such segmentation in the framework of the large deformation diffeomorphic metric mapping (LDDMM) registration method with reference to atlases and parameters. First we report the application of a multi-atlas segmentation approach to define basal ganglia structures in healthy and diseased kids' brains. The segmentation accuracy of the multi-atlas approach is compared with the single atlas LDDMM implementation and two state-of-the-art segmentation algorithms—Freesurfer and FSL—by computing the overlap errors between automatic and manual segmentations of the six basal ganglia nuclei in healthy subjects as well as subjects with diseases including ADHD and Autism. The high accuracy of multi-atlas segmentation is obtained at the cost of increasing the computational complexity because of the calculations necessary between the atlases and a subject. Second, we examine the effect of parameters on total LDDMM computation time and segmentation accuracy for basal ganglia structures. Single atlas LDDMM method is used to automatically segment the structures in a population of 16 subjects using different sets of parameters. The results show that a cascade approach and using fewer time steps can reduce computational complexity as much as five times while maintaining reliable segmentations. PMID:23986653

  7. All-atom molecular dynamics analysis of multi-peptide systems reproduces peptide solubility in line with experimental observations

    PubMed Central

    Kuroda, Yutaka; Suenaga, Atsushi; Sato, Yuji; Kosuda, Satoshi; Taiji, Makoto

    2016-01-01

    In order to investigate the contribution of individual amino acids to protein and peptide solubility, we carried out 100 ns molecular dynamics (MD) simulations of 106 Å3 cubic boxes containing ~3 × 104 water molecules and 27 tetra-peptides regularly positioned at 23 Å from each other and composed of a single amino acid type for all natural amino acids but cysteine and glycine. The calculations were performed using Amber with a standard force field on a special purpose MDGRAPE-3 computer, without introducing any “artificial” hydrophobic interactions. Tetra-peptides composed of I, V, L, M, N, Q, F, W, Y, and H formed large amorphous clusters, and those containing A, P, S, and T formed smaller ones. Tetra-peptides made of D, E, K, and R did not cluster at all. These observations correlated well with experimental solubility tendencies as well as hydrophobicity scales with correlation coefficients of 0.5 to > 0.9. Repulsive Coulomb interactions were dominant in ensuring high solubility, whereas both Coulomb and van der Waals (vdW) energies contributed to the aggregations of low solubility amino acids. Overall, this very first all-atom molecular dynamics simulation of a multi-peptide system appears to reproduce the basic properties of peptide solubility, essentially in line with experimental observations. PMID:26817663

  8. On-column digestion of protein for peptide mapping by capillary zone electrophoresis with laser-induced native fluorescence detection

    SciTech Connect

    Chang, H.T.; Yeung, E.S. Iowa State Univ., Ames, IA )

    1993-10-15

    We have developed a novel technique to separate and detect peptide fragments which are digested on the same column. In this procedure, pepsin is used to digest low femtomole amounts of [beta]-lactoglobulin on the column. Then, CZE and LINF are applied to separate and detect the peptide fragments. The advantages of this method are its simplicity, high sensitivity, high selectivity, efficient operation, and high speed. 38 refs., 6 figs., 2 tabs.

  9. NMR-Based Mapping of Disulfide Bridges in Cysteine-Rich Peptides: Application to the μ-Conotoxin SxIIIA*

    PubMed Central

    Walewska, Aleksandra; Skalicky, Jack J.; Davis, Darrell R.; Zhang, Min-Min; Lopez-Vera, Estuardo; Watkins, Maren; Han, Tiffany S.; Yoshikami, Doju; Olivera, Baldomero M.; Bulaj, Grzegorz

    2009-01-01

    Disulfide-rich peptides represent a megadiverse group of natural products with very promising therapeutic potential. To accelerate their functional characterization, high-throughput chemical synthesis and folding methods are required, including efficient mapping of multiple disulfide bridges. Here, we describe a novel approach for such mapping and apply it to a three-disulfide bridged conotoxin, μ-SxIIIA (from the venom of Conus striolatus) whose discovery is also reported here for the first time. μ-SxIIIA was chemically synthesized with three cysteine residues labeled 100% with 15N/13C, while the remaining three cysteine residues were incorporated using a mixture of 70%:30% unlabeled:labeled Fmoc-protected residues. After oxidative folding, the major product was analyzed by NMR spectroscopy. Sequence-specific resonance assignments for the isotope-enriched Cys residues were determined with 2D versions of standard triple resonance (1H,13C,15N) NMR experiments and 2D [13C,1H] HSQC. Disulfide patterns were directly determined with cross-disulfide NOEs confirming that the oxidation product had the disulfide connectivities characteristic of μ-conotoxins. μ-SxIIIA was found to be a potent blocker of the sodium channel subtype NaV1.4 (IC50 = 7 nM). These results suggest that differential incorporation of isotope-labeled cysteine residues is an efficient strategy to map disulfides and should facilitate the discovery and structure-function studies of many bioactive peptides. PMID:18831583

  10. Epitope mapping of anti-myelin oligodendrocyte glycoprotein (MOG) antibodies in a mouse model of multiple sclerosis: microwave-assisted synthesis of the peptide antigens and ELISA screening.

    PubMed

    Pacini, Giulia; Ieronymaki, Matthaia; Nuti, Francesca; Sabatino, Giuseppina; Larregola, Maud; Aharoni, Rina; Papini, Anna Maria; Rovero, Paolo

    2016-01-01

    The role of pathologic auto-antibodies against myelin oligodendrocyte glycoprotein (MOG) in multiple sclerosis is a highly controversial matter. As the use of animal models may enable to unravel the molecular mechanisms of the human disorder, numerous studies on multiple sclerosis are carried out using experimental autoimmune encephalomyelitis (EAE). In particular, the most extensively used EAE model is obtained by immunizing C57BL/6 mice with the immunodominant peptide MOG(35-55). In this scenario, we analyzed the anti-MOG antibody response in this model using the recombinant refolded extracellular domain of the protein, MOG(1-117). To assess the presence of a B-cell intramolecular epitope spreading mechanism, we tested also five synthetic peptides mapping the 1-117 sequence of MOG, including MOG(35-55). For this purpose, we cloned, expressed in Escherichia coli and on-column refolded MOG(1-117), and we applied an optimized microwave-assisted solid-phase synthetic strategy to obtain the designed peptide sequences. Subsequently, we set up a solid-phase immunoenzymatic assay testing both naïve and EAE mice sera and using MOG protein and peptides as antigenic probes. The results obtained disclose an intense IgG antibody response against both the recombinant protein and the immunizing peptide, while no response was observed against the other synthetic fragments, thus excluding the presence of an intramolecular epitope spreading mechanism. Furthermore, as the properly refolded recombinant probe is able to bind antibodies with greater efficiency compared with MOG(35-55), we hypothesize the presence of both linear and conformational epitopes on MOG(35-55) sequence. PMID:26663200

  11. Quantitative analysis of single amino acid variant peptides associated with pancreatic cancer in serum by an isobaric labeling quantitative method.

    PubMed

    Nie, Song; Yin, Haidi; Tan, Zhijing; Anderson, Michelle A; Ruffin, Mack T; Simeone, Diane M; Lubman, David M

    2014-12-01

    Single amino acid variations are highly associated with many human diseases. The direct detection of peptides containing single amino acid variants (SAAVs) derived from nonsynonymous single nucleotide polymorphisms (SNPs) in serum can provide unique opportunities for SAAV associated biomarker discovery. In the present study, an isobaric labeling quantitative strategy was applied to identify and quantify variant peptides in serum samples of pancreatic cancer patients and other benign controls. The largest number of SAAV peptides to date in serum including 96 unique variant peptides were quantified in this quantitative analysis, of which five variant peptides showed a statistically significant difference between pancreatic cancer and other controls (p-value < 0.05). Significant differences in the variant peptide SDNCEDTPEAGYFAVAVVK from serotransferrin were detected between pancreatic cancer and controls, which was further validated by selected reaction monitoring (SRM) analysis. The novel biomarker panel obtained by combining α-1-antichymotrypsin (AACT), Thrombospondin-1 (THBS1) and this variant peptide showed an excellent diagnostic performance in discriminating pancreatic cancer from healthy controls (AUC = 0.98) and chronic pancreatitis (AUC = 0.90). These results suggest that large-scale analysis of SAAV peptides in serum may provide a new direction for biomarker discovery research. PMID:25393578

  12. Mapping Creativity: Creativity Measurements Network Analysis

    ERIC Educational Resources Information Center

    Pinheiro, Igor Reszka; Cruz, Roberto Moraes

    2014-01-01

    This article borrowed network analysis tools to discover how the construct formed by the set of all measures of creativity configures itself. To this end, using a variant of the meta-analytical method, a database was compiled simulating 42,381 responses to 974 variables centered on 64 creativity measures. Results, although preliminary, indicate…

  13. Analysis of novel angiotensin-I-converting enzyme inhibitory peptides from protease-hydrolyzed marine shrimp Acetes chinensis.

    PubMed

    Hai-Lun, He; Xiu-Lan, Chen; Cai-Yun, Sun; Yu-Zhong, Zhang; Bai-Cheng, Zhou

    2006-11-01

    Acetes chinensis is an underutilized shrimp species thriving in the Bo Hai Gulf of China. In a previous study, we had used the protease from Bacillus sp. SM98011 to digest this kind of shrimp and found that the oligopeptide-enriched hydrolysate possessed antioxidant activity and high angiotensin I-converting enzyme (ACE) inhibitory activity with an IC50 value of 0.97 mg/ml. In this paper, by ultrafiltration, gel permeation chromatography and reversed-phase high-performance liquid chromatography (RP-HPLC), five peptides with high ACE inhibitory activity were purified from the shrimp hydrolysates and their sequences were identified by amino acid composition analysis and molecular weight (MW) analysis. Three of them, FCVLRP (a), IFVPAF (f) and KPPETV (j), were novel ACE inhibitory peptides. Their IC50 values were 12.3 microM, 3.4 microM and 24.1 microM, respectively, and their recoveries were 30 mg/100 g (solid basis of shrimp), 19 mg/100 g and 33 mg/100 g, respectively. Lineweaver-Burk plots for the three novel peptides showed that they are all competitive inhibitors. To test the ACE inhibitory activity of peptide a, f, j after they were digested by digestive enzymes in vivo, 12 derived peptides from FCVLRP and IFVPAF were synthesized based on their amino acid sequences and the cleavage sites of digestive enzymes. No digestive enzyme cleavage site was found in KPPETV. The IC50 values of the derived peptides were determined and the result showed that except for VPAF, FC and FCVL, the ACE inhibitory activity of the other nine derived peptides did not significantly change when compared with their original peptides. Surprisingly, five peptides had lower IC50 values than their original peptides, particularly for RP (IC50 value = 0.39 microM), which is about 30 times lower than its original peptide and almost the lowest IC50 value for ACE inhibitory peptides reported. Therefore, the novel peptides identified from A. chinensis hydrolysates probably still maintain a high ACE

  14. Modular Automated Processing System (MAPS) for analysis of biological samples.

    SciTech Connect

    Gil, Geun-Cheol; Chirica, Gabriela S.; Fruetel, Julia A.; VanderNoot, Victoria A.; Branda, Steven S.; Schoeniger, Joseph S.; Throckmorton, Daniel J.; Brennan, James S.; Renzi, Ronald F.

    2010-10-01

    We have developed a novel modular automated processing system (MAPS) that enables reliable, high-throughput analysis as well as sample-customized processing. This system is comprised of a set of independent modules that carry out individual sample processing functions: cell lysis, protein concentration (based on hydrophobic, ion-exchange and affinity interactions), interferent depletion, buffer exchange, and enzymatic digestion of proteins of interest. Taking advantage of its unique capacity for enclosed processing of intact bioparticulates (viruses, spores) and complex serum samples, we have used MAPS for analysis of BSL1 and BSL2 samples to identify specific protein markers through integration with the portable microChemLab{trademark} and MALDI.

  15. Automated thermal mapping techniques using chromatic image analysis

    NASA Technical Reports Server (NTRS)

    Buck, Gregory M.

    1989-01-01

    Thermal imaging techniques are introduced using a chromatic image analysis system and temperature sensitive coatings. These techniques are used for thermal mapping and surface heat transfer measurements on aerothermodynamic test models in hypersonic wind tunnels. Measurements are made on complex vehicle configurations in a timely manner and at minimal expense. The image analysis system uses separate wavelength filtered images to analyze surface spectral intensity data. The system was initially developed for quantitative surface temperature mapping using two-color thermographic phosphors but was found useful in interpreting phase change paint and liquid crystal data as well.

  16. Molecular genetic analysis of a locus required for resistance to antimicrobial peptides in Salmonella typhimurium.

    PubMed Central

    Parra-Lopez, C; Baer, M T; Groisman, E A

    1993-01-01

    The innate immunity of vertebrates and invertebrates to microbial infection is mediated in part by small cationic peptides with antimicrobial activity. Successful pathogens have evolved mechanisms to withstand the antibiotic activity of these molecules. We have isolated a set of genes from Salmonella typhimurium which are required for virulence and resistance to the antimicrobial peptides melittin and protamine. Sequence analysis of a 5.7 kb segment from the wild-type plasmid conferring resistance to protamine contained five open reading frames: sapA, sapB, sapC, sapD and sapF, organized in an operon structure and transcribed as a 5.3 kb mRNA. SapD and SapF exhibited similarity with the 'ATP binding cassette' family of transporters including the bacterial Opp and SpoOK, involved in the uptake of oligopeptides; the yeast STE6, necessary for the export of a peptide pheromone; and the mammalian mdr, which mediates resistance to chemotherapeutic agents in cancer cells. SapA showed identity with other periplasmic solute binding proteins involved in peptide transport. The SapABCDF system constitutes a novel transporter for enteric bacteria and the first one harboring a periplasmic component with a role in virulence. Images PMID:8223423

  17. Strain mapping analysis of textile composites

    NASA Astrophysics Data System (ADS)

    Ivanov, Dmitry; Ivanov, Sergey; Lomov, Stepan; Verpoest, Ignaas

    2009-03-01

    The focus of the work is meso-scale analysis (scale level of the fabric unit cell) of textile composite deformation and failure. The surface strain measurement is used for: (1) experimental investigation, which includes study of strain distribution at various stages of deformation, plasticity detection, damage initiation; (2) numerical validation of the correspondent finite element (FE) models. Two examples are considered: carbon-epoxy triaxial-braided and glass polypropylene-woven composite. The surface strain measurement (by digital image correlation technique) accompanies the tensile tests, aiming at: (1) elastic anisotropic constants characterisation, (2) study of non-linear material behaviour (for the thermoplastic composite), (3) control of homogeneity of the macro-strain distribution, and (4) analysis of damage initiation in brittle composites. Validation of meso-FE models by strain measurements encounters difficulties arising from (1) resolution of the strain measurements, (2) irregularities of the initial structure such as random layer nesting, ply interaction, and deviation of yarns from their theoretical position, which affects the measured strain fields. The paper discusses these difficulties and demonstrates a qualitative agreement with the FE analysis of idealised composite configurations.

  18. Pooled-Peptide Epitope Mapping Strategies Are Efficient and Highly Sensitive: An Evaluation of Methods for Identifying Human T Cell Epitope Specificities in Large-Scale HIV Vaccine Efficacy Trials

    PubMed Central

    Fiore-Gartland, Andrew; Manso, Bryce A.; Friedrich, David P.; Gabriel, Erin E.; Finak, Greg; Moodie, Zoe; Hertz, Tomer; De Rosa, Stephen C.; Frahm, Nicole; Gilbert, Peter B.; McElrath, M. Juliana

    2016-01-01

    The interferon gamma, enzyme-linked immunospot (IFN-γ ELISpot) assay is widely used to identify viral antigen-specific T cells is frequently employed to quantify T cell responses in HIV vaccine studies. It can be used to define T cell epitope specificities using panels of peptide antigens, but with sample and cost constraints there is a critical need to improve the efficiency of epitope mapping for large and variable pathogens. We evaluated two epitope mapping strategies, based on group testing, for their ability to identify vaccine-induced T-cells from participants in the Step HIV-1 vaccine efficacy trial, and compared the findings to an approach of assaying each peptide individually. The group testing strategies reduced the number of assays required by >7-fold without significantly altering the accuracy of T-cell breadth estimates. Assays of small pools containing 7–30 peptides were highly sensitive and effective at detecting single positive peptides as well as summating responses to multiple peptides. Also, assays with a single 15-mer peptide, containing an identified epitope, did not always elicit a response providing validation that 15-mer peptides are not optimal antigens for detecting CD8+ T cells. Our findings further validate pooling-based epitope mapping strategies, which are critical for characterizing vaccine-induced T-cell responses and more broadly for informing iterative vaccine design. We also show ways to improve their application with computational peptide:MHC binding predictors that can accurately identify the optimal epitope within a 15-mer peptide and within a pool of 15-mer peptides. PMID:26863315

  19. Pooled-Peptide Epitope Mapping Strategies Are Efficient and Highly Sensitive: An Evaluation of Methods for Identifying Human T Cell Epitope Specificities in Large-Scale HIV Vaccine Efficacy Trials.

    PubMed

    Fiore-Gartland, Andrew; Manso, Bryce A; Friedrich, David P; Gabriel, Erin E; Finak, Greg; Moodie, Zoe; Hertz, Tomer; De Rosa, Stephen C; Frahm, Nicole; Gilbert, Peter B; McElrath, M Juliana

    2016-01-01

    The interferon gamma, enzyme-linked immunospot (IFN-γ ELISpot) assay is widely used to identify viral antigen-specific T cells is frequently employed to quantify T cell responses in HIV vaccine studies. It can be used to define T cell epitope specificities using panels of peptide antigens, but with sample and cost constraints there is a critical need to improve the efficiency of epitope mapping for large and variable pathogens. We evaluated two epitope mapping strategies, based on group testing, for their ability to identify vaccine-induced T-cells from participants in the Step HIV-1 vaccine efficacy trial, and compared the findings to an approach of assaying each peptide individually. The group testing strategies reduced the number of assays required by >7-fold without significantly altering the accuracy of T-cell breadth estimates. Assays of small pools containing 7-30 peptides were highly sensitive and effective at detecting single positive peptides as well as summating responses to multiple peptides. Also, assays with a single 15-mer peptide, containing an identified epitope, did not always elicit a response providing validation that 15-mer peptides are not optimal antigens for detecting CD8+ T cells. Our findings further validate pooling-based epitope mapping strategies, which are critical for characterizing vaccine-induced T-cell responses and more broadly for informing iterative vaccine design. We also show ways to improve their application with computational peptide:MHC binding predictors that can accurately identify the optimal epitope within a 15-mer peptide and within a pool of 15-mer peptides. PMID:26863315

  20. Modified capillary electrophoresis system for peptide, protein and double-stranded DNA analysis.

    PubMed

    Belenkii, B G; Kassalainen, G E; Nasledov, D G

    2000-05-26

    The results of high-performance capillary electrophoresis (HPCE) studies of peptide, protein and double-stranded DNA separations on a laboratory-made HPCE system are presented. Parameters of the HPCE system are given. The new method of capillary surface modification by grafting poly(glycidyl methacrylate) is described. The problems of HPCE biopolymer analysis connected with the sample-wall interactions are discussed. PMID:10893035

  1. Interrogating the repertoire: broadening the scope of peptide-MHC multimer analysis.

    PubMed

    Davis, Mark M; Altman, John D; Newell, Evan W

    2011-08-01

    Labelling antigen-specific T cells with peptide-MHC multimers has provided an invaluable way to monitor T cell-mediated immune responses. A number of recent developments in this technology have made these multimers much easier to make and use in large numbers. Furthermore, enrichment techniques have provided a greatly increased sensitivity that allows the analysis of the naive T cell repertoire directly. Thus, we can expect a flood of new information to emerge in the coming years. PMID:21760610

  2. Negative electron-transfer dissociation nLC-MS/MS facilitates the analysis of thousands of acidic peptides

    PubMed Central

    McAlister, Graeme C.; Russell, Jason D.; Rumachik, Neil G.; Hebert, Alexander S.; Syka, John E. P.; Geer, Lewis Y.; Westphall, Michael S.; Pagliarini, David J.; Coon, Joshua J.

    2012-01-01

    We describe the first implementation of negative electron-transfer dissociation (NETD) on a hybrid ion trap-orbitrap mass spectrometer and its application to high-throughput sequencing of peptide anions. NETD – coupled with high pH separations, negative electrospray ionization (ESI), and an NETD compatible version of OMSSA – is part of a complete workflow that includes the formation, interrogation and sequencing of peptide anions. Together these interlocking pieces facilitated the identification of more than 2,000 unique peptides from Saccharomyces cerevisiae representing the most comprehensive analysis of peptide anions by tandem mass spectrometry to date. The same S. cerevisiae samples were interrogated using traditional, positive modes of peptide LC-MS/MS analysis (e.g., acidic LC separations, positive ESI, and collision activated dissociation), and the resulting peptide identifications of the different workflows were compared. Due to a decreased flux of peptide anions, and a tendency to produced lowly charged precursors, the NETD-based LC-MS/MS workflow was not as sensitive as the positive mode methods. However, the use of NETD readily permits access to underrepresented acidic portions of the proteome by identifying peptides that tended to have lower pI values. As such NETD improves sequence coverage, filling out the acidic portions of proteins that are often overlooked by the other methods. PMID:22335612

  3. Mapping.

    ERIC Educational Resources Information Center

    Kinney, Douglas M.; McIntosh, Willard L.

    1979-01-01

    The area of geological mapping in the United States in 1978 increased greatly over that reported in 1977; state geological maps were added for California, Idaho, Nevada, and Alaska last year. (Author/BB)

  4. Global land cover mapping: a review and uncertainty analysis

    USGS Publications Warehouse

    Congalton, Russell G.; Gu, Jianyu; Yadav, Kamini; Thenkabail, Prasad S.; Ozdogan, Mutlu

    2014-01-01

    Given the advances in remotely sensed imagery and associated technologies, several global land cover maps have been produced in recent times including IGBP DISCover, UMD Land Cover, Global Land Cover 2000 and GlobCover 2009. However, the utility of these maps for specific applications has often been hampered due to considerable amounts of uncertainties and inconsistencies. A thorough review of these global land cover projects including evaluating the sources of error and uncertainty is prudent and enlightening. Therefore, this paper describes our work in which we compared, summarized and conducted an uncertainty analysis of the four global land cover mapping projects using an error budget approach. The results showed that the classification scheme and the validation methodology had the highest error contribution and implementation priority. A comparison of the classification schemes showed that there are many inconsistencies between the definitions of the map classes. This is especially true for the mixed type classes for which thresholds vary for the attributes/discriminators used in the classification process. Examination of these four global mapping projects provided quite a few important lessons for the future global mapping projects including the need for clear and uniform definitions of the classification scheme and an efficient, practical, and valid design of the accuracy assessment.

  5. Dissociation Behavior of a TEMPO-Active Ester Cross-Linker for Peptide Structure Analysis by Free Radical Initiated Peptide Sequencing (FRIPS) in Negative ESI-MS

    NASA Astrophysics Data System (ADS)

    Hage, Christoph; Ihling, Christian H.; Götze, Michael; Schäfer, Mathias; Sinz, Andrea

    2016-07-01

    We have synthesized a homobifunctional amine-reactive cross-linking reagent, containing a TEMPO (2,2,6,6-tetramethylpiperidine-1-oxy) and a benzyl group (Bz), termed TEMPO-Bz-linker, to derive three-dimensional structural information of proteins. The aim for designing this novel cross-linker was to facilitate the mass spectrometric analysis of cross-linked products by free radical initiated peptide sequencing (FRIPS). In an initial study, we had investigated the fragmentation behavior of TEMPO-Bz-derivatized peptides upon collision activation in (+)-electrospray ionization collision-induced dissociation tandem mass spectrometry (ESI-CID-MS/MS) experiments. In addition to the homolytic NO-C bond cleavage FRIPS pathway delivering the desired odd-electron product ions, an alternative heterolytic NO-C bond cleavage, resulting in even-electron product ions mechanism was found to be relevant. The latter fragmentation route clearly depends on the protonation of the TEMPO-Bz-moiety itself, which motivated us to conduct (-)-ESI-MS, CID-MS/MS, and MS3 experiments of TEMPO-Bz-cross-linked peptides to further clarify the fragmentation behavior of TEMPO-Bz-peptide molecular ions. We show that the TEMPO-Bz-linker is highly beneficial for conducting FRIPS in negative ionization mode as the desired homolytic cleavage of the NO-C bond is the major fragmentation pathway. Based on characteristic fragments, the isomeric amino acids leucine and isoleucine could be discriminated. Interestingly, we observed pronounced amino acid side chain losses in cross-linked peptides if the cross-linked peptides contain a high number of acidic amino acids.

  6. Small interacting peptides. Part II: Interaction of cyclohexapeptides with immobilised model peptides. Comparison of infrared investigations, principal components analysis and force field calculations

    NASA Astrophysics Data System (ADS)

    Palmer, Frauke; Stingel, Christiane; Tünnemann, Rolf; Mack, Hans-Georg; Jung, Günther; Hoffmann, Volker

    2004-07-01

    The interaction of cyclic peptides with surface-bound model peptides was investigated by ATR-FTIR spectroscopy, principal components analysis and force field calculations. Information about the interacting functional COOH, COO -, and NH 3+ groups and the peptide backbone was gained through a set of cyclohexapeptides (seven of the type c(X 1KX 2KX 3K) (K = L-lysine) and one of the type c(X 1KX 2KX 3k) (k = D-lysine), which are interacting with L-arginine- or tripeptide-coated Si-ATR crystals. All measurements were performed in aqueous solutions. Spectra evaluation in the range 1800-1500 cm -1 was done by band and principal components analysis (PCA). Only adsorbed molecules were present in these spectra. The coatings were investigated by ATR-FTIR spectroscopy too in order to characterise their functional groups. Based on this knowledge, the spectra of the interacting partners could be evaluated in relation to cyclohexapeptides and coatings. As a result, it was possible to identify the distinct differences in the bonding behaviour of the various peptides.

  7. Identification and expression analysis of the zebrafish orthologues of the mammalian MAP1LC3 gene family.

    PubMed

    Ganesan, Swamynathan; Moussavi Nik, Seyyed Hani; Newman, Morgan; Lardelli, Michael

    2014-10-15

    Autophagy is the principle pathway within cells involved in clearing damaged proteins and organelles. Therefore autophagy is necessary to maintain the turnover balance of peptides and homoeostasis. Autophagy occurs at basal levels under normal conditions but can be upregulated by chemical inducers or stress conditions. The zebrafish (Danio rerio) serves as a versatile tool to understand the functions of genes implicated in autophagy. We report the identification of the zebrafish orthologues of mammalian genes MAP1LC3A (map1lc3a) and MAP1LC3B (map1lc3b) by phylogenetic and conserved synteny analysis and we examine their expression during embryonic development. The zebrafish map1lc3a and map1lc3b genes both show maternally contributed transcripts in early embryogenesis. However, levels of map1lc3a transcript steadily increase until at least 120h post-fertilisation while the levels of map1lc3b show a more variable pattern across developmental time. We have also validated the LC3I ratio/LC3I immunoblot autophagy assay in the presence of chloroquine (a lysosomal proteolysis inhibitor). We found that the LC3II/LC3I ratio is significantly increased in the presence of sodium azide with chloroquine supporting that hypoxia induces autophagy in zebrafish. This was supported by our qPCR assay that showed increased map1lc3a transcript levels in the presence of sodium azide. In contrast, levels of map1lc3b transcripts were reduced in the presence of rapamycin but the decrease in the presence of sodium azide did not reach statistical significance. Our study supports the use of zebrafish for analysing the interplay between hypoxia, development and autophagy. PMID:25051050

  8. Computational Analysis and Mapping of ijCSCL Content

    ERIC Educational Resources Information Center

    Lonchamp, Jacques

    2012-01-01

    The purpose of this empirical study is to analyze and map the content of the "International Journal of Computer-Supported Collaborative Learning" since its inception in 2006. Co-word analysis is the general approach that is used. In this approach, patterns of co-occurrence of pairs of items (words or phrases) identify relationships among ideas.…

  9. WAMI: a web server for the analysis of minisatellite maps

    PubMed Central

    2010-01-01

    Background Minisatellites are genomic loci composed of tandem arrays of short repetitive DNA segments. A minisatellite map is a sequence of symbols that represents the tandem repeat array such that the set of symbols is in one-to-one correspondence with the set of distinct repeats. Due to variations in repeat type and organization as well as copy number, the minisatellite maps have been widely used in forensic and population studies. In either domain, researchers need to compare the set of maps to each other, to build phylogenetic trees, to spot structural variations, and to study duplication dynamics. Efficient algorithms for these tasks are required to carry them out reliably and in reasonable time. Results In this paper we present WAMI, a web-server for the analysis of minisatellite maps. It performs the above mentioned computational tasks using efficient algorithms that take the model of map evolution into account. The WAMI interface is easy to use and the results of each analysis task are visualized. Conclusions To the best of our knowledge, WAMI is the first server providing all these computational facilities to the minisatellite community. The WAMI web-interface and the source code of the underlying programs are available at http://www.nubios.nileu.edu.eg/tools/wami. PMID:20525398

  10. PHASTpep: Analysis Software for Discovery of Cell-Selective Peptides via Phage Display and Next-Generation Sequencing

    PubMed Central

    Dasa, Siva Sai Krishna; Kelly, Kimberly A.

    2016-01-01

    Next-generation sequencing has enhanced the phage display process, allowing for the quantification of millions of sequences resulting from the biopanning process. In response, many valuable analysis programs focused on specificity and finding targeted motifs or consensus sequences were developed. For targeted drug delivery and molecular imaging, it is also necessary to find peptides that are selective—targeting only the cell type or tissue of interest. We present a new analysis strategy and accompanying software, PHage Analysis for Selective Targeted PEPtides (PHASTpep), which identifies highly specific and selective peptides. Using this process, we discovered and validated, both in vitro and in vivo in mice, two sequences (HTTIPKV and APPIMSV) targeted to pancreatic cancer-associated fibroblasts that escaped identification using previously existing software. Our selectivity analysis makes it possible to discover peptides that target a specific cell type and avoid other cell types, enhancing clinical translatability by circumventing complications with systemic use. PMID:27186887

  11. Epitope Mapping of Antigenic MUC1 Peptides to Breast Cancer Antibody Fragment B27.29: A Heteronuclear NMR Study

    SciTech Connect

    Grinstead, Jeffrey S.; Schuman, Jason T.; Campbell, Ann P.

    2003-11-13

    MUC1 mucin is a breast cancer-associated transmembrane glycoprotein, of which the extracellular domain is formed by the repeating 20-amino acid sequence GVTSAPDTRPAPGSTAPPAH. In neoplastic breast tissue, the highly immunogenic sequence PDTRPAP (in bold above) is exposed. Antibodies raised directly against MUC1-expressing tumors offer unique access to this neoplastic state, as they represent immunologically relevant ''reverse templates'' of the tumor-associated mucin. In a previous study [Grinstead, J. S., et al. (2002) Biochemistry 41, 9946-9961], 1H NMR methods were used to correlate the effects of cryptic glycosylation outside of the PDTRPAP core epitope sequence on the recognition and binding of Mab B27.29, a monoclonal antibody raised against breast tumor cells. In the study presented here, isotope-edited NMR methods, including 15N and 13C relaxation measurements, were used to probe the recognition and binding of the PDTRPAP epitope sequence to Fab B27.29. Two peptides were studied: a one-repeat MUC1 16mer peptide of the sequence GVTSAPDTRPAPGSTA and a two-repeat MUC1 40mer peptide of the sequence (VTSAPDTRPAPGSTAPPAHG)2. 15N and 13C NMR relaxation parameters were measured for both peptides free in solution and bound to Fab B27.29. The 13CR T1 values best represent changes in the local correlation time of the peptide epitope upon binding antibody, and demonstrate that the PDTRPAP sequence is immobilized in the antibody-combining site. This result is also reflected in the appearance of the 15N- and 13C-edited HSQC spectra, where line broadening of the same peptide epitope resonances is observed. The PDTRPAP peptide epitope expands upon the peptide epitope identified previously in our group as PDTRP by homonuclear NMR experiments [Grinstead, J. S., et al. (2002) Biochemistry 41, 9946-9961], and illustrates the usefulness of the heteronuclear NMR experiments. The implications of these results are discussed within the context of MUC1 breast cancer vaccine design.

  12. Sequence analysis and mapping of a novel human mitochondrial ATP synthase subunit 9 cDNA (ATP5G3)

    SciTech Connect

    Yan, W.L.; Gusella, J.F. |; Haines, J.L. |

    1994-11-15

    The authors describe the cloning, sequence analysis, and chromosomal mapping of a novel mitochondrial ATP synthase subunit 9 cDNA, P3. Subunit 9 transports protons across the inner mitochondrial membrane to the F{sub 1}-ATPase protruding on the matrix side, resulting in the generation of ATP. Sequence analysis of the P3 cDNA reveals only 80% identity with the human subunit 9 genes P1 and P2 in the DNA sequence encoding the mature protein identical to P1 and P2. The predicted sequence of the P3 leader peptide differs from the P1 and P2 leaders, but retains the {open_quotes}RFS{close_quotes} motif critical for mitochondrial import and maturation. The P3 gene (ATP5G3) maps to chromosome 2. 8 refs., 1 fig., 1 tab.

  13. 3D Regression Heat Map Analysis of Population Study Data.

    PubMed

    Klemm, Paul; Lawonn, Kai; Glaßer, Sylvia; Niemann, Uli; Hegenscheid, Katrin; Völzke, Henry; Preim, Bernhard

    2016-01-01

    Epidemiological studies comprise heterogeneous data about a subject group to define disease-specific risk factors. These data contain information (features) about a subject's lifestyle, medical status as well as medical image data. Statistical regression analysis is used to evaluate these features and to identify feature combinations indicating a disease (the target feature). We propose an analysis approach of epidemiological data sets by incorporating all features in an exhaustive regression-based analysis. This approach combines all independent features w.r.t. a target feature. It provides a visualization that reveals insights into the data by highlighting relationships. The 3D Regression Heat Map, a novel 3D visual encoding, acts as an overview of the whole data set. It shows all combinations of two to three independent features with a specific target disease. Slicing through the 3D Regression Heat Map allows for the detailed analysis of the underlying relationships. Expert knowledge about disease-specific hypotheses can be included into the analysis by adjusting the regression model formulas. Furthermore, the influences of features can be assessed using a difference view comparing different calculation results. We applied our 3D Regression Heat Map method to a hepatic steatosis data set to reproduce results from a data mining-driven analysis. A qualitative analysis was conducted on a breast density data set. We were able to derive new hypotheses about relations between breast density and breast lesions with breast cancer. With the 3D Regression Heat Map, we present a visual overview of epidemiological data that allows for the first time an interactive regression-based analysis of large feature sets with respect to a disease. PMID:26529689

  14. In silico prediction of peptide binding affinity to class I mouse major histocompatibility complexes: a comparative molecular similarity index analysis (CoMSIA) study.

    PubMed

    Hattotuwagama, Channa K; Doytchinova, Irini A; Flower, Darren R

    2005-01-01

    Current methods for the in silico identification of T cell epitopes (which form the basis of many vaccines, diagnostics, and reagents) rely on the accurate prediction of peptide-major histocompatibility complex (MHC) affinity. A three-dimensional quantitative structure-activity relationship (3D-QSAR) for the prediction of peptide binding to class I MHC molecules was established using the comparative molecular similarity index analysis (CoMSIA) method. Three MHC alleles were studied: H2-D(b), H2-K(b), and H2-K(k). Models were produced for each allele. Each model consisted of five physicochemical descriptors-steric bulk, electrostatic potentials, hydrophobic interactions, and hydrogen-bond donor and hydrogen-bond acceptor abilities. The models have an acceptable level of predictivity: cross-validation leave-one-out statistical terms q2 and SEP (standard error of prediction) ranged between 0.490 and 0.679 and between 0.525 and 0.889, respectively. The non-cross-validated statistical terms r2 and SEE (standard error of estimate) ranged between 0.913 and 0.979 and between 0.167 and 0.248, respectively. The use of coefficient contour maps, which indicate favored and disfavored areas for each position of the MHC-bound peptides, allowed the binding specificity of each allele to be identified, visualized, and understood. The present study demonstrates the effectiveness of CoMSIA as a method for studying peptide-MHC interactions. The peptides used in this study are available on the Internet (http://www.jenner.ac.uk/AntiJen). The partial least-squares method is available commercially in the SYBYL molecular modeling software package. PMID:16180918

  15. Analysis of variance of thematic mapping experiment data.

    USGS Publications Warehouse

    Rosenfield, G.H.

    1981-01-01

    As an example of the methodology, data from an experiment using three scales of land-use and land-cover mapping have been analyzed. The binomial proportions of correct interpretations have been analyzed untransformed and transformed by both the arcsine and the logit transformations. A weighted analysis of variance adjustment has been used. There is evidence of a significant difference among the three scales of mapping (1:24 000, 1:100 000 and 1:250 000) using the transformed data. Multiple range tests showed that all three scales are different for the arcsine transformed data. - from Author

  16. “On silico” peptide microarrays for high-resolution mapping of antibody epitopes and diverse protein-protein interactions

    PubMed Central

    Price, Jordan V; Tangsombatvisit, Stephanie; Xu, Guangyu; Levy, Dan; Baechler, Emily C.; Gozani, Or; Varma, Madoo; Liu, Chih Long

    2011-01-01

    We have developed a novel, silicon-based peptide array for broad biological applications, including potential for development as a real-time point-of-care platform. We employed photolithography on silicon wafers to synthesize microarrays (Intel arrays), containing every possible overlapping peptide within a linear protein sequence covering the N-terminal tail of human histone H2B. Arrays also included peptides with acetylated and methylated lysine residues reflecting post-translational modifications of H2B. We defined minimum binding epitopes for commercial antibodies recognizing modified and unmodified H2B peptides. We further demonstrated that this platform is suitable for highly sensitive methyltransferase and kinase substrate characterization. Intel arrays also revealed specific H2B epitopes recognized by autoantibodies in individuals with systemic lupus erythematosus (SLE) that have increased disease severity. By combining emerging nonfluorescence-based detection methods with an underlying integrated circuit, we are now poised to create a truly transformative proteomics platform with applications in bioscience, drug development, and clinical diagnostics. PMID:22902875

  17. A cost-benefit analysis of The National Map

    USGS Publications Warehouse

    Halsing, David L.; Theissen, Kevin; Bernknopf, Richard

    2003-01-01

    The Geography Discipline of the U.S. Geological Survey (USGS) has conducted this cost-benefit analysis (CBA) of The National Map. This analysis is an evaluation of the proposed Geography Discipline initiative to provide the Nation with a mechanism to access current and consistent digital geospatial data. This CBA is a supporting document to accompany the Exhibit 300 Capital Asset Plan and Business Case of The National Map Reengineering Program. The framework for estimating the benefits is based on expected improvements in processing information to perform any of the possible applications of spatial data. This analysis does not attempt to determine the benefits and costs of performing geospatial-data applications. Rather, it estimates the change in the differences between those benefits and costs with The National Map and the current situation without it. The estimates of total costs and benefits of The National Map were based on the projected implementation time, development and maintenance costs, rates of data inclusion and integration, expected usage levels over time, and a benefits estimation model. The National Map provides data that are current, integrated, consistent, complete, and more accessible in order to decrease the cost of implementing spatial-data applications and (or) improve the outcome of those applications. The efficiency gains in per-application improvements are greater than the cost to develop and maintain The National Map, meaning that the program would bring a positive net benefit to the Nation. The average improvement in the net benefit of performing a spatial data application was multiplied by a simulated number of application implementations across the country. The numbers of users, existing applications, and rates of application implementation increase over time as The National Map is developed and accessed by spatial data users around the country. Results from the 'most likely' estimates of model parameters and data inputs indicate that

  18. Mapping of the SecA signal peptide binding site and dimeric interface by using the substituted cysteine accessibility method.

    PubMed

    Bhanu, Meera K; Zhao, Ping; Kendall, Debra A

    2013-10-01

    SecA is an ATPase nanomotor critical for bacterial secretory protein translocation. Secretory proteins carry an amino-terminal signal peptide that is recognized and bound by SecA followed by its transfer across the SecYEG translocon. While this process is crucial for the onset of translocation, exactly where the signal peptide interacts with SecA is unclear. SecA protomers also interact among themselves to form dimers in solution, yet the oligomeric interface and the residues involved in dimerization are unknown. To address these issues, we utilized the substituted cysteine accessibility method (SCAM); we generated a library of 23 monocysteine SecA mutants and probed for the accessibility of each mutant cysteine to maleimide-(polyethylene glycol)2-biotin (MPB), a sulfhydryl-labeling reagent, both in the presence and absence of a signal peptide. Dramatic differences in MPB labeling were observed, with a select few mutants located at the preprotein cross-linking domain (PPXD), the helical wing domain (HWD), and the helical scaffold domain (HSD), indicating that the signal peptide binds at the groove formed between these three domains. The exposure of this binding site is varied under different conditions and could therefore provide an ideal mechanism for preprotein transfer into the translocon. We also identified residues G793, A795, K797, and D798 located at the two-helix finger of the HSD to be involved in dimerization. Adenosine-5'-(γ-thio)-triphosphate (ATPγS) alone and, more extensively, in conjunction with lipids and signal peptides strongly favored dimer dissociation, while ADP supports dimerization. This study provides key insight into the structure-function relationships of SecA preprotein binding and dimer dissociation. PMID:23935053

  19. SIM-XL: A powerful and user-friendly tool for peptide cross-linking analysis.

    PubMed

    Lima, Diogo B; de Lima, Tatiani B; Balbuena, Tiago S; Neves-Ferreira, Ana Gisele C; Barbosa, Valmir C; Gozzo, Fábio C; Carvalho, Paulo C

    2015-11-01

    Chemical cross-linking has emerged as a powerful approach for the structural characterization of proteins and protein complexes. However, the correct identification of covalently linked (cross-linked or XL) peptides analyzed by tandem mass spectrometry is still an open challenge. Here we present SIM-XL, a software tool that can analyze data generated through commonly used cross-linkers (e.g., BS3/DSS). Our software introduces a new paradigm for search-space reduction, which ultimately accounts for its increase in speed and sensitivity. Moreover, our search engine is the first to capitalize on reporter ions for selecting tandem mass spectra derived from cross-linked peptides. It also makes available a 2D interaction map and a spectrum-annotation tool unmatched by any of its kind. We show SIM-XL to be more sensitive and faster than a competing tool when analyzing a data set obtained from the human HSP90. The software is freely available for academic use at http://patternlabforproteomics.org/sim-xl. A video demonstrating the tool is available at http://patternlabforproteomics.org/sim-xl/video. SIM-XL is the first tool to support XL data in the mzIdentML format; all data are thus available from the ProteomeXchange consortium (identifier PXD001677). This article is part of a Special Issue entitled: Computational Proteomics. PMID:25638023

  20. Global proteogenomic analysis of human MHC class I-associated peptides derived from non-canonical reading frames.

    PubMed

    Laumont, Céline M; Daouda, Tariq; Laverdure, Jean-Philippe; Bonneil, Éric; Caron-Lizotte, Olivier; Hardy, Marie-Pierre; Granados, Diana P; Durette, Chantal; Lemieux, Sébastien; Thibault, Pierre; Perreault, Claude

    2016-01-01

    In view of recent reports documenting pervasive translation outside of canonical protein-coding sequences, we wished to determine the proportion of major histocompatibility complex (MHC) class I-associated peptides (MAPs) derived from non-canonical reading frames. Here we perform proteogenomic analyses of MAPs eluted from human B cells using high-throughput mass spectrometry to probe the six-frame translation of the B-cell transcriptome. We report that ∼ 10% of MAPs originate from allegedly noncoding genomic sequences or exonic out-of-frame translation. The biogenesis and properties of these 'cryptic MAPs' differ from those of conventional MAPs. Cryptic MAPs come from very short proteins with atypical C termini, and are coded by transcripts bearing long 3'UTRs enriched in destabilizing elements. Relative to conventional MAPs, cryptic MAPs display different MHC class I-binding preferences and harbour more genomic polymorphisms, some of which are immunogenic. Cryptic MAPs increase the complexity of the MAP repertoire and enhance the scope of CD8 T-cell immunosurveillance. PMID:26728094

  1. Comprehensive Analysis of the Naturally Processed Peptide Repertoire: Differences between HLA-A and B in the Immunopeptidome

    PubMed Central

    Spijkers, Sanne N. M.; Poelen, Martien C. M.; van Gaans-van den Brink, Jacqueline A. M.; van der Poel, Kees; Costa, Ana I.; van Els, Cecile A. C. M.; van Baarle, Debbie; Kesmir, Can

    2015-01-01

    The cytotoxic T cell (CTL) response is determined by the peptide repertoire presented by the HLA class I molecules of an individual. We performed an in-depth analysis of the peptide repertoire presented by a broad panel of common HLA class I molecules on four B lymphoblastoid cell-lines (BLCL). Peptide elution and mass spectrometry analysis were utilised to investigate the number and abundance of self-peptides. Altogether, 7897 unique self-peptides, derived of 4344 proteins, were eluted. After viral infection, the number of unique self-peptides eluted significantly decreased compared to uninfected cells, paralleled by a decrease in the number of source proteins. In the overall dataset, the total number of unique self-peptides eluted from HLA-B molecules was larger than from HLA-A molecules, and they were derived from a larger number of source proteins. These results in B cells suggest that HLA-B molecules possibly present a more diverse repertoire compared to their HLA-A counterparts, which may contribute to their immunodominance. This study provides a unique data set giving new insights into the complex system of antigen presentation for a broad panel of HLA molecules, many of which were never studied this extensively before. PMID:26375851

  2. A novel node-structural map for angiogenesis analysis

    NASA Astrophysics Data System (ADS)

    Xiong, Yizhi; Zhao, Tong; Talavera, Dodanim; Honigmann, Rocio S.; Farkas, Daniel L.

    2005-04-01

    We introduce a novel node-structural map method for digital image-based analysis of angiogenesis, and apply it to quantitate the effect of pro-angiogenic (e.g. VEGF) and anti-angiogenic (e.g. anti-VEGF) treatments on blood vessel patterns in the quail chorioallantoic membrane (CAM) in vivo model. After vessel segmentation and skeletonization, a node-structural map is derived to represent the structural property of each pixel in the skeletonized image, such as end nodes (root and leaf), branch and furcation/junction nodes. By combining the node-structural map with vascular thickness map, our proposed method provides more detailed morphometric and structural measurement of vascular angiogenesis, such as average diameter, average branch length, branch thickness distribution, density of branch and furcation nodes, etc. Furthermore, the concept of vascular generations will be proposed. Accordingly, more detailed measurements related to the generations of the vascular tree can be easily evaluated. From the quantitative analysis results, it correctly shows the fact that VEGF/anti-VEGF can modify the blood vessel pattern and increase/decrease the vessel density in CAM significantly, compared to the phosphate-buffered saline treated controls.

  3. Processing of chromatographic data for chemometric analysis of peptide profiles from cheese extracts: a novel approach.

    PubMed

    Piraino, Paolo; Parente, Eugenio; McSweeney, Paul L H

    2004-11-17

    Chemometric analysis of chromatograms plays a fundamental role in characterization of foods or in detection of adulteration. Data for multivariate analysis of chromatographic profiles are usually obtained by visual matching (VM) of peaks, the identities of which, as for peptide profiles from cheese extracts, are often unknown. To avoid the main disadvantages of VM, which is subjective and time-consuming, a novel approach was developed. Fuzzy logic was employed to handle in a systematic way uncertainty in the position of peptide peaks, and chromatograms were processed by a rule-based membership function. Processed data consisted of classes of retention time wherein peak heights were accumulated by using the distance from the center of the class as a weight. The novel approach (fuzzy approach, FA) was compared with VM by using a real data set and by performing multivariate descriptive statistical techniques (principal component analysis, multidimensional scaling, and nonhierarchical cluster analysis). FA provided a fast, reliable, and objective alternative to VM and could be successfully applied for chemometric analysis of chromatographic profiles whenever knowledge of the identity of peaks is lacking or unnecessary. PMID:15537294

  4. Sequences encoding identical peptides for the analysis and manipulation of coding DNA

    PubMed Central

    Sánchez, Joaquín

    2013-01-01

    The use of sequences encoding identical peptides (SEIP) for the in silico analysis of coding DNA from different species has not been reported; the study of such sequences could directly reveal properties of coding DNA that are independent of peptide sequences. For practical purposes SEIP might also be manipulated for e.g. heterologous protein expression. We extracted 1,551 SEIP from human and E. coli and 2,631 SEIP from human and D. melanogaster. We then analyzed codon usage and intercodon dinucleotide tendencies and found differences in both, with more conspicuous disparities between human and E. coli than between human and D. melanogaster. We also briefly manipulated SEIP to find out if they could be used to create new coding sequences. We hence attempted replacement of human by E. coli codons via dicodon exchange but found that full replacement was not possible, this indicated robust species-specific dicodon tendencies. To test another form of codon replacement we isolated SEIP from human and the jellyfish green fluorescent protein (GFP) and we then re-constructed the GFP coding DNA with human tetra-peptide-coding sequences. Results provide proof-of-principle that SEIP may be used to reveal differences in the properties of coding DNA and to reconstruct in pieces a protein coding DNA with sequences from a different organism, the latter might be exploited in heterologous protein expression. PMID:23861567

  5. Sequences encoding identical peptides for the analysis and manipulation of coding DNA.

    PubMed

    Sánchez, Joaquín

    2013-01-01

    The use of sequences encoding identical peptides (SEIP) for the in silico analysis of coding DNA from different species has not been reported; the study of such sequences could directly reveal properties of coding DNA that are independent of peptide sequences. For practical purposes SEIP might also be manipulated for e.g. heterologous protein expression. We extracted 1,551 SEIP from human and E. coli and 2,631 SEIP from human and D. melanogaster. We then analyzed codon usage and intercodon dinucleotide tendencies and found differences in both, with more conspicuous disparities between human and E. coli than between human and D. melanogaster. We also briefly manipulated SEIP to find out if they could be used to create new coding sequences. We hence attempted replacement of human by E. coli codons via dicodon exchange but found that full replacement was not possible, this indicated robust species-specific dicodon tendencies. To test another form of codon replacement we isolated SEIP from human and the jellyfish green fluorescent protein (GFP) and we then re-constructed the GFP coding DNA with human tetra-peptide-coding sequences. Results provide proof-of-principle that SEIP may be used to reveal differences in the properties of coding DNA and to reconstruct in pieces a protein coding DNA with sequences from a different organism, the latter might be exploited in heterologous protein expression. PMID:23861567

  6. Analysis of Peptides and Proteins in Their Binding to GroEL

    PubMed Central

    Li, Yali; Zheng, Zhida; Ramsey, Andrew; Chen, Lingling

    2010-01-01

    The GroEL-GroES is an essential molecular chaperon system that assists protein folding in cell. Binding of various substrate proteins to GroEL is one of the key aspects in GroEL-assisted protein folding. Small peptides may mimic segments of the substrate proteins in contact with GroEL, and allow detailed structural analysis of the interactions. A model peptide SBP has been shown to bind to a region in GroEL that is important for binding of substrate proteins. Here, we investigated whether the observed GroEL-SBP interaction represented those of GroEL-substrate proteins, and whether SBP was able to mimic various aspects of substrate proteins in GroE-assisted protein folding cycle. We found that SBP competed with substrate proteins, including α-lactalbumin, rhodanese, and malate dehydrogenase, in binding to GroEL. SBP stimulated GroEL ATP hydrolysis rate in a manner similar to that of α-lactalbumin. SBP did not prevent GroES from binding to GroEL, and GroES association reduced the ATPase rates of GroEL/SBP and GroEL/α-lactalbumin to a comparable extent. Binding of both SBP and α-lactalbumin to apo GroEL was dominated by hydrophobic interaction. Interestingly, association of α-lactalbumin to GroEL/GroES was thermodynamically distinct from that to GroEL with reduced affinity and decreased contribution from hydrophobic interaction. However, SBP did not display such differential binding behaviors to apo GroEL and GroEL/GroES, likely due to the lack of a contiguous polypeptide chain that links all of the bound peptide fragments. Nevertheless, studies using peptides provide valuable information on the nature of GroEL-substrate protein interaction, which is central to understand the mechanism of GroEL-assisted protein folding. PMID:20814869

  7. Analysis and prediction of affinity of TAP binding peptides using cascade SVM.

    PubMed

    Bhasin, Manoj; Raghava, G P S

    2004-03-01

    The generation of cytotoxic T lymphocyte (CTL) epitopes from an antigenic sequence involves number of intracellular processes, including production of peptide fragments by proteasome and transport of peptides to endoplasmic reticulum through transporter associated with antigen processing (TAP). In this study, 409 peptides that bind to human TAP transporter with varying affinity were analyzed to explore the selectivity and specificity of TAP transporter. The abundance of each amino acid from P1 to P9 positions in high-, intermediate-, and low-affinity TAP binders were examined. The rules for predicting TAP binding regions in an antigenic sequence were derived from the above analysis. The quantitative matrix was generated on the basis of contribution of each position and residue in binding affinity. The correlation of r = 0.65 was obtained between experimentally determined and predicted binding affinity by using a quantitative matrix. Further a support vector machine (SVM)-based method has been developed to model the TAP binding affinity of peptides. The correlation (r = 0.80) was obtained between the predicted and experimental measured values by using sequence-based SVM. The reliability of prediction was further improved by cascade SVM that uses features of amino acids along with sequence. An extremely good correlation (r = 0.88) was obtained between measured and predicted values, when the cascade SVM-based method was evaluated through jackknife testing. A Web service, TAPPred (http://www.imtech.res.in/raghava/tappred/ or http://bioinformatics.uams.edu/mirror/tappred/), has been developed based on this approach. PMID:14978300

  8. Structural analysis of peptide fragments following the hydrolysis of bovine serum albumin by trypsin and chymotrypsin.

    PubMed

    Özyiğit, İbrahim Ethem; Akten, E Demet; Pekcan, Önder

    2016-05-01

    Peptide bond hydrolysis of bovine serum albumin (BSA) by chymotrypsin and trypsin was investigated by employing time-resolved fluorescence spectroscopy. As a fluorescent cross-linking reagent, N-(1-pyrenyl) maleimide (PM) was attached to BSA, through all free amine groups of arginine, lysine, and/or single free thiol (Cys34). Time-resolved fluorescence spectroscopy was used to monitor fluorescence decays analyzed by exponential series method to obtain the changes in lifetime distributions. After the exposure of synthesized protein substrate PM-BSA to chymotrypsin and trypsin, it is observed that each protease produced a distinct change in the lifetime distribution profile, which was attributed to distinct chemical environments created by short peptide fragments in each hydrolysate. The persistence of excimer emission at longer lifetime regions for chymotrypsin, as opposed to trypsin, suggested the presence of small-scale hydrophobic clusters that might prevent some excimers from being completely quenched. It is most likely that the formation of these clusters is due to hydrophobic end groups of peptide fragments in chymotrypsin hydrolysate. A similar hydrophobic shield was not suggested for trypsin hydrolysis, as the end groups of peptide fragments would be either arginine or lysine. Overall, in case the target protein's 3D structure is known, the structural analysis of possible excimer formation presented here can be used as a tool to explain the differences in activity between two proteases, i.e. the peak's intensity and location in the profile. Furthermore, this structural evaluation might be helpful in obtaining the optimum experimental conditions in order to generate the highest amount of PM-BSA complexes. PMID:26169062

  9. Porcine MAP3K5 analysis: molecular cloning, characterization, tissue expression pattern, and copy number variations associated with residual feed intake.

    PubMed

    Pu, L; Zhang, L C; Zhang, J S; Song, X; Wang, L G; Liang, J; Zhang, Y B; Liu, X; Yan, H; Zhang, T; Yue, J W; Li, N; Wu, Q Q; Wang, L X

    2016-01-01

    Mitogen-activated protein kinase kinase kinase 5 (MAP3K5) is essential for apoptosis, proliferation, differentiation, and immune responses, and is a candidate marker for residual feed intake (RFI) in pig. We cloned the full-length cDNA sequence of porcine MAP3K5 by rapid-amplification of cDNA ends. The 5451-bp gene contains a 5'-untranslated region (UTR) (718 bp), a coding region (3738 bp), and a 3'-UTR (995 bp), and encodes a peptide of 1245 amino acids, which shares 97, 99, 97, 93, 91, and 84% sequence identity with cattle, sheep, human, mouse, chicken, and zebrafish MAP3K5, respectively. The deduced MAP3K5 protein sequence contains two conserved domains: a DUF4071 domain and a protein kinase domain. Phylogenetic analysis showed that porcine MAP3K5 forms a separate branch to vicugna and camel MAP3K5. Tissue expression analysis using real-time quantitative polymerase chain reaction (qRT-PCR) revealed that MAP3K5 was expressed in the heart, liver, spleen, lung, kidney, muscle, fat, pancrea, ileum, and stomach tissues. Copy number variation was detected for porcine MAP3K5 and validated by qRT-PCR. Furthermore, a significant increase in average copy number was detected in the low RFI group when compared to the high RFI group in a Duroc pig population. These results provide useful information regarding the influence of MAP3K5 on RFI in pigs. PMID:27525933

  10. Homogenization of soil properties map by Principal Component Analysis

    NASA Astrophysics Data System (ADS)

    Valverde Arias, Omar; Garrido, Alberto; Villeta, Maria; Tarquis, Ana Maria

    2016-04-01

    It is widely known that extreme climatic phenomena occur with more intensity and frequency. This fact has put more pressure over farming, becoming very important to implement agriculture risk management policies by governments and institutions. One of the main strategies is transfer risk by agriculture insurance. Agriculture insurance based in indexes has gained importance in the last decade. And consist in a comparison between measured index values with a defined threshold that triggers damage losses. However, based index insurance could not be based on an isolated measurement. It is necessary to be integrated in a complete monitoring system that uses many sources of information and tools. For example, index influence areas, crop production risk maps, crop yields, claim statistics, and so on. To establish index influence area is necessary to have a secondary information that show us homogeneous climatic and soil areas, which inside of each homogeneous classes, index measurements on crops of interest are going to be similar, and in this way reduce basis risk. But it is necessary an efficient method to accomplish this aim, to get homogeneous areas that not depends on only in expert criteria and that could be widely used, for this reason this study asses two conventional agricultural and geographic methods (control and climatic maps) based in expert criteria, and one classical statistical method of multi-factorial analysis (factorial map), all of them to homogenize soil and climatic characteristics. Resulting maps were validated by agricultural and spatial analysis, obtaining very good results in statistical method (Factorial map) that proves to be an efficient and accuracy method that could be used for similar porpoises.

  11. Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays

    PubMed Central

    Ghorbani, Sarieh; Lin, Yao-Cheng; Parizot, Boris; Fernandez, Ana; Njo, Maria Fransiska; Van de Peer, Yves; Beeckman, Tom; Hilson, Pierre

    2015-01-01

    Plant genomes encode numerous small secretory peptides (SSPs) whose functions have yet to be explored. Based on structural features that characterize SSP families known to take part in postembryonic development, this comparative genome analysis resulted in the identification of genes coding for oligopeptides potentially involved in cell-to-cell communication. Because genome annotation based on short sequence homology is difficult, the criteria for the de novo identification and aggregation of conserved SSP sequences were first benchmarked across five reference plant species. The resulting gene families were then extended to 32 genome sequences, including major crops. The global phylogenetic pattern common to the functionally characterized SSP families suggests that their apparition and expansion coincide with that of the land plants. The SSP families can be searched online for members, sequences and consensus (http://bioinformatics.psb.ugent.be/webtools/PlantSSP/). Looking for putative regulators of root development, Arabidopsis thaliana SSP genes were further selected through transcriptome meta-analysis based on their expression at specific stages and in specific cell types in the course of the lateral root formation. As an additional indication that formerly uncharacterized SSPs may control development, this study showed that root growth and branching were altered by the application of synthetic peptides matching conserved SSP motifs, sometimes in very specific ways. The strategy used in the study, combining comparative genomics, transcriptome meta-analysis and peptide functional assays in planta, pinpoints factors potentially involved in non-cell-autonomous regulatory mechanisms. A similar approach can be implemented in different species for the study of a wide range of developmental programmes. PMID:26195730

  12. Design and analysis of structure-activity relationship of novel antimicrobial peptides derived from the conserved sequence of cecropin.

    PubMed

    Hao, Gang; Shi, Yong-Hui; Han, Jing-Hui; Li, Qi-Hui; Tang, Ya-Li; Le, Guo-Wei

    2008-03-01

    We have de novo designed four antimicrobial peptides AMP-A/B/C/D, the 51-residues peptides, which are based on the conserved sequence of cecropin. In the present study, the four peptides were chemically synthesized and their activities assayed. Their secondary structure, amphipathic property, electric field distribution and transmembrane domain were subsequently predicted by bioinformatics tools. Finally, the structure-activity relationship was analyzed from the results of activity experiments and prediction. The results of activity experiments indicated that AMP-B/C/D clearly possessed excellent broad-spectrum activity against bacteria, whereas AMP-A was almost inactive against most of the bacterial strains tested. AMP-B/C/D showed more potent activity against Gram-positive bacteria than against Gram-negative bacteria. By utilizing bioinformatics analysis tools, we found that the secondary structure of the four cation peptides was mainly alpha-helix, and the result of CD spectrum also displayed that all the peptides had considerable alpha-helix in the presence of either 50% TFE or SDS micelles. AMP-C showed much better activity than other peptides against most of the bacteria tested, owing to its remarkable cation property and the amphipathic character of its N-terminal. The study of structure-activity relationship of the designed peptides confirmed that amphipathic structure and high net positive charge were prerequisites for maintaining their activities. PMID:17929330

  13. Isolation and sequence analysis of peptides from the skin secretion of the Middle East tree frog Hyla savignyi.

    PubMed

    Langsdorf, Markus; Ghassempour, Alireza; Römpp, Andreas; Spengler, Bernhard

    2010-12-01

    Novel peptides were identified in the skin secretion of the tree frog Hyla savignyi. Skin secretions were collected by mild electrical stimulation. Peptides were separated by reversed-phase high-performance liquid chromatography. Mass spectra were acquired by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), and fragment ion spectra were obtained after collision-induced dissociation and electron capture dissociation. Peptides were analyzed by manual de novo sequencing and composition-based sequencing (CBS). Sequence analyses of three so far undescribed, structurally unrelated peptides are presented in this paper, having the sequences DDSEEEEVE-OH, P*EEVEEERJK-OH, and GJJDPJTGJVGGJJ-NH(2). The glutamate-rich sequences are assumed to be acidic spacer peptides of the prepropeptide. One of these peptides contains the modified amino acid hydroxyproline, as identified and localized by high-accuracy FTICR-MS. Combination of CBS and of experience-based manual sequence analysis as complementary and database-independent sequencing strategies resulted in peptide identification with high reliability. PMID:20835817

  14. A frequency domain analysis of spatial organization of epicardial maps.

    PubMed

    Sih, H J; Sahakian, A V; Arentzen, C E; Swiryn, S

    1995-07-01

    Mapping of organized rhythms like sinus rhythm uses activation times from individual electrograms, and often assumes that the map for a single activation is similar to maps for subsequent activations. However, during fibrillation, activation times and electrograms are not easy to define, and maps change from activation to activation. Volume and complexity of data make analysis of more than a few seconds of fibrillation difficult. Magnitude Squared Coherence (MSC), a frequency domain measure of the phase consistency between two signals, can be used to help interpret longer data segments without defining activation times or electrograms. Sinus rhythm, flutter, and fibrillation in humans and swine were mapped with an array of unipolar electrodes (2.5 mm apart) at 240 sites on the atrial or ventricular epicardium. Four-second data segments were analyzed. One site near the center of the array was chosen ad hoc as a reference. MSC maps were made by measuring mean MSC from 0-50 Hz between every point in the array relative to the reference. Isocoherence contours were drawn. The effects of bias in the coherence estimate due to misalignment were investigated. Average MSC versus distance from the reference was measured for all rhythms. Results indicate that in a 4-s segment of fibrillation, there can exist some phase consistency between one site and the reference and little or none between a second site and the reference even when both sites are equidistant from the reference. In fibrillation, isocoherence contours are elongated and irregularly shaped, reflecting long-term, but nonuniform, spatial organization. That is, activation during fibrillation cannot be considered as random over a 4-s interval. Bias in the coherence estimate due to misalignment is significant for sinus rhythm and flutter, but can be corrected by manual realignment. Average MSC drops with distance for all rhythms, being most pronounced for fibrillation, MSC maps may provide insights into long

  15. Protein separation and characterization by np-RP-HPLC followed by intact MALDI-TOF mass spectrometry and peptide mass mapping analyses

    PubMed Central

    Dauly, Claire; Perlman, David H.; Costello, Catherine E.; McComb, Mark E.

    2008-01-01

    Due to their complexity, the separation of intact proteins from complex mixtures is an important step to comparative proteomics and the identification and characterization of the proteins by mass spectrometry (MS). In the study reported, we evaluated the use of non-porous-reversed-phase (np-RP) HPLC for intact protein separation prior to MS analyses. The separation system was characterized and compared to 1D-SDS-PAGE electrophoresis in terms of resolution and sensitivity. We demonstrate that np-RP HPLC protein separation is highly reproducible and provides intact protein fractions which can be directly analyzed by MALDI-TOF MS for intact molecular weight determination. An in-well digestion protocol was developed, allowing for rapid protein identification by peptide mass fingerprinting (PMF) and resulted in comparable or improved peptide recovery compared with in-gel digestion. The np-RP sensitivity of detection by UV absorbance at 214 nm for intact proteins was at the low ng level and the sensitivity of peptide analysis by MALDI-TOF MS was in the 10–50 pg level. A membrane protein fraction was characterized to demonstrate application of this methodology. Among the identified proteins, multiple forms of vimentin were observed. Overall we demonstrate that np-RP HPLC followed by MALDI-TOF MS allows for rapid, sensitive and reproducible protein fractionation and very specific protein characterization by integration of PMF analysis with MS intact molecular weight information. PMID:16823977

  16. Analysis of peptides synthesized in the presence of SAz-1 montmorillonite and Cu(2+) exchanged hectorite.

    PubMed

    Porter, T L; Eastman, M P; Bain, E; Begay, S

    2001-07-01

    We have investigated the synthesis of oligopeptides containing glycine and tyrosine in the presence of the clay minerals montmorillonite (non-exchanged, SAz-1) and Cu(2+) exchanged hectorite. In both cases, homopolymers of the two amino acids are formed, as are mixed peptides. In the case of Cu(2+) hectorite, mixed oligopeptides up to trimers are detected in small amounts. For montmorillonite, heterogeneous oligopeptides up to hexamers are detected. Our experiments indicate montmorillonite is more effective in promoting oligopeptide formation than Cu(2+) hectorite. Analysis of the oligopeptide sequences formed on the montmorillonite surfaces indicates preferential synthesis of certain Gly-Tyr sequences over others. PMID:11429201

  17. Theoretical conformational analysis of the bovine adrenal medulla 12 residue peptide molecule

    NASA Astrophysics Data System (ADS)

    Akhmedov, N. A.; Tagiyev, Z. H.; Hasanov, E. M.; Akverdieva, G. A.

    2003-02-01

    The spatial structure and conformational properties of the bovine adrenal medulla 12 residue peptide Tyr1-Gly2-Gly3-Phe4-Met5-Arg6-Arg7-Val8-Gly9-Arg10-Pro11-Glu12 (BAM-12P) molecule were studied by theoretical conformational analysis. It is revealed that this molecule can exist in several stable states. The energy and geometrical parameters for the low-energy conformations are obtained. The conformationally rigid and labile segments of this molecule were revealed.

  18. Exploratory data analysis using set operations and ordinal mapping.

    PubMed

    Churches, Tim

    2003-05-01

    Exploratory data analysis requires the ability to issue ad hoc queries to filter and summarise data sets. As the sizes of health data sets grow, traditional methods of processing data have difficulty in providing acceptable response times for such queries. An alternative method is described which combines complete vertical partitioning of data with set operations on ordinal mappings (SOOM). An initial implementation of the technique provides significantly better performance than a conventional SQL database on typical exploratory data analysis queries. The use of parallel, distributed computation to further increase the performance of the technique appears to be feasible. PMID:12725961

  19. Analysis of gene expression data using self-organizing maps.

    PubMed

    Törönen, P; Kolehmainen, M; Wong, G; Castrén, E

    1999-05-21

    DNA microarray technologies together with rapidly increasing genomic sequence information is leading to an explosion in available gene expression data. Currently there is a great need for efficient methods to analyze and visualize these massive data sets. A self-organizing map (SOM) is an unsupervised neural network learning algorithm which has been successfully used for the analysis and organization of large data files. We have here applied the SOM algorithm to analyze published data of yeast gene expression and show that SOM is an excellent tool for the analysis and visualization of gene expression profiles. PMID:10371154

  20. Lassa fever virus peptides predicted by computational analysis induce epitope-specific cytotoxic-T-lymphocyte responses in HLA-A2.1 transgenic mice.

    PubMed

    Boesen, Agnieszka; Sundar, Krishnan; Coico, Richard

    2005-10-01

    Lassa fever is a hemorrhagic disease caused by Lassa fever virus (LV). Although the precise host defense mechanism(s) that affords protection against LV is not completely understood, cellular immunity mediated by cytotoxic T lymphocytes (CTLs) plays a pivotal role in controlling viral replication and LV infection. To date, there have been no reports mapping major histocompatibility complex (MHC) class I-binding CTL epitopes for LV. Using computer-assisted algorithms, we identified five HLA-A2.1-binding peptides of LV glycoprotein (GP) and two peptides from LV nucleoprotein (NP). Synthesized peptides were examined for their ability to bind to MHC class I molecules using a flow cytometric assay that measures peptide stabilization of class I. Three of the LV-GP peptides tested (LLGTFTWTL, SLYKGVYEL, and YLISIFLHL) stabilized HLA-A2. The LV-NP peptides tested failed to stabilize this HLA-A2. We then investigated the ability of the HLA-A2-binding LV-GP peptides to generate peptide-specific CTLs in HLA-A2.1 transgenic mice. Functional assays used to confirm CTL activation included gamma interferon enzyme-linked immunospot (ELISPOT) assays and intracellular cytokine staining of CD8+ T cells from peptide-primed mice. CTL assays were also performed to verify the cytolytic activity of peptide-pulsed target cells. Each of the LV-GP peptides induced CTL responses in HLA-A2-transgenic mice. MHC class I tetramers prepared using one LV-GP peptide that showed the highest cytolytic index (LLGTFTWTL) confirmed that peptide-binding CD8+ T cells were present in pooled lymphocytes harvested from peptide-primed mice. These findings provide direct evidence for the existence of LV-derived GP epitopes that may be useful in the development of protective immunogens for this hemorrhagic virus. PMID:16210487

  1. Lassa Fever Virus Peptides Predicted by Computational Analysis Induce Epitope-Specific Cytotoxic-T-Lymphocyte Responses in HLA-A2.1 Transgenic Mice

    PubMed Central

    Boesen, Agnieszka; Sundar, Krishnan; Coico, Richard

    2005-01-01

    Lassa fever is a hemorrhagic disease caused by Lassa fever virus (LV). Although the precise host defense mechanism(s) that affords protection against LV is not completely understood, cellular immunity mediated by cytotoxic T lymphocytes (CTLs) plays a pivotal role in controlling viral replication and LV infection. To date, there have been no reports mapping major histocompatibility complex (MHC) class I-binding CTL epitopes for LV. Using computer-assisted algorithms, we identified five HLA-A2.1-binding peptides of LV glycoprotein (GP) and two peptides from LV nucleoprotein (NP). Synthesized peptides were examined for their ability to bind to MHC class I molecules using a flow cytometric assay that measures peptide stabilization of class I. Three of the LV-GP peptides tested (LLGTFTWTL, SLYKGVYEL, and YLISIFLHL) stabilized HLA-A2. The LV-NP peptides tested failed to stabilize this HLA-A2. We then investigated the ability of the HLA-A2-binding LV-GP peptides to generate peptide-specific CTLs in HLA-A2.1 transgenic mice. Functional assays used to confirm CTL activation included gamma interferon enzyme-linked immunospot (ELISPOT) assays and intracellular cytokine staining of CD8+ T cells from peptide-primed mice. CTL assays were also performed to verify the cytolytic activity of peptide-pulsed target cells. Each of the LV-GP peptides induced CTL responses in HLA-A2-transgenic mice. MHC class I tetramers prepared using one LV-GP peptide that showed the highest cytolytic index (LLGTFTWTL) confirmed that peptide-binding CD8+ T cells were present in pooled lymphocytes harvested from peptide-primed mice. These findings provide direct evidence for the existence of LV-derived GP epitopes that may be useful in the development of protective immunogens for this hemorrhagic virus. PMID:16210487

  2. Mapping photoautotrophic metabolism with isotopically nonstationary (13)C flux analysis.

    PubMed

    Young, Jamey D; Shastri, Avantika A; Stephanopoulos, Gregory; Morgan, John A

    2011-11-01

    Understanding in vivo regulation of photoautotrophic metabolism is important for identifying strategies to improve photosynthetic efficiency or re-route carbon fluxes to desirable end products. We have developed an approach to reconstruct comprehensive flux maps of photoautotrophic metabolism by computational analysis of dynamic isotope labeling measurements and have applied it to determine metabolic pathway fluxes in the cyanobacterium Synechocystis sp. PCC6803. Comparison to a theoretically predicted flux map revealed inefficiencies in photosynthesis due to oxidative pentose phosphate pathway and malic enzyme activity, despite negligible photorespiration. This approach has potential to fill important gaps in our understanding of how carbon and energy flows are systemically regulated in cyanobacteria, plants, and algae. PMID:21907300

  3. Adapting and testing a portable Raman spectrometer for SERS analysis of amino acids and small peptides

    NASA Astrophysics Data System (ADS)

    Brambilla, A.; Philippidis, A.; Nevin, A.; Comelli, D.; Valentini, G.; Anglos, D.

    2013-07-01

    Surface-Enhanced Raman Spectroscopy (SERS), a powerful spectrochemical technique enabling highly sensitive analysis of organic and biological materials, is investigated for applications in the analysis of archaeological materials including in situ screening. In this work, a compact mobile Raman spectrometer is employed for acquiring Surface-Enhanced Raman spectra from natural amino acids (L-Arg, L-Phe, L-Met) and a tripeptide (Glutathione), adsorbed on silver colloids. The detection limits of the portable Raman spectrometer, together with an optimization of sample preparation and experimental parameters, are reported. The collection and interpretation of SER spectra of amino acids and peptides is a starting point for the optimization of the instrumentation and its application in the study of more complex biological molecules in the context of detection and analysis of archaeological materials and residues.

  4. Why Map Issues? On Controversy Analysis as a Digital Method

    PubMed Central

    2015-01-01

    This article takes stock of recent efforts to implement controversy analysis as a digital method in the study of science, technology, and society (STS) and beyond and outlines a distinctive approach to address the problem of digital bias. Digital media technologies exert significant influence on the enactment of controversy in online settings, and this risks undermining the substantive focus of controversy analysis conducted by digital means. To address this problem, I propose a shift in thematic focus from controversy analysis to issue mapping. The article begins by distinguishing between three broad frameworks that currently guide the development of controversy analysis as a digital method, namely, demarcationist, discursive, and empiricist. Each has been adopted in STS, but only the last one offers a digital “move beyond impartiality.” I demonstrate this approach by analyzing issues of Internet governance with the aid of the social media platform Twitter. PMID:26336325

  5. Two-dimensional nuclear magnetic resonance analysis of a labeled peptide bound to a class II major histocompatibility complex molecule.

    PubMed

    Driscoll, P C; Altman, J D; Boniface, J J; Sakaguchi, K; Reay, P A; Omichinski, J G; Appella, E; Davis, M M

    1993-07-20

    The formation of peptide/major histocompatibility complex (MHC) complexes and their subsequent recognition by T cells is a pivotal event in the initiation of an immune response. While X-ray crystal structures are now available for class I MHC/peptide complexes, little detailed structural information is known about the class II MHC equivalent, and there are no solution structure data for either. A 16 amino acid residue moth cytochrome c peptide (residues 88 to 103) was 13C-labeled for two-dimensional isotope-edited NMR analysis. The peptide was labeled either selectively in the methyl groups of alanine residues or uniformly at every carbon position, and bound to unlabeled soluble mouse I-Ek class II MHC molecules. Although alpha-helical in the native cytochrome c protein and with no uniform structure in solution, the peptide is bound to the I-Ek molecule with the alpha-carbon atoms of the 11 C-terminal residues held in the binding groove. This indicates that the class II MHC peptide binding site is somewhat larger than that of class I MHC molecules (> or = 11 amino acid residues versus 8 to 10 amino acid residues), consistent with recent data on eluted peptides. Despite the large size of the complex (approximately 70 kDa), nuclear Overhauser effects are clearly detectable between peptide side-chains and the MHC molecule. Indications of the buried or exposed nature of particular side-chains within the bound peptide are derived from the NMR data and these are used together with information from previous biological studies to propose a crude model of the interaction of the peptide with the groove of the MHC molecule. We find no evidence for a conformational change in the peptide/MHC complex in the spectra at pH 5.0 versus pH 7.0, despite a 40-fold faster on-rate for the peptide at the lower pH value. PMID:8393933

  6. A LiDAR based analysis of hydraulic hazard mapping

    NASA Astrophysics Data System (ADS)

    Cazorzi, F.; De Luca, A.; Checchinato, A.; Segna, F.; Dalla Fontana, G.

    2012-04-01

    Mapping hydraulic hazard is a ticklish procedure as it involves technical and socio-economic aspects. On the one hand no dangerous areas should be excluded, on the other hand it is important not to exceed, beyond the necessary, with the surface assigned to some use limitations. The availability of a high resolution topographic survey allows nowadays to face this task with innovative procedures, both in the planning (mapping) and in the map validation phases. The latter is the object of the present work. It should be stressed that the described procedure is proposed purely as a preliminary analysis based on topography only, and therefore does not intend in any way to replace more sophisticated analysis methods requiring based on hydraulic modelling. The reference elevation model is a combination of the digital terrain model and the digital building model (DTM+DBM). The option of using the standard surface model (DSM) is not viable, as the DSM represents the vegetation canopy as a solid volume. This has the consequence of unrealistically considering the vegetation as a geometric obstacle to water flow. In some cases the topographic model construction requires the identification and digitization of the principal breaklines, such as river banks, ditches and similar natural or artificial structures. The geometrical and topological procedure for the validation of the hydraulic hazard maps is made of two steps. In the first step the whole area is subdivided into fluvial segments, with length chosen as a reasonable trade-off between the need to keep the hydrographical unit as complete as possible, and the need to separate sections of the river bed with significantly different morphology. Each of these segments is made of a single elongated polygon, whose shape can be quite complex, especially for meandering river sections, where the flow direction (i.e. the potential energy gradient associated to the talweg) is often inverted. In the second step the segments are analysed

  7. Children's Understanding of Large-Scale Mapping Tasks: An Analysis of Talk, Drawings, and Gesture

    ERIC Educational Resources Information Center

    Kotsopoulos, Donna; Cordy, Michelle; Langemeyer, Melanie

    2015-01-01

    This research examined how children represent motion in large-scale mapping tasks that we referred to as "motion maps". The underlying mathematical content was transformational geometry. In total, 19 children, 8- to 10-year-old, created motion maps and captured their motion maps with accompanying verbal description digitally. Analysis of…

  8. Saturation of an Intra-Gene Pool Linkage Map: Towards a Unified Consensus Linkage Map for Fine Mapping and Synteny Analysis in Common Bean

    PubMed Central

    Galeano, Carlos H.; Fernandez, Andrea C.; Franco-Herrera, Natalia; Cichy, Karen A.; McClean, Phillip E.; Vanderleyden, Jos; Blair, Matthew W.

    2011-01-01

    Map-based cloning and fine mapping to find genes of interest and marker assisted selection (MAS) requires good genetic maps with reproducible markers. In this study, we saturated the linkage map of the intra-gene pool population of common bean DOR364×BAT477 (DB) by evaluating 2,706 molecular markers including SSR, SNP, and gene-based markers. On average the polymorphism rate was 7.7% due to the narrow genetic base between the parents. The DB linkage map consisted of 291 markers with a total map length of 1,788 cM. A consensus map was built using the core mapping populations derived from inter-gene pool crosses: DOR364×G19833 (DG) and BAT93×JALO EEP558 (BJ). The consensus map consisted of a total of 1,010 markers mapped, with a total map length of 2,041 cM across 11 linkage groups. On average, each linkage group on the consensus map contained 91 markers of which 83% were single copy markers. Finally, a synteny analysis was carried out using our highly saturated consensus maps compared with the soybean pseudo-chromosome assembly. A total of 772 marker sequences were compared with the soybean genome. A total of 44 syntenic blocks were identified. The linkage group Pv6 presented the most diverse pattern of synteny with seven syntenic blocks, and Pv9 showed the most consistent relations with soybean with just two syntenic blocks. Additionally, a co-linear analysis using common bean transcript map information against soybean coding sequences (CDS) revealed the relationship with 787 soybean genes. The common bean consensus map has allowed us to map a larger number of markers, to obtain a more complete coverage of the common bean genome. Our results, combined with synteny relationships provide tools to increase marker density in selected genomic regions to identify closely linked polymorphic markers for indirect selection, fine mapping or for positional cloning. PMID:22174773

  9. C6 Peptide-Based Multiplex Phosphorescence Analysis (PHOSPHAN) for Serologic Confirmation of Lyme Borreliosis

    PubMed Central

    Pomelova, Vera G.; Korenberg, Edward I.

    2015-01-01

    Background A single-tier immunoassay using the C6 peptide of VlsE (C6) from Borrelia burgdorferi sensu stricto (Bb) has been proposed as a potential alternative to conventional two-tier testing for the serologic diagnosis of Lyme disease in the United States and Europe. Objective To evaluate the performance of C6 peptide based multiplex Phosphorescence Analysis (PHOSPHAN) for the serologic confirmation of Lyme borreliosis (LB) in Russian patients. Methods Serum samples (n = 351) were collected from 146 patients with erythema migrans (EM); samples from 131 of these patients were taken several times prior to treatment and at different stages of recovery. The control group consisted of 197 healthy blood donors and 31 patients with other diseases, all from the same highly endemic region of Russia. All samples were analyzed by PHOSPHAN for IgM and IgG to Bb C6, recombinant OspC and VlsE proteins, and C6 peptides from B. garinii and B. afzelii. Results IgM and IgG to Bb C6 were identified in 43 and 95 out of 131 patients (32.8 and 72.5%, respectively); seroconversion of IgM antibodies was observed in about half of the patients (51.2%), and of IgG antibodies, in almost all of them (88.4%). Additional detection of OspC-IgM and VlsE-IgM or IgG to C6 from B. garinii or B. afzelii did not contribute significantly to the overall sensitivity of the multiplex immunoassay. Conclusions The multiplex phosphorescence immunoassay is a promising method for simultaneously revealing the spectrum of antibodies to several Borrelia antigens. Detection of IgM and IgG to Bb C6 in the sera of EM patients provides effective serologic confirmation of LB and, with high probability, indicates an active infection process. PMID:26147441

  10. “Proteomic analysis of peptides tagged with dimedone and related probes”

    PubMed Central

    Martínez-Acedo, Pablo; Gupta, Vinayak; Carroll, Kate S.

    2014-01-01

    Owing to its labile nature, a new role for cysteine sulfenic acid (-SOH) modification has emerged. This oxidative modification modulates protein function by acting as a redox switch during cellular signaling. The identification of proteins that undergo this modification represents a methodological challenge, and its resolution remains a matter of current interest. The development of strategies to chemically modify cysteinyl-containing peptides for LC-MS/MS analysis has increased significantly within the past decade. The method of choice to selectively label sulfenic acid is based on the use of dimedone or its derivatives. For these chemical probes to be effective on a proteome-wide level, their reactivity toward -SOH must be high to ensure reaction completion. In addition, the presence of an adduct should not interfere with electrospray ionization, the efficiency of induced dissociation in MS/MS experiments, or with identification of Cys-modified peptides by automated database searching algorithms. Herein, we employ a targeted proteomics approach to study the electrospray ionization and fragmentation effects of different –SOH specific probes, and compared them to commonly used alkylating agents. We then extend our study to a whole proteome extract using shotgun proteomic approaches. These experiments enable us to demonstrate that dimedone adducts do not interfere with electrospray by suppressing the ionization nor impedes product ion assignment by automated search engines, which detect a + 138 Da increase from unmodified peptides. Collectively, these results suggest dimedone can be a powerful tool to identify sulfenic acid modifications by high-throughput shotgun proteomics of a whole proteome. PMID:24719340

  11. Peptidomic analysis of the extensive array of host-defense peptides in skin secretions of the dodecaploid frog Xenopus ruwenzoriensis (Pipidae).

    PubMed

    Coquet, Laurent; Kolodziejek, Jolanta; Jouenne, Thierry; Nowotny, Norbert; King, Jay D; Conlon, J Michael

    2016-09-01

    The Uganda clawed frog Xenopus ruwenzoriensis with a karyotype of 2n=108 is one of the very few vertebrates with dodecaploid status. Peptidomic analysis of norepinephrine-stimulated skin secretions from this species led to the isolation and structural characterization of 23 host-defense peptides belonging to the following families: magainin (3 peptides), peptide glycine-leucine-amide (PGLa; 6 peptides), xenopsin precursor fragment (XPF; 3 peptides), caerulein precursor fragment (CPF; 8 peptides), and caerulein precursor fragment-related peptide (CPF-RP; 3 peptides). In addition, the secretions contained caerulein, identical to the peptide from Xenopus laevis, and two peptides that were identified as members of the trefoil factor family (TFF). The data indicate that silencing of the host-defense peptide genes following polyploidization has been appreciable and non-uniform. Consistent with data derived from comparison of nucleotide sequences of mitochrondrial and nuclear genes, cladistic analyses based upon the primary structures of the host-defense peptides provide support for an evolutionary scenario in which X. ruwenzoriensis arose from an allopolyploidization event involving an octoploid ancestor of the present-day frogs belonging to the Xenopus amieti species group and a tetraploid ancestor of Xenopus pygmaeus. PMID:27290612

  12. Application of automated multispectral analysis to Delaware's coastal vegetation mapping

    NASA Technical Reports Server (NTRS)

    Klemas, V. (Principal Investigator); Daiber, D.; Bartlett, D. S.; Crichton, O. W.; Fornes, A. O.

    1973-01-01

    There are no author-identified significant results in this report. Overlay maps of Delaware's wetlands have been prepared, showing the dominant species or group of species of vegetation present. Five such categories of vegetation were used indicating marshes dominated by: (1) salt marsh cord grass; (2) salt marsh hay and spike grass; (3) reed grass; (4) high tide bush and sea myrtle; and (5) a group of fresh water species found in impounded areas built to attract water fowl. Fifteen such maps cover Delaware's wetlands from the Pennsylvania to the Maryland borders. The mapping technique employed utilizes the General Electric multispectral data processing system. This system is a hybrid analog-digital system designed as an analysis tool to be used by an operator whose own judgment and knowledge of ground truth can be incorporated at any time into the analyzing process. The result is a high speed, cost effective method for producing enhanced photomaps showing a number of spectral classes, each enhanced spectral class being representative of a vegetative species or group of species.

  13. CAD system for automatic analysis of CT perfusion maps

    NASA Astrophysics Data System (ADS)

    Hachaj, T.; Ogiela, M. R.

    2011-03-01

    In this article, authors present novel algorithms developed for the computer-assisted diagnosis (CAD) system for analysis of dynamic brain perfusion, computer tomography (CT) maps, cerebral blood flow (CBF), and cerebral blood volume (CBV). Those methods perform both quantitative analysis [detection and measurement and description with brain anatomy atlas (AA) of potential asymmetries/lesions] and qualitative analysis (semantic interpretation of visualized symptoms). The semantic interpretation (decision about type of lesion: ischemic/hemorrhagic, is the brain tissue at risk of infraction or not) of visualized symptoms is done by, so-called, cognitive inference processes allowing for reasoning on character of pathological regions based on specialist image knowledge. The whole system is implemented in.NET platform (C# programming language) and can be used on any standard PC computer with.NET framework installed.

  14. AHTPDB: a comprehensive platform for analysis and presentation of antihypertensive peptides

    PubMed Central

    Kumar, Ravi; Chaudhary, Kumardeep; Sharma, Minakshi; Nagpal, Gandharva; Chauhan, Jagat Singh; Singh, Sandeep; Gautam, Ankur; Raghava, Gajendra P.S.

    2015-01-01

    AHTPDB (http://crdd.osdd.net/raghava/ahtpdb/) is a manually curated database of experimentally validated antihypertensive peptides. Information pertaining to peptides with antihypertensive activity was collected from research articles and from various peptide repositories. These peptides were derived from 35 major sources that include milk, egg, fish, pork, chicken, soybean, etc. In AHTPDB, most of the peptides belong to a family of angiotensin-I converting enzyme inhibiting peptides. The current release of AHTPDB contains 5978 peptide entries among which 1694 are unique peptides. Each entry provides detailed information about a peptide like sequence, inhibitory concentration (IC50), toxicity/bitterness value, source, length, molecular mass and information related to purification of peptides. In addition, the database provides structural information of these peptides that includes predicted tertiary and secondary structures. A user-friendly web interface with various tools has been developed to retrieve and analyse the data. It is anticipated that AHTPDB will be a useful and unique resource for the researchers working in the field of antihypertensive peptides. PMID:25392419

  15. A new strategy for site-specific protein modification: analysis of a Tat peptide-TAR RNA interaction.

    PubMed

    Tamilarasu, N; Zhang, J; Hwang, S; Rana, T M

    2001-01-01

    Site-specific modification of proteins and peptides with reporter molecules provides a powerful research tool in chemistry and biology. We report the synthesis and application of a tyrosine analogue, N-alpha-Fmoc-3-acetyl-L-tyrosine, for selective modification of proteins. As a model system, we synthesized the human immunodeficiency virus type 1 (HIV-1) Tat peptide (amino acids 47-56) containing the arginine rich RNA-binding region and replaced the Tyr-47 with 3-acetyl-tyrosine. The acetyl-Tyr-Tat peptide was subsequently labeled with a fluorescein derivative to study RNA-protein interactions by fluorescence energy transfer experiments. Our results showed that the Tat peptide binds to the rhodamine labeled TAR RNA with a dissociation constant (KD) of 1.0 +/- 0.5 nM. This strategy of selective protein modification offers a versatile new procedure for labeling peptides of biological interest at a desired site when several nucleophilic side chains of lysine and cysteine are present. These methods would provide tools for postsynthetic peptide modification and introducing biophysical probes for structural and functional analysis of proteins. PMID:11312672

  16. Stakeholder analysis and mapping as targeted communication strategy.

    PubMed

    Shirey, Maria R

    2012-09-01

    This department highlights change management strategies that may be successful in strategically planning and executing organizational change initiatives. With the goal of presenting practical approaches helpful to nurse leaders advancing organizational change, content includes evidence-based projects, tools, and resources that mobilize and sustain organizational change initiatives. In this article, the author highlights the importance of stakeholder theory and discusses how to apply the theory to conduct a stakeholder analysis. This article also provides an explanation of how to use related stakeholder mapping techniques with targeted communication strategies. PMID:22922747

  17. Membrane-targeting peptides for nanoparticle-facilitated cellular imaging and analysis

    NASA Astrophysics Data System (ADS)

    Breger, Joyce; Delehanty, James B.; Boeneman Gemmill, Kelly; Field, Lauren D.; Blanco-Canosa, Juan B.; Dawson, Philip E.; Huston, Alan L.; Medintz, Igor L.

    2015-03-01

    The controlled delivery of nanomaterials to the plasma membrane is critical for the development of nanoscale probes that can eventually enable cellular imaging and analysis of membrane processes. Chief among the requisite criteria are delivery/targeting modalities that result in the long-term residence (e.g., days) of the nanoparticles on the plasma membrane while simultaneously not interfering with regular cellular physiology and homeostasis. Our laboratory has developed a suite of peptidyl motifs that target semiconductor nanocrystals (quantum dots (QDs) to the plasma membrane where they remain resident for up to three days. Notably, only small a percentage of the QDs are endocytosed over this time course and cellular viability is maintained. This talk will highlight the utility of these peptide-QD constructs for cellular imaging and analysis.

  18. The good, the bad, the ugly: validating the mass spectrometric analysis of modified peptides.

    PubMed

    Beck, Florian; Lewandrowski, Urs; Wiltfang, Matthias; Feldmann, Ingo; Geiger, Jörg; Sickmann, Albert; Zahedi, René Peiman

    2011-03-01

    Mass spectrometric characterization of protein modifications is usually based on single peptides. With the advent of large-scale PTM-focussed MS studies, vast amounts of data are generated continuously, providing biologists extremely valuable and virtually never-ending sources for targeted functional research. However, even more than for proteomics in general, appropriate strategies for quality control of the different steps of the analytical strategy are imperative to prevent functional researchers from doing Sisyphos work on false-positive and unconfident PTM assignments. Here, we describe strategies to address the important issue of quality control for PTM analysis on various levels of the analytical pipeline: sample preparation/processing, analysis/identification and finally data interpretation, for qualitative as well as quantitative studies. PMID:21298789

  19. Transcriptomic Analysis of Neuropeptides and Peptide Hormones in the Barnacle Balanus amphitrite: Evidence of Roles in Larval Settlement

    PubMed Central

    Yan, Xing-Cheng; Chen, Zhang-Fan; Sun, Jin; Matsumura, Kiyotaka; Wu, Rudolf S. S.; Qian, Pei-Yuan

    2012-01-01

    The barnacle Balanus amphitrite is a globally distributed marine crustacean and has been used as a model species for intertidal ecology and biofouling studies. Its life cycle consists of seven planktonic larval stages followed by a sessile juvenile/adult stage. The transitional processes between larval stages and juveniles are crucial for barnacle development and recruitment. Although some studies have been conducted on the neuroanatomy and neuroactive substances of the barnacle, a comprehensive understanding of neuropeptides and peptide hormones remains lacking. To better characterize barnacle neuropeptidome and its potential roles in larval settlement, an in silico identification of putative transcripts encoding neuropeptides/peptide hormones was performed, based on transcriptome of the barnacle B. amphitrite that has been recently sequenced. Potential cleavage sites andstructure of mature peptides were predicted through homology search of known arthropod peptides. In total, 16 neuropeptide families/subfamilies were predicted from the barnacle transcriptome, and 14 of them were confirmed as genuine neuropeptides by Rapid Amplification of cDNA Ends. Analysis of peptide precursor structures and mature sequences showed that some neuropeptides of B. amphitrite are novel isoforms and shared similar characteristics with their homologs from insects. The expression profiling of predicted neuropeptide genes revealed that pigment dispersing hormone, SIFamide, calcitonin, and B-type allatostatin had the highest expression level in cypris stage, while tachykinin-related peptide was down regulated in both cyprids and juveniles. Furthermore, an inhibitor of proprotein convertase related to peptide maturation effectively delayed larval metamorphosis. Combination of real-time PCR results and bioassay indicated that certain neuropeptides may play an important role in cypris settlement. Overall, new insight into neuropeptides/peptide hormones characterized in this study shall

  20. Mechanism of interaction of optimized Limulus-derived cyclic peptides with endotoxins: thermodynamic, biophysical and microbiological analysis

    PubMed Central

    Andrä, Jörg; Howe, Jörg; Garidel, Patrick; Rössle, Manfred; Richter, Walter; Leiva-León, José; Moriyon, Ignacio; Bartels, Rainer; Gutsmann, Thomas; Brandenburg, Klaus

    2007-01-01

    On the basis of formerly investigated peptides corresponding to the endotoxin-binding domain from LALF [Limulus anti-LPS (lipopolysaccharide) factor], a protein from Limulus polyphemus, we have designed and synthesized peptides of different lengths with the aim of obtaining potential therapeutic agents against septic shock syndrome. For an understanding of the mechanisms of action, we performed a detailed physicochemical and biophysical analysis of the interaction of rough mutant LPS with these peptides by applying FTIR (Fourier-transform infrared) spectroscopy, SAXS (small-angle X-ray scattering), calorimetric techniques [DSC (differential scanning calorimetry) and ITC (isothermal titration calorimetry)] and FFTEM (freeze-fracture transmission electron microscopy). Also, the action of the peptides on bacteria of different origin in microbial assays was investigated. Using FTIR and DSC, our results indicated a strong fluidization of the lipid A acyl chains due to peptide binding, with a decrease in the endothermic melting enthalpy change of the acyl chains down to a complete disappearance in the 1:0.5 to 1:2 [LPS]:[peptide] molar ratio range. Via ITC, it was deduced that the binding is a clearly exothermic process which becomes saturated at a 1:0.5 to 1:2 [LPS]:[peptide] molar ratio range. The results obtained with SAXS indicated a drastic change of the aggregate structures of LPS into a multilamellar stack, which was visualized in electron micrographs as hundreds of lamellar layers. This can be directly correlated with the inhibition of the LPS-induced production of tumour necrosis factor α in human mononuclear cells, but not with the action of the peptides on bacteria. PMID:17501719

  1. Mitochondrial DAMPs from femoral reamings activate neutrophils via formyl peptide receptors and P44/42 MAP Kinase

    PubMed Central

    Hauser, Carl J.; Sursal, Tolga; Rodriguez, Edward K.; Appleton, Paul T.; Zhang, Qin; Itagaki, Kiyoshi

    2010-01-01

    Hypothesis Fractures and femoral reaming are associated with lung injury. The mechanisms linking fractures and inflammation are unclear; but tissue disruption might release mitochondria. Mitochondria are evolutionarily derived from bacteria and contain “Damage Associated Molecular Patterns” (DAMPs) like formylated peptides that can activate immunocytes. We therefore studied whether fracture reaming releases mitochondrial DAMPs (MTD) and how MTD act on immune cells. Methods Femur fracture reamings (FFx) from 10 patients were spun to remove bone particulates. Supernatants were assayed for mitochondrial DNA (mtDNA). Mitochondria were isolated from the residual reaming slurry, sonicated and spun at 12,000g. The resultant MTD were assayed for their ability to cause neutrophil (PMN) Ca2+ transient production, p44/42 MAPK phosphorylation, IL-8 release and matrix metalloproteinase-9 (MMP9) release with and without formyl peptide receptor-1 (FPR1) blockade. Rats were injected with MTD and whole lung assayed for p44/42 activation. Results mtDNA appears at many thousand fold normal plasma levels in FFx and at intermediate levels in patients’ plasma, suggesting release from fracture to plasma. FFx MTD caused brisk PMN Ca2+ flux, activated PMN p44/42 MAPK and caused PMN release of IL-8 and MMP9. Responses to MTD were inhibited by FPR1 blockade using Cyclosporin H and anti-FPR1. MTD injection caused P44/42 phosphorylation in rat lung. Conclusions FFx reaming releases mitochondria into the wound and circulation. MTD then activates PMN. Release of damage signals like MTD from FFx may underlie activation of the cytokine cascades known to be associated with facture fixation and lung injury. PMID:20736789

  2. Automated carboxy-terminal sequence analysis of peptides and proteins using diphenyl phosphoroisothiocyanatidate.

    PubMed Central

    Bailey, J. M.; Nikfarjam, F.; Shenoy, N. R.; Shively, J. E.

    1992-01-01

    peptides covalently attached to carboxylic acid-modified polyethylene and proteins (200 pmol to 5 nmol) noncovalently applied to Zitex (porous Teflon). The generality of our automated C-terminal sequencing methodology was examined by sequencing model peptides containing all 20 of the common amino acids. All of the amino acids tested were found to sequence in good yield except for proline, which was found not to be capable of derivatization. In spite of this limitation, the methodology should be a valuable tool for the C-terminal sequence analysis of peptides and proteins.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:1304893

  3. Chemical genetic analysis reveals the effects of NMU2R on the expression of peptide hormones.

    PubMed

    Fang, Liyan; Zhang, Mancang; Li, Chunxia; Dong, Suzhen; Hu, Yinghe

    2006-08-14

    Neuromedin U 2 receptor (NMU2R) plays important roles for the regulation of food intake and body weight. However, the molecular mechanism underlying the action of NMU2R has not been clearly defined. We have taken chemical genetic approach to examine the involvement of peptides in the regulation of NMU2R effects. A cell-based reporter gene assay has been developed and used for the screening of human NMU2R agonist. Three natural product compounds, EUK2010, EUK2011 and EUK2012, were identified that could activate the reporter gene expression in the cell-based functional assay. Although these compounds showed high EC50 at hundreds micro-molar range, in vitro pharmacological analysis suggested that they were specific agonists for the human NMU2R. The natural compounds could decrease food intake and lead to the reduction of body weight in different animal models. To understand the molecular basis of the NMU2R regulation of food intake and body weight, we examined the expression of a number of key genes in hypothalamus and adipose tissues after oral administration of EUK2010 in mice. Our results demonstrated that the expression levels of a number of neuropeptide genes were altered after the treatment of EUK2010. Interestingly, EUK2010 increased the expression of Leptin in white fat. These results suggested that these peptides may participate in the regulation of NMU2R effects in mice. PMID:16781063

  4. Combined autoradiographic-immunocytochemical analysis of opioid receptors and opioid peptide neuronal systems in brain

    SciTech Connect

    Lewis, M.E.; Khachaturian, H.; Watson, S.J.

    1985-01-01

    Using adjacent section autoradiography-immunocytochemistry, the distribution of (TH)naloxone binding sites was studied in relation to neuronal systems containing (Leu)enkephalin, dynorphin A, or beta-endorphin immunoreactivity in rat brain. Brain sections from formaldehyde-perfused rats show robust specific binding of (TH)naloxone, the pharmacological (mu-like) properties of which appear unaltered. In contrast, specific binding of the delta ligand (TH)D-Ala2,D-Leu5-enkephalin was virtually totally eliminated as a result of formaldehyde perfusion. Using adjacent section analysis, the authors have noted associations between (TH)naloxone binding sites and one, two, or all three opioid systems in different brain regions; however, in some areas, no apparent relationship could be observed. Within regions, the relationship was complex. The complexity of the association between (TH)naloxone binding sites and the multiple opioid systems, and previous reports of co-localization of mu and kappa receptors in rat brain, are inconsistent with a simple-one-to-one relationship between a given opioid precursor and opioid receptor subtype. Instead, since differential processing of the three precursors gives rise to peptides of varying receptor subtype potencies and selectivities, the multiple peptide-receptor relationships may point to a key role of post-translational processing in determining the physiological consequences of opioid neurotransmission.

  5. Frames of reference for helicopter electronic maps - The relevance of spatial cognition and componential analysis

    NASA Technical Reports Server (NTRS)

    Harwood, Kelly; Wickens, Christopher D.

    1991-01-01

    Computer-generated map displays for NOE and low-level helicopter flight were formed according to prior research on maps, navigational problem solving, and spatial cognition in large-scale environments. The north-up map emphasized consistency of object location, wheareas, the track-up map emphasized map-terrain congruency. A component analysis indicates that different cognitive components, e.g., orienting and absolute object location, are supported to varying degrees by properties of different frames of reference.

  6. Large areas elemental mapping by ion beam analysis techniques

    NASA Astrophysics Data System (ADS)

    Silva, T. F.; Rodrigues, C. L.; Curado, J. F.; Allegro, P.; Moro, M. V.; Campos, P. H. O. V.; Santos, S. B.; Kajiya, E. A. M.; Rizzutto, M. A.; Added, N.; Tabacniks, M. H.

    2015-07-01

    The external beam line of the Laboratory for Material Analysis with Ion Beams (LAMFI) is a versatile setup for multi-technique analysis. X-ray detectors for Particle Induced X-rays Emission (PIXE) measurements, a Gamma-ray detector for Particle Induced Gamma- ray Emission (PIGE), and a particle detector for scattering analysis, such as Rutherford Backscattering Spectrometry (RBS), were already installed. In this work, we present some results, using a large (60-cm range) XYZ computer controlled sample positioning system, completely developed and build in our laboratory. The XYZ stage was installed at the external beam line and its high spacial resolution (better than 5 μm over the full range) enables positioning the sample with high accuracy and high reproducibility. The combination of a sub-millimeter beam with the large range XYZ robotic stage is being used to produce elemental maps of large areas in samples like paintings, ceramics, stones, fossils, and all sort of samples. Due to its particular characteristics, this is a unique device in the sense of multi-technique analysis of large areas. With the continuous development of the external beam line at LAMFI, coupled to the robotic XYZ stage, it is becoming a robust and reliable option for regular analysis of trace elements (Z > 5) competing with the traditional in-vacuum ion-beam-analysis with the advantage of automatic rastering.

  7. Halvade: scalable sequence analysis with MapReduce

    PubMed Central

    Decap, Dries; Reumers, Joke; Herzeel, Charlotte; Costanza, Pascal; Fostier, Jan

    2015-01-01

    Motivation: Post-sequencing DNA analysis typically consists of read mapping followed by variant calling. Especially for whole genome sequencing, this computational step is very time-consuming, even when using multithreading on a multi-core machine. Results: We present Halvade, a framework that enables sequencing pipelines to be executed in parallel on a multi-node and/or multi-core compute infrastructure in a highly efficient manner. As an example, a DNA sequencing analysis pipeline for variant calling has been implemented according to the GATK Best Practices recommendations, supporting both whole genome and whole exome sequencing. Using a 15-node computer cluster with 360 CPU cores in total, Halvade processes the NA12878 dataset (human, 100 bp paired-end reads, 50× coverage) in <3 h with very high parallel efficiency. Even on a single, multi-core machine, Halvade attains a significant speedup compared with running the individual tools with multithreading. Availability and implementation: Halvade is written in Java and uses the Hadoop MapReduce 2.0 API. It supports a wide range of distributions of Hadoop, including Cloudera and Amazon EMR. Its source is available at http://bioinformatics.intec.ugent.be/halvade under GPL license. Contact: jan.fostier@intec.ugent.be Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25819078

  8. Amplitude-Phase Analysis of Cosmic Microwave Background Maps

    NASA Astrophysics Data System (ADS)

    Novikov, D.; Naselsky, P.; Silk, J.

    We suggest the amplitude-phase analysis (APA) as a new method for the CMB image reconstruction. This method has been adopted for any kind of possible noise in the CMB observational data ( like point sources, dust emission, pixel and radiometer noise and so on). The important advantage of our scheme is that unlike other methods the phase analysis doesn't require any information about the expected CMB power spectra to subtract the noise. The only assumption we made is that the initial cosmological signal has a Gaussian nature. This method is very efficient computationally because it requires only O(Nln (N)) operations, where N is the number of pixels. Therefore, the full advantage of our scheme can be reached on very large data sets. Its efficiency has been successfully tested on simulated signals corresponding to MAP, PLANCK and RATAN-600 angular resolutions. P. Naselsky (TAC, Denmark), I. Novikov (TAC, Denmark)

  9. Analysis of radiotracking data using digitized habitat maps

    USGS Publications Warehouse

    Gilmer, D.S.; Miller, S.E.; Cowardin, L.M.

    1973-01-01

    A method is described that provides a rapid and accurate analysis of habitat used by radio-equipped animals. The digitizer (basically an X-Y plotter in reverse) converts maps into digital form by describing each habitat unit as a polygon that closely approximates the actual shape of the unit. The coordinates of each polygon are then stored on magnetic tape. Habitat classification data and other information are coded and combined with the proper polygon coordinates. This results in one file containing all habitat data. A computer program with inputs of tracking data and habitat data provides a listing of the habitat used by the animals studied. Analysis of habitat used by radio-equipped ducks is demonstrated using this method.

  10. New Mexico Play Fairway Analysis: Particle Tracking ArcGIS Map Packages

    SciTech Connect

    Jeff Pepin

    2015-11-15

    These are map packages used to visualize geochemical particle-tracking analysis results in ArcGIS. It includes individual map packages for several regions of New Mexico including: Acoma, Rincon, Gila, Las Cruces, Socorro and Truth or Consequences.

  11. Photo-Assisted Peptide Enrichment in Protein Complex Cross-Linking Analysis of a Model Homodimeric Protein Using Mass Spectrometry

    PubMed Central

    Yan, Funing; Che, Fa-Yun; Nieves, Edward; Weiss, Louis M.; Angeletti, Ruth H.; Fiser, Andras

    2012-01-01

    Mass spectrometry analysis of cross-linked peptides can be used to probe protein contact sites in macromolecular complexes. We have developed a photo-cleavable cross-linker that enhances peptide enrichment, improving the signal-to-noise ratio of the cross-linked peptides in mass spectrometry analysis. This cross-linker utilizes nitro-benzyl alcohol group that can be cleaved by UV irradiation and is stable during the multiple washing steps used for peptide enrichment. The enrichment method utilizes a cross-linker that aids in eliminating contamination resulting from protein based retrieval systems, and thus, facilitates the identification of cross-linked peptides. Homodimeric pilM protein from Pseudomonas aeruginosa 2192 (pilM) was investigated to test the specificity and experimental conditions. As predicted, the known pair of lysine side chains within 14Å was cross-linked. An unexpected cross-link involving the protein’s amino terminus was also detected. This is consistent with the predicted mobility of the amino terminus that may bring the amino groups within 19Å of one another in solution. These technical improvements allow this method to be used for investigating protein-protein interactions in complex biological samples. PMID:21834138

  12. Develop Advanced Nonlinear Signal Analysis Topographical Mapping System

    NASA Technical Reports Server (NTRS)

    Jong, Jen-Yi

    1997-01-01

    During the development of the SSME, a hierarchy of advanced signal analysis techniques for mechanical signature analysis has been developed by NASA and AI Signal Research Inc. (ASRI) to improve the safety and reliability for Space Shuttle operations. These techniques can process and identify intelligent information hidden in a measured signal which is often unidentifiable using conventional signal analysis methods. Currently, due to the highly interactive processing requirements and the volume of dynamic data involved, detailed diagnostic analysis is being performed manually which requires immense man-hours with extensive human interface. To overcome this manual process, NASA implemented this program to develop an Advanced nonlinear signal Analysis Topographical Mapping System (ATMS) to provide automatic/unsupervised engine diagnostic capabilities. The ATMS will utilize a rule-based Clips expert system to supervise a hierarchy of diagnostic signature analysis techniques in the Advanced Signal Analysis Library (ASAL). ASAL will perform automatic signal processing, archiving, and anomaly detection/identification tasks in order to provide an intelligent and fully automated engine diagnostic capability. The ATMS has been successfully developed under this contract. In summary, the program objectives to design, develop, test and conduct performance evaluation for an automated engine diagnostic system have been successfully achieved. Software implementation of the entire ATMS system on MSFC's OISPS computer has been completed. The significance of the ATMS developed under this program is attributed to the fully automated coherence analysis capability for anomaly detection and identification which can greatly enhance the power and reliability of engine diagnostic evaluation. The results have demonstrated that ATMS can significantly save time and man-hours in performing engine test/flight data analysis and performance evaluation of large volumes of dynamic test data.

  13. Interaction of glycine zipper fragments of Aβ-peptides with neuronal nitric oxide synthase: kinetic, thermodynamic and spectrofluorimetric analysis.

    PubMed

    Padayachee, E R; Whiteley, C G

    2013-06-01

    Five peptide fragments [Aβ(17-21); Aβ(25-29); Aβ(29-33); Aβ(33-37); Aβ(25-37)] of the toxic Aβ(1-40(42)) amyloid peptide were shown to bind with neuronal nitric oxide synthase by means of hydrophobic-hydrophobic forces. The enzyme has a single site for the amyloid peptide binding, which resulted in a quenching of the intrinsic fluorescence of the enzyme. Binding constants determined from Stern-Volmer analysis were between 9×10(-3) and 1.8×10(-2) μM(-1). As temperature increased these binding constants increased reflecting that the interaction of the amyloid peptides with nNOS was endothermic and the quenching was dynamic. Kinetic analysis revealed a non-competitive interaction of the amyloid peptides to the enzyme with inhibitor constants of 5.1 μM for Aβ(17-21) to about 8-12 μM for the other peptides. According to the van't Hoff relationship the thermodynamic parameters, ΔH, ΔS and ΔG for the interaction of the amyloid peptides were all positive and between 41.28 and 77.86 kJ mol(-1)K(-1), 104.92 and 220.82 J mol(-1)K(-1) and 9.92 and 13.13 kJ mol(-1)K(-1), respectively. This suggested that the transition state, created by the amyloid peptide-nNOS complex and generated during the initial stages of Aβ aggregation had to, initially, overcome an activation barrier. Since the ΔG values decreased as temperature increased it not only implied a non-spontaneous interaction but that hydrophobic forces were operative during the binding. By FRET analysis the distance between the donor enzyme and the acceptor amyloid peptide was between 2.7 and 2.8 nm. As the temperature increased from 298 K through 313 K (and higher) the fraction of these tryptophan residues that became exposed increased, to approach a value of 1. There was strong support for the initial interaction being through the glycine zipper regions of Aβ(25-37). PMID:23375441

  14. Epitope mapping of B-cell determinants on the 15-kilodalton lipoprotein of Treponema pallidum (Tpp15) with synthetic peptides.

    PubMed Central

    Baughn, R E; Demecs, M; Taber, L H; Musher, D M

    1996-01-01

    The antigenicity of the 15-kDa lipoprotein of Treponema pallidum (Tpp15 or TpN15) was comprehensively evaluated in epitope-scanning studies with overlapping deca- and octapeptides and polygonal rabbit and human infant immunoglobulins (Igs) and antisera. This approach enabled us to identify potentially important regions and to determine the optimal dilutions of Igs or antisera for use in further studies. IgM and IgG from both species were capable of recognizing multiple, continuous epitopes. A total of 13 peptides, principally clustered in the central regions of the protein, were recognized by all syphilitic sera and Ig fractions. On the basis of window analyses, frequency profiles, and alanine substitution studies, five heptapeptides were selected for mimetic studies. Two of these five immunodominant, continuous epitopes initially appeared to be species specific; however, antisera elicited against mimetics of all five epitopes were polyspecific, recognizing similar motifs on several other treponemal proteins, including those of avirulent organisms. The only mimetic which yielded positive reactions with infant IgM and syphilitic sera in the absence of cross-reactions with rabbit antisera to avirulent treponemes was the variant of the VMYASSG motif. These findings are relevant to the development of simple, inexpensive assays for the serodiagnosis of active syphilis. PMID:8698467

  15. Proteomic Characterization of Helicobacter pylori CagA Antigen Recognized by Child Serum Antibodies and Its Epitope Mapping by Peptide Array

    PubMed Central

    Akada, Junko; Okuda, Masumi; Hiramoto, Narumi; Kitagawa, Takao; Zhang, Xiulian; Kamei, Shuichi; Ito, Akane; Nakamura, Mikiko; Uchida, Tomohisa; Hiwatani, Tomoko; Fukuda, Yoshihiro; Nakazawa, Teruko; Kuramitsu, Yasuhiro; Nakamura, Kazuyuki

    2014-01-01

    Serum antibodies against pathogenic bacteria play immunologically protective roles, and can be utilized as diagnostic markers of infection. This study focused on Japanese child serum antibodies against Helicobacter pylori, a chronically-infected gastric bacterium which causes gastric cancer in adults. Serological diagnosis for H. pylori infection is well established for adults, but it needs to be improved for children. Serum samples from 24 children, 22 H. pylori (Hp)-positive and 2 Hp-negative children, were used to catalogue antigenic proteins of a Japanese strain CPY2052 by two-dimensional electrophoresis followed by immunoblot and LC-MS/MS analysis. In total, 24 proteins were identified as candidate antigen proteins. Among these, the major virulence factor, cytotoxin-associated gene A protein (CagA) was the most reactive antigen recognized by all the Hp-positive sera even from children under the age of 3 years. The major antigenic part of CagA was identified in the middle region, and two peptides containing CagA epitopes were identified using a newly developed peptide/protein-combined array chip method, modified from our previous protein chip method. Each of the epitopes was found to contain amino acid residue(s) unique to East Asian CagA. Epitope analysis of CagA indicated importance of the regional CagA antigens for serodiagnosis of H. pylori infection in children. PMID:25141238

  16. Source separation in astrophysical maps using independent factor analysis.

    PubMed

    Kuruoğlu, Ercan E; Bedini, Luigi; Paratore, Maria T; Salerno, Emanuele; Tonazzini, Anna

    2003-01-01

    A microwave sky map results from a combination of signals from various astrophysical sources, such as cosmic microwave background radiation, synchrotron radiation and galactic dust radiation. To derive information about these sources, one needs to separate them from the measured maps on different frequency channels. Our insufficient knowledge of the weights to be given to the individual signals at different frequencies makes this a difficult task. Recent work on the problem led to only limited success due to ignoring the noise and to the lack of a suitable statistical model for the sources. In this paper, we derive the statistical distribution of some source realizations, and check the appropriateness of a Gaussian mixture model for them. A source separation technique, namely, independent factor analysis, has been suggested recently in the literature for Gaussian mixture sources in the presence of noise. This technique employs a three layered neural network architecture which allows a simple, hierarchical treatment of the problem. We modify the algorithm proposed in the literature to accommodate for space-varying noise and test its performance on simulated astrophysical maps. We also compare the performances of an expectation-maximization and a simulated annealing learning algorithm in estimating the mixture matrix and the source model parameters. The problem with expectation-maximization is that it does not ensure global optimization, and thus the choice of the starting point is a critical task. Indeed, we did not succeed to reach good solutions for random initializations of the algorithm. Conversely, our experiments with simulated annealing yielded initialization-independent results. The mixing matrix and the means and coefficients in the source model were estimated with a good accuracy while some of the variances of the components in the mixture model were not estimated satisfactorily. PMID:12672442

  17. Geologic map and structural analysis of the Victoria quadrangle, Mercury

    NASA Astrophysics Data System (ADS)

    Galluzzi, Valentina; Di Achille, Gaetano; Ferranti, Luigi; Rothery, David A.; Palumbo, Pasquale

    2015-04-01

    In this work we present a new geologic map and structural analysis of the Victoria quadrangle (H2) of Mercury, along with a reconnaissance study of the geometry and kinematics of lobate scarps in this area. To this end, we produced a 1:3,000,000 geologic map of the area using the images provided by the NASA spacecraft MESSENGER, which has been orbiting the planet since March, 2011. The geologic map shows the distribution of smooth plains, intermediate plains, intercrater plains units and a classification of crater materials based on an empirical distinction among three stages of degradation. Structural mapping shows that the H2 quadrangle is dominated by N-S faults (here grouped into the Victoria system) to the east and NE-SW faults (Larrocha system) to the west, with the secondary existence of NW-SE-trending faults (Carnegie system) in the north-western area of the quadrangle. A systematic analysis of these systems has led to the following results. 1) the Victoria system is characterized by a main array of faults located along Victoria Rupes - Endeavour Rupes - Antoniadi Dorsum. The segmentation of this array into three different sectors changes from north to south and is spatially linked to the presence of three volcanic vents located at the boundaries between each sector and at the northern end of the Victoria Rupes sector , suggesting that volcanism and faulting are interrelated 2) The main array of Carnegie system is kinematically linked and antithetical to the Victoria system. Both systems have arguably controlled the growth of a longitudinal, fault-free, crustal and gravimetric bulge in the central area of the Victoria quadrangle, which is interpreted as a regional contractional pop-up. 3) The Larrocha system is interrupted against the central bulge and thus is probably older than the Victoria and Carnegie systems. Buffered crater counting performed on the Victoria system confirms the young relative age of its fault segments with respect to the map units

  18. Performance metrics for evaluating system suitability in liquid chromatography—Mass spectrometry peptide mass mapping of protein therapeutics and monoclonal antibodies

    PubMed Central

    Zhou, Mowei; Gucinski, Ashley C; Boyne, Michael T

    2015-01-01

    The use of liquid chromatography – mass spectrometry (LC-MS) for the characterization of proteins can provide a plethora of information related to their structure, including amino acid sequence determination and analysis of posttranslational modifications. The variety of LC-MS based applications has led to the use of LC-MS characterization of therapeutic proteins and monoclonal antibodies as an integral part of the regulatory approval process. However, the improper use of an LC-MS system, related to intrinsic instrument limitations, improper tuning parameters, or poorly optimized methods may result in the production of low quality data. Improper system performance may arise from subtle changes in operating conditions that limit the ability to detect low abundance species. To address this issue, we systematically evaluated LC-MS/MS operating parameters to identify a set of metrics that can be used in a workflow to determine if a system is suitable for its intended purpose. Development of this workflow utilized a bovine serum albumin (BSA) digest standard spiked with synthetic peptides present at 0.1% to 100% of the BSA digest peptide concentration to simulate the detection of low abundance species using a traditional bottom-up workflow and data-dependent MS2 acquisition. BSA sequence coverage, a commonly used indicator for instrument performance did not effectively identify settings that led to limited dynamic range or poorer absolute mass accuracy on 2 separate LC-MS systems. Additional metrics focusing on the detection limit and sensitivity for peptide identification were determined to be necessary to establish system suitability for protein therapeutic characterization by LC-MS. PMID:26218711

  19. Performance analysis of unmanned vehicle positioning and obstacle mapping

    NASA Astrophysics Data System (ADS)

    Bostelman, Roger; Hong, Tsai; Madhavan, Raj; Chang, Tommy; Scott, Harry

    2006-05-01

    As unmanned ground vehicles take on more and more intelligent tasks, determination of potential obstacles and accurate estimation of their position become critical for successful navigation and path planning. The performance analysis of obstacle mapping and unmanned vehicle positioning in outdoor environments is the subject of this paper. Recently, the National Institute of Standards and Technology's (NIST) Intelligent Systems Division has been a part of the Defense Advanced Research Project Agency LAGR (Learning Applied to Ground Robots) Program. NIST's objective for the LAGR Project is to insert learning algorithms into the modules that make up the NIST 4D/RCS (Four Dimensional/Real-Time Control System) standard reference model architecture which has been successfully applied to many intelligent systems. We detail world modeling techniques used in the 4D/RCS architecture and then analyze the high precision maps generated by the vehicle world modeling algorithms as compared to ground truth obtained from an independent differential GPS system operable throughout most of the NIST campus. This work has implications, not only for outdoor vehicles but also, for indoor automated guided vehicles where future systems will have more and more onboard intelligence requiring non-contact sensors to provide accurate vehicle and object positioning.

  20. Mapping of normal fault scarps in airborne laser swath mapping data using wavelet analysis

    NASA Astrophysics Data System (ADS)

    Sare, R.; Hilley, G. E.

    2015-12-01

    Wavelet analysis of Digital Elevation Models (DEMs) successfully identifies degraded fault scarps where earthquakes produce topographic steps and provides an estimate of their morphologic age. However, these methods may fail to detect relatively young, sloping scarps created by more gently-dipping normal faults, misidentifying them as mature, highly-degraded vertical scarps if they are detected at all. We present new wavelet templates incorporating initial scarp slope and above- and below-scarp surface angles to better describe the curvature of observed fault scarps. These templates are based on an analytic solution for scarp curvature, allowing for more accurate estimation of the relative age of the scarp. Synthetic tests show that scarp-like landforms that went largely undetected by a vertical-scarp template are more clearly detected using profile geometries that reflect subtle changes in curvature due to scarp and far-field slope angles. Analysis of DEMs from sites in Surprise Valley in the northwestern Basin and Range and near Jenny Lake on the Teton rangefront illustrates the effects of along-strike variability in scarp morphology on best-fit template parameters. Where normal fault scarps have high slopes, they are identified by filters designed to detect topographic step functions. Scarps with finite initial slopes, as well as those that cut surfaces with different angles above and below the scarp, can be resolved with higher signal-to-noise ratios using more sophisticated template functions. Adaptive use of different wavelet templates could reduce the number of false negatives in wavelet analysis of data from complex faulting regimes, improving the robustness of these methods and enabling automated fault mapping of large areas.

  1. Construction and Analysis of High-Density Linkage Map Using High-Throughput Sequencing Data

    PubMed Central

    Liu, Min; Liu, Hui; Zeng, Huaping; Deng, Dejing; Xin, Huaigen; Song, Jun; Xu, Chunhua; Sun, Xiaowen; Hou, Xilin; Wang, Xiaowu; Zheng, Hongkun

    2014-01-01

    Linkage maps enable the study of important biological questions. The construction of high-density linkage maps appears more feasible since the advent of next-generation sequencing (NGS), which eases SNP discovery and high-throughput genotyping of large population. However, the marker number explosion and genotyping errors from NGS data challenge the computational efficiency and linkage map quality of linkage study methods. Here we report the HighMap method for constructing high-density linkage maps from NGS data. HighMap employs an iterative ordering and error correction strategy based on a k-nearest neighbor algorithm and a Monte Carlo multipoint maximum likelihood algorithm. Simulation study shows HighMap can create a linkage map with three times as many markers as ordering-only methods while offering more accurate marker orders and stable genetic distances. Using HighMap, we constructed a common carp linkage map with 10,004 markers. The singleton rate was less than one-ninth of that generated by JoinMap4.1. Its total map distance was 5,908 cM, consistent with reports on low-density maps. HighMap is an efficient method for constructing high-density, high-quality linkage maps from high-throughput population NGS data. It will facilitate genome assembling, comparative genomic analysis, and QTL studies. HighMap is available at http://highmap.biomarker.com.cn/. PMID:24905985

  2. Sensitivity analysis and scale issues in landslide susceptibility mapping

    NASA Astrophysics Data System (ADS)

    Catani, Filippo; Lagomarsino, Daniela; Segoni, Samuele; Tofani, Veronica

    2013-04-01

    Despite the large number of recent advances and developments in landslide susceptibility mapping (LSM) there is still a lack of studies focusing on specific aspects of LSM model sensitivity. For example, the influence of factors of paramount importance such as the survey scale of the landslide conditioning variables (LCVs), the resolution of the mapping unit (MUR) and the optimal number and ranking of LCVs have never been investigated analytically, especially on large datasets. In this paper we attempt this experimentation concentrating on the impact of model tuning choice on the final result, rather than on the comparison of methodologies. To this end, we adopt a simple implementation of the random forest (RF) classification family to produce an ensamble of landslide susceptibility maps for a set of different model settings, input data types and scales. RF classification and regression methods offer a very flexible environment for testing model parameters and mapping hypotheses, allowing for a direct quantification of variable importance. The model choice is, in itself, quite innovative since it is the first time that such technique, widely used in remote sensing for image classification, is used in this form for the production of a LSM. Random forest is a combination of tree (usually binary) bayesian predictors that permits to relate a set of contributing factors with the actual landslides occurrence. Being it a nonparametric model, it is possible to incorporate a range of numeric or categorical data layers and there is no need to select unimodal training data. Many classical and widely acknowledged landslide predisposing factors have been taken into account as mainly related to: the lithology, the land use, the land surface geometry (derived from DTM), the structural and anthropogenic constrains. In addition, for each factor we also included in the parameter set the standard deviation (for numerical variables) or the variety (for categorical ones). The use of

  3. Historical shoreline mapping (II): application of the Digital Shoreline Mapping and Analysis Systems (DSMS/DSAS) to shoreline change mapping in Puerto Rico

    USGS Publications Warehouse

    Thieler, E. Robert; Danforth, William W.

    1994-01-01

    A new, state-of-the-art method for mapping historical shorelines from maps and aerial photographs, the Digital Shoreline Mapping System (DSMS), has been developed. The DSMS is a freely available, public domain software package that meets the cartographic and photogrammetric requirements of precise coastal mapping, and provides a means to quantify and analyze different sources of error in the mapping process. The DSMS is also capable of resolving imperfections in aerial photography that commonly are assumed to be nonexistent. The DSMS utilizes commonly available computer hardware and software, and permits the entire shoreline mapping process to be executed rapidly by a single person in a small lab. The DSMS generates output shoreline position data that are compatible with a variety of Geographic Information Systems (GIS). A second suite of programs, the Digital Shoreline Analysis System (DSAS) has been developed to calculate shoreline rates-of-change from a series of shoreline data residing in a GIS. Four rate-of-change statistics are calculated simultaneously (end-point rate, average of rates, linear regression and jackknife) at a user-specified interval along the shoreline using a measurement baseline approach. An example of DSMS and DSAS application using historical maps and air photos of Punta Uvero, Puerto Rico provides a basis for assessing the errors associated with the source materials as well as the accuracy of computed shoreline positions and erosion rates. The maps and photos used here represent a common situation in shoreline mapping: marginal-quality source materials. The maps and photos are near the usable upper limit of scale and accuracy, yet the shoreline positions are still accurate ±9.25 m when all sources of error are considered. This level of accuracy yields a resolution of ±0.51 m/yr for shoreline rates-of-change in this example, and is sufficient to identify the short-term trend (36 years) of shoreline change in the study area.

  4. Canonical integration and analysis of periodic maps using non-standard analysis and life methods

    SciTech Connect

    Forest, E.; Berz, M.

    1988-06-01

    We describe a method and a way of thinking which is ideally suited for the study of systems represented by canonical integrators. Starting with the continuous description provided by the Hamiltonians, we replace it by a succession of preferably canonical maps. The power series representation of these maps can be extracted with a computer implementation of the tools of Non-Standard Analysis and analyzed by the same tools. For a nearly integrable system, we can define a Floquet ring in a way consistent with our needs. Using the finite time maps, the Floquet ring is defined only at the locations s/sub i/ where one perturbs or observes the phase space. At most the total number of locations is equal to the total number of steps of our integrator. We can also produce pseudo-Hamiltonians which describe the motion induced by these maps. 15 refs., 1 fig.

  5. Electricity Consumption Risk Map - The use of Urban Climate Mapping for smarter analysis: Case study for Birmingham, UK.

    NASA Astrophysics Data System (ADS)

    Antunes Azevedo, Juliana; Burghardt, René; Chapman, Lee; Katzchner, Lutz; Muller, Catherine L.

    2015-04-01

    Climate is a key driving factor in energy consumption. However, income, vegetation, building mass structure, topography also impact on the amount of energy consumption. In a changing climate, increased temperatures are likely to lead to increased electricity consumption, affecting demand, distribution and generation. Furthermore, as the world population becomes more urbanized, increasing numbers of people will need to deal with not only increased temperatures from climate change, but also from the unintentional modification of the urban climate in the form of urban heat islands. Hence, climate and climate change needs to be taken into account for future urban planning aspects to increase the climate and energy resilience of the community and decrease the future social and economic costs. Geographical Information Systems provide a means to create urban climate maps as part of the urban planning process. Geostatistical analyses linking these maps with demographic and social data, enables a geo-statistical analysis to identify linkages to high-risk groups of the community and vulnerable areas of town and cities. Presently, the climatope classification is oriented towards thermal aspects and the ventilation quality (roughness) of the urban areas but can also be adapted to take into account other structural "environmental factors". This study aims to use the climatope approach to predict areas of potential high electricity consumption in Birmingham, UK. Several datasets were used to produce an average surface temperature map, vegetation map, land use map, topography map, building height map, built-up area roughness calculations, an average air temperature map and a domestic electricity consumption map. From the correlations obtained between the layers it is possible to average the importance of each factor and create a map for domestic electricity consumption to understand the influence of environmental aspects on spatial energy consumption. Based on these results city

  6. Synthesis and Kinetic Analysis of Two Conformationally Restricted Peptide Substrates of Escherichia coli Penicillin-Binding Protein 5.

    PubMed

    Nemmara, Venkatesh V; Nicholas, Robert A; Pratt, R F

    2016-07-26

    Escherichia coli PBP5 (penicillin-binding protein 5) is a dd-carboxypeptidase involved in bacterial cell wall maturation. Beyond the C-terminal d-alanyl-d-alanine moiety, PBP5, like the essential high-molecular mass PBPs, has little specificity for other elements of peptidoglycan structure, at least as elicited in vitro by small peptidoglycan fragments. On the basis of the crystal structure of a stem pentapeptide derivative noncovalently bound to E. coli PBP6 (Protein Data Bank entry 3ITB ), closely similar in structure to PBP5, we have modeled a pentapeptide structure at the active site of PBP5. Because the two termini of the pentapeptide are directed into solution in the PBP6 crystal structure, we then modeled a 19-membered cyclic peptide analogue by cross-linking the terminal amines by succinylation. An analogous smaller, 17-membered cyclic peptide, in which the l-lysine of the original was replaced by l-diaminobutyric acid, could also be modeled into the active site. We anticipated that, just as the reactivity of stem peptide fragments of peptidoglycan with PBPs in vivo may be entropically enhanced by immobilization in the polymer, so too would that of our cyclic peptides with respect to their acyclic analogues in vitro. This paper describes the synthesis of the peptides described above that were required to examine this hypothesis and presents an analysis of their structures and reaction kinetics with PBP5. PMID:27420403

  7. PepBind: a comprehensive database and computational tool for analysis of protein-peptide interactions.

    PubMed

    Das, Arindam Atanu; Sharma, Om Prakash; Kumar, Muthuvel Suresh; Krishna, Ramadas; Mathur, Premendu P

    2013-08-01

    Protein-peptide interactions, where one partner is a globular protein (domain) and the other is a flexible linear peptide, are key components of cellular processes predominantly in signaling and regulatory networks, hence are prime targets for drug design. To derive the details of the protein-peptide interaction mechanism is often a cumbersome task, though it can be made easier with the availability of specific databases and tools. The Peptide Binding Protein Database (PepBind) is a curated and searchable repository of the structures, sequences and experimental observations of 3100 protein-peptide complexes. The web interface contains a computational tool, protein inter-chain interaction (PICI), for computing several types of weak or strong interactions at the protein-peptide interaction interface and visualizing the identified interactions between residues in Jmol viewer. This initial database release focuses on providing protein-peptide interface information along with structure and sequence information for protein-peptide complexes deposited in the Protein Data Bank (PDB). Structures in PepBind are classified based on their cellular activity. More than 40% of the structures in the database are found to be involved in different regulatory pathways and nearly 20% in the immune system. These data indicate the importance of protein-peptide complexes in the regulation of cellular processes. PMID:23896518

  8. High colloidal stability of gold nanorods coated with a peptide-ethylene glycol: Analysis by cyanide-mediated etching and nanoparticle tracking analysis.

    PubMed

    Free, Paul; Conger, Gao; Siji, Wu; Zhang, Jing Bo; Fernig, David G

    2016-10-01

    The stability of gold nanorods was assessed following coating with various charged or uncharged ligands, mostly peptides. Highly stable monodispersed gold nanorods were obtained by coating CTAB-stabilized gold nanorods with a pentapeptide with C-terminal ethylene glycol units (peptide-EG). UV-vis spectroscopy of these nanorods suspended in saline solutions indicated no signs of aggregation, and they were easily purified using size-exclusion chromatography. A more stringent measure of nanorod stability involved observing changes in the UV-vis absorbance of gold nanorods subjected to etching with cyanide. The λmax absorbance of peptide-EG coated nanorods red-shifted in etchant solution. The hypothesis that changes in the nanorod aspect ratio led to this red-shift was confirmed by TEM analysis, which showed pit formation along the transverse axis. The etching process was followed in solution using nanoparticle tracking analysis. The red-shift was shown to occur while the particles remained mono-dispersed, and so was not due to aggregation. Adding both etchant solution and peptide-EG to the nanorods was further shown to allow modulation of the Δλmax red-shift and increase the etchant resistance of peptide-EG nanorods. Thus, very stable gold nanorods can be produced using the peptide-EG coating approach and their optical properties modulated with etchant. PMID:27455407

  9. Oregon Cascades Play Fairway Analysis: Faults and Heat Flow maps

    SciTech Connect

    Adam Brandt

    2015-11-15

    This submission includes a fault map of the Oregon Cascades and backarc, a probability map of heat flow, and a fault density probability layer. More extensive metadata can be found within each zip file.

  10. Symplectic maps for the n-body problem - Stability analysis

    NASA Technical Reports Server (NTRS)

    Wisdom, Jack; Holman, Matthew

    1992-01-01

    The stability of new symplectic n-body maps is examined from the point of view of nonlinear dynamics. The resonances responsible for the principal artifacts are identified. These are resonances between the stepsize and the difference of mean motions between pairs of planets. For larger stepsizes resonant perturbations are evident in the variation of the energy of the system corresponding to these stepsize resonances. It is shown that the principal instability of the method can be predicted and corresponds to the overlap of the stepsize resonances. It is noted that the analysis suggests that other artifacts will occur. For example, the overlap of a stepsize resonance with a resonance of the actual system may also give a region of chaotic behavior that is an artifact. It is pointed out that the fact that the principal artifacts corresponds to a particular set of stepsize resonances suggests that it may be possible to perturbatively remove the effect when the stepsize resonances are nonoverlapping.

  11. Silicone/graphite coating for on-target desalting and improved peptide mapping performance of matrix-assisted laser desorption/ionization-mass spectrometry targets in proteomic experiments.

    PubMed

    Li, Xinping; Wilm, Matthias; Franz, Thomas

    2005-04-01

    In two-dimensional gel electrophoresis-based proteomic experiments matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) peptide mass fingerprinting is often the technique of choice in identifying proteins. Here, we present a novel surface coating technique for MALDI-MS targets that improves manual and automatic sample analysis. A mixture of silicone and graphite is spread in the form of a thin layer over the target. Due to the hydrophobicity of the coating, aqueous solutions can be applied to relatively small spots very precisely using a robotic system. At least four times more liquid can be concentrated on the same area compared to uncoated steel targets. alpha-cyano-4-hydrocinnamic acid crystallizes in form of very small crystals evenly distributed over the surface. The search for "hot spots" during the analysis is not necessary, which supports the automatic acquisition of data. The homogeneous crystal layer can be very effectively washed on-target without encountering major sample losses. This efficient washing and the focused application of aqueous samples replace expensive and time-consuming reversed phase micro column based sample clean-ups. When analyzing peptide mixtures, the signal intensities are up to five times higher than with preparations of the same un-desalted samples on steel targets, since four times more sample can be loaded. The mass resolution remains unaffected by the surface coating. After usage the coating can be removed, followed by a new coating avoiding any carry-over of sample to the next analysis. All these properties make the precoating of MALDI-MS targets with a silicone/graphite layer an ideal technique for routine analysis in large-scale proteomic experiments. PMID:15838907

  12. Modern methods of documentation for conservation - digital mapping in metigo® MAP, Software for documentation, mapping and quantity survey and analysis

    NASA Astrophysics Data System (ADS)

    Siedler, Gunnar; Vetter, Sebastian

    2015-04-01

    Several years of experience of heritage documentation have given a background to develop methods of cartography and digital evaluation. The outcome of which is the development of a 2D-mapping software with integrated image rectification over a period of more then 10 years and that became the state of the art software in Germany initially and now elsewhere for Conservation and Restoration projects. If there are no mapping bases (image plan or CAD-drawing), the user can create its own image plans using different types of rectification functions. Based on true to scale mappings, quantity surveys of areas and lines can be calculated automatically. Digital maps were used for the documentation and analysis of materials and damages, for planning of required action and for calculation of costs. With the help of the hierarchy even large mapping projects with many sub projects can be managed. The results of quantification can be exported to excel spreadsheets for further processing. The combination of image processing and CAD-functionality makes operation of the programm user-friendly, both in the office and on-site. metigo MAP was developed in close cooperation with conservators and restorers. Based on simple equipment consisting of digital camera, laser measuring instrument for measuring distances or total station and standard notebook the mapping software is used in many restoration companies.

  13. An Analysis of Prospective Teachers' Knowledge for Constructing Concept Maps

    ERIC Educational Resources Information Center

    Subramaniam, Karthigeyan; Esprívalo Harrell, Pamela

    2015-01-01

    Background: Literature contends that a teacher's knowledge of concept map-based tasks influence how their students perceive the task and execute the creation of acceptable concept maps. Teachers who are skilled concept mappers are able to (1) understand and apply the operational terms to construct a hierarchical/non-hierarchical concept map; (2)…

  14. Optimization of field-amplified sample injection for analysis of peptides by capillary electrophoresis-mass spectrometry.

    PubMed

    Yang, Yuanzhong; Boysen, Reinhard I; Hearn, Milton T W

    2006-07-15

    A versatile experimental approach is described to achieve very high sensitivity analysis of peptides by capillary electrophoresis-mass spectrometry with sheath flow configuration based on optimization of field-amplified sample injection. Compared to traditional hydrodynamic injection methods, signal enhancement in terms of detection sensitivity of the bioanalytes by more than 3000-fold can be achieved. The effects of injection conditions, composition of the acid and organic solvent in the sample solution, length of the water plug, sample injection time, and voltage on the efficiency of the sample stacking have been systematically investigated, with peptides in the low-nanomolar (10(-9) M) range readily detected under the optimized conditions. Linearity of the established stacking method was found to be excellent over 2 orders of magnitude of concentration. The method was further evaluated for the analysis of low concentration bioactive peptide mixtures and tryptic digests of proteins. A distinguishing feature of the described approach is that it can be employed directly for the analysis of low-abundance protein fragments generated by enzymatic digestion and a reversed-phase-based sample-desalting procedure. Thus, rapid identification of protein fragments as low-abundance analytes can be achieved with this new approach by comparison of the actual tandem mass spectra of selected peptides with the predicted fragmentation patterns using online database searching algorithms. PMID:16841892

  15. 76 FR 78015 - Revised Analysis and Mapping Procedures for Non-Accredited Levees

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-15

    ... SECURITY Federal Emergency Management Agency Revised Analysis and Mapping Procedures for Non-Accredited... Management Agency (FEMA) is accepting comments on the proposed solution for Revised Analysis and Mapping Procedures for Non-Accredited Levees. This document proposes a revised procedure for the analysis and...

  16. A Comparative Analysis of Global Cropping Systems Models and Maps

    NASA Astrophysics Data System (ADS)

    Anderson, W. B.; You, L.; Wood, S.; Wood-Sichra, U.; Wu, W.

    2013-12-01

    Agricultural practices have dramatically altered the land cover of the Earth, but the spatial extent and intensity of these practices is often difficult to catalogue. Cropland accounts for nearly 15 million km2 of the Earth's land cover - amounting to 12% of the Earth's ice-free land surface - yet information on the distribution and performance of specific crops is often available only through national or sub-national statistics. While remote sensing products offer spatially disaggregated information, those currently available on a global scale are ill-suited for many applications due to the limited separation of crop types within the area classified as cropland. Recently, however, there have been multiple independent efforts to incorporate the detailed information available from statistical surveys with supplemental spatial information to produce a spatially explicit global dataset specific to individual cropss for the year 2000. While these datasets provide analysts and decision makers with improved information on global cropping systems, the final global cropping maps differ from one another substantially. This study aims to explore and quantify systematic similarities and differences between four major global cropping systems products: the monthly irrigated and rainfed crop areas around the year 2000 (MIRAC2000) dataset, the spatial production allocation model (SPAM), the global agro-ecological zone (GAEZ) dataset, and the dataset developed by Monfreda et al., 2008. The analysis explores not only the final cropping systems maps but also the interdependencies of each product, methodological differences and modeling assumptions, which will provide users with information vital for discerning between datasets in selecting a product appropriate for each intended application.

  17. Large-scale analysis of peptide sequence variants: the case for high-field asymmetric waveform ion mobility spectrometry.

    PubMed

    Creese, Andrew J; Smart, Jade; Cooper, Helen J

    2013-05-21

    Large scale analysis of proteins by mass spectrometry is becoming increasingly routine; however, the presence of peptide isomers remains a significant challenge for both identification and quantitation in proteomics. Classes of isomers include sequence inversions, structural isomers, and localization variants. In many cases, liquid chromatography is inadequate for separation of peptide isomers. The resulting tandem mass spectra are composite, containing fragments from multiple precursor ions. The benefits of high-field asymmetric waveform ion mobility spectrometry (FAIMS) for proteomics have been demonstrated by a number of groups, but previously work has focused on extending proteome coverage generally. Here, we present a systematic study of the benefits of FAIMS for a key challenge in proteomics, that of peptide isomers. We have applied FAIMS to the analysis of a phosphopeptide library comprising the sequences GPSGXVpSXAQLX(K/R) and SXPFKXpSPLXFG(K/R), where X = ADEFGLSTVY. The library has defined limits enabling us to make valid conclusions regarding FAIMS performance. The library contains numerous sequence inversions and structural isomers. In addition, there are large numbers of theoretical localization variants, allowing false localization rates to be determined. The FAIMS approach is compared with reversed-phase liquid chromatography and strong cation exchange chromatography. The FAIMS approach identified 35% of the peptide library, whereas LC-MS/MS alone identified 8% and LC-MS/MS with strong cation exchange chromatography prefractionation identified 17.3% of the library. PMID:23646896

  18. Accounting for the kinetics in order parameter analysis: Lessons from theoretical models and a disordered peptide

    NASA Astrophysics Data System (ADS)

    Berezovska, Ganna; Prada-Gracia, Diego; Mostarda, Stefano; Rao, Francesco

    2012-11-01

    Molecular simulations as well as single molecule experiments have been widely analyzed in terms of order parameters, the latter representing candidate probes for the relevant degrees of freedom. Notwithstanding this approach is very intuitive, mounting evidence showed that such descriptions are inaccurate, leading to ambiguous definitions of states and wrong kinetics. To overcome these limitations a framework making use of order parameter fluctuations in conjunction with complex network analysis is investigated. Derived from recent advances in the analysis of single molecule time traces, this approach takes into account the fluctuations around each time point to distinguish between states that have similar values of the order parameter but different dynamics. Snapshots with similar fluctuations are used as nodes of a transition network, the clusterization of which into states provides accurate Markov-state-models of the system under study. Application of the methodology to theoretical models with a noisy order parameter as well as the dynamics of a disordered peptide illustrates the possibility to build accurate descriptions of molecular processes on the sole basis of order parameter time series without using any supplementary information.

  19. Peptide mapping and amino acid sequencing of two catechol 1,2-dioxygenases (CD I1 and CD I2) from Acinetobacter lwoffii K24.

    PubMed

    Kim, S I; Ha, K S

    1997-10-31

    The partial amino acid sequences of two catechol 1,2-dioxygenases (CD I1 and CD I2) from Acinetobacter lwoffii K24 have been determined by analysis of peptides after cleavages with endopeptidase Lys-C, endopeptidase Glu-C, trypsin, and chemicals (cyanogen bromide and BNPS-skatole). They include 248 amino acid sequences (4 fragments) of CD I1 and 211 amino acid sequences (5 fragments) of CD I2. Two enzymes have more than 50% sequence homology with type I catechol 1,2-dioxygenases and less than 30% sequence homology with type II catechol 1,2-dioxygenases. Two enzymes have similar hydropathy profiles in the N-terminal region, suggesting that they have similar secondary structures. PMID:9387151

  20. Effectiveness of CID, HCD, and ETD with FT MS/MS for degradomic-peptidomic analysis: comparison of peptide identification methods

    PubMed Central

    Shen, Yufeng; Tolić, Nikola; Xie, Fang; Zhao, Rui; Purvine, Samuel O.; Schepmoes, Athena A.; Ronald, J. Moore; Anderson, Gordon A.; Smith, Richard D.

    2011-01-01

    We report on the effectiveness of CID, HCD, and ETD for LC-FT MS/MS analysis of peptides using a tandem linear ion trap-Orbitrap mass spectrometer. A range of software tools and analysis parameters were employed to explore the use of CID, HCD, and ETD to identify peptides isolated from human blood plasma without the use of specific “enzyme rules”. In the evaluation of an FDR-controlled SEQUEST scoring method, the use of accurate masses for fragments increased the numbers of identified peptides (by ~50%) compared to the use of conventional low accuracy fragment mass information, and CID provided the largest contribution to the identified peptide datasets compared to HCD and ETD. The FDR-controlled Mascot scoring method provided significantly fewer peptide identifications than with SEQUEST (by 1.3–2.3 fold) at the same confidence levels, and CID, HCD, and ETD provided similar contributions to identified peptides. Evaluation of de novo sequencing and the UStags method for more intense fragment ions revealed that HCD afforded more sequence consecutive residues (e.g., ≥7 amino acids) than either CID or ETD. Both the FDR-controlled SEQUEST and Mascot scoring methods provided peptide datasets that were affected by the decoy database and mass tolerances applied (e.g., the identical peptides between the datasets could be limited to ~70%), while the UStags method provided the most consistent peptide datasets (>90% overlap) with extremely low (near zero) numbers of false positive identifications. The m/z ranges in which CID, HCD, and ETD contributed the largest number of peptide identifications were substantially overlapping. This work suggests that the three peptide ion fragmentation methods are complementary, and that maximizing the number of peptide identifications benefits significantly from a careful match with the informatics tools and methods applied. These results also suggest that the decoy strategy may inaccurately estimate identification FDRs. PMID:21678914

  1. Integrating Recent Land Cover Mapping Efforts to Update the National Gap Analysis Program's Species Habitat Map

    NASA Astrophysics Data System (ADS)

    McKerrow, A. J.; Davidson, A.; Earnhardt, T. S.; Benson, A. L.

    2014-11-01

    Over the past decade, great progress has been made to develop national extent land cover mapping products to address natural resource issues. One of the core products of the GAP Program is range-wide species distribution models for nearly 2000 terrestrial vertebrate species in the U.S. We rely on deductive modeling of habitat affinities using these products to create models of habitat availability. That approach requires that we have a thematically rich and ecologically meaningful map legend to support the modeling effort. In this work, we tested the integration of the Multi-Resolution Landscape Characterization Consortium's National Land Cover Database 2011 and LANDFIRE's Disturbance Products to update the 2001 National GAP Vegetation Dataset to reflect 2011 conditions. The revised product can then be used to update the species models. We tested the update approach in three geographic areas (Northeast, Southeast, and Interior Northwest). We used the NLCD product to identify areas where the cover type mapped in 2011 was different from what was in the 2001 land cover map. We used Google Earth and ArcGIS base maps as reference imagery in order to label areas identified as "changed" to the appropriate class from our map legend. Areas mapped as urban or water in the 2011 NLCD map that were mapped differently in the 2001 GAP map were accepted without further validation and recoded to the corresponding GAP class. We used LANDFIRE's Disturbance products to identify changes that are the result of recent disturbance and to inform the reassignment of areas to their updated thematic label. We ran species habitat models for three species including Lewis's Woodpecker (Melanerpes lewis) and the White-tailed Jack Rabbit (Lepus townsendii) and Brown Headed nuthatch (Sitta pusilla). For each of three vertebrate species we found important differences in the amount and location of suitable habitat between the 2001 and 2011 habitat maps. Specifically, Brown headed nuthatch habitat in

  2. Application of GelC-MS/MS to Proteomic Profiling of Chikungunya Virus Infection: Preparation of Peptides for Analysis.

    PubMed

    Paemanee, Atchara; Wikan, Nitwara; Roytrakul, Sittiruk; Smith, Duncan R

    2016-01-01

    Gel-enhanced liquid chromatography coupled with tandem mass spectrometry (GeLC-MS/MS) is a labor intensive, but relatively straightforward methodology that generates high proteome coverage which can be applied to the proteome analysis of a range of starting materials such as cells or patient specimens. Sample proteins are resolved electrophoretically in one dimension through a sodium dodecyl sulfate (SDS) polyacrylamide gel after which the lanes are sliced into sections. The sections are further diced and the gel cubes generated are subjected to in-gel tryptic digestion. The resultant peptides can then be analyzed by tandem mass spectroscopy to identify the proteins by database searching. The methodology can routinely detect several thousand proteins in one analysis. The protocol we describe here has been used with both cells in culture that have been infected with chikungunya virus and specimens from Chikungunya fever patients. This protocol details the process for generating peptides for subsequent mass spectroscopic and bioinformatic analysis. PMID:27233271

  3. Prediction and Analysis of Quorum Sensing Peptides Based on Sequence Features

    PubMed Central

    Rajput, Akanksha; Gupta, Amit Kumar; Kumar, Manoj

    2015-01-01

    Quorum sensing peptides (QSPs) are the signaling molecules used by the Gram-positive bacteria in orchestrating cell-to-cell communication. In spite of their enormous importance in signaling process, their detailed bioinformatics analysis is lacking. In this study, QSPs and non-QSPs were examined according to their amino acid composition, residues position, motifs and physicochemical properties. Compositional analysis concludes that QSPs are enriched with aromatic residues like Trp, Tyr and Phe. At the N-terminal, Ser was a dominant residue at maximum positions, namely, first, second, third and fifth while Phe was a preferred residue at first, third and fifth positions from the C-terminal. A few motifs from QSPs were also extracted. Physicochemical properties like aromaticity, molecular weight and secondary structure were found to be distinguishing features of QSPs. Exploiting above properties, we have developed a Support Vector Machine (SVM) based predictive model. During 10-fold cross-validation, SVM achieves maximum accuracy of 93.00%, Mathew’s correlation coefficient (MCC) of 0.86 and Receiver operating characteristic (ROC) of 0.98 on the training/testing dataset (T200p+200n). Developed models performed equally well on the validation dataset (V20p+20n). The server also integrates several useful analysis tools like “QSMotifScan”, “ProtFrag”, “MutGen” and “PhysicoProp”. Our analysis reveals important characteristics of QSPs and on the basis of these unique features, we have developed a prediction algorithm “QSPpred” (freely available at: http://crdd.osdd.net/servers/qsppred). PMID:25781990

  4. Digital floodplain mapping and an analysis of errors involved

    USGS Publications Warehouse

    Hamblen, C.S.; Soong, D.T.; Cai, X.

    2007-01-01

    Mapping floodplain boundaries using geographical information system (GIS) and digital elevation models (DEMs) was completed in a recent study. However convenient this method may appear at first, the resulting maps potentially can have unaccounted errors. Mapping the floodplain using GIS is faster than mapping manually, and digital mapping is expected to be more common in the future. When mapping is done manually, the experience and judgment of the engineer or geographer completing the mapping and the contour resolution of the surface topography are critical in determining the flood-plain and floodway boundaries between cross sections. When mapping is done digitally, discrepancies can result from the use of the computing algorithm and digital topographic datasets. Understanding the possible sources of error and how the error accumulates through these processes is necessary for the validation of automated digital mapping. This study will evaluate the procedure of floodplain mapping using GIS and a 3 m by 3 m resolution DEM with a focus on the accumulated errors involved in the process. Within the GIS environment of this mapping method, the procedural steps of most interest, initially, include: (1) the accurate spatial representation of the stream centerline and cross sections, (2) properly using a triangulated irregular network (TIN) model for the flood elevations of the studied cross sections, the interpolated elevations between them and the extrapolated flood elevations beyond the cross sections, and (3) the comparison of the flood elevation TIN with the ground elevation DEM, from which the appropriate inundation boundaries are delineated. The study area involved is of relatively low topographic relief; thereby, making it representative of common suburban development and a prime setting for the need of accurately mapped floodplains. This paper emphasizes the impacts of integrating supplemental digital terrain data between cross sections on floodplain delineation

  5. Develop advanced nonlinear signal analysis topographical mapping system

    NASA Technical Reports Server (NTRS)

    1994-01-01

    The Space Shuttle Main Engine (SSME) has been undergoing extensive flight certification and developmental testing, which involves some 250 health monitoring measurements. Under the severe temperature, pressure, and dynamic environments sustained during operation, numerous major component failures have occurred, resulting in extensive engine hardware damage and scheduling losses. To enhance SSME safety and reliability, detailed analysis and evaluation of the measurements signal are mandatory to assess its dynamic characteristics and operational condition. Efficient and reliable signal detection techniques will reduce catastrophic system failure risks and expedite the evaluation of both flight and ground test data, and thereby reduce launch turn-around time. The basic objective of this contract are threefold: (1) develop and validate a hierarchy of innovative signal analysis techniques for nonlinear and nonstationary time-frequency analysis. Performance evaluation will be carried out through detailed analysis of extensive SSME static firing and flight data. These techniques will be incorporated into a fully automated system; (2) develop an advanced nonlinear signal analysis topographical mapping system (ATMS) to generate a Compressed SSME TOPO Data Base (CSTDB). This ATMS system will convert tremendous amount of complex vibration signals from the entire SSME test history into a bank of succinct image-like patterns while retaining all respective phase information. High compression ratio can be achieved to allow minimal storage requirement, while providing fast signature retrieval, pattern comparison, and identification capabilities; and (3) integrate the nonlinear correlation techniques into the CSTDB data base with compatible TOPO input data format. Such integrated ATMS system will provide the large test archives necessary for quick signature comparison. This study will provide timely assessment of SSME component operational status, identify probable causes of

  6. Develop advanced nonlinear signal analysis topographical mapping system

    NASA Technical Reports Server (NTRS)

    Jong, Jen-Yi

    1993-01-01

    The SSME has been undergoing extensive flight certification and developmental testing, which involves some 250 health monitoring measurements. Under the severe temperature pressure, and dynamic environments sustained during operation, numerous major component failures have occurred, resulting in extensive engine hardware damage and scheduling losses. To enhance SSME safety and reliability, detailed analysis and evaluation of the measurements signal are mandatory to assess its dynamic characteristics and operational condition. Efficient and reliable signal detection techniques will reduce catastrophic system failure risks and expedite the evaluation of both flight and ground test data, and thereby reduce launch turn-around time. The basic objective of this contract are threefold: (1) Develop and validate a hierarchy of innovative signal analysis techniques for nonlinear and nonstationary time-frequency analysis. Performance evaluation will be carried out through detailed analysis of extensive SSME static firing and flight data. These techniques will be incorporated into a fully automated system. (2) Develop an advanced nonlinear signal analysis topographical mapping system (ATMS) to generate a Compressed SSME TOPO Data Base (CSTDB). This ATMS system will convert tremendous amounts of complex vibration signals from the entire SSME test history into a bank of succinct image-like patterns while retaining all respective phase information. A high compression ratio can be achieved to allow the minimal storage requirement, while providing fast signature retrieval, pattern comparison, and identification capabilities. (3) Integrate the nonlinear correlation techniques into the CSTDB data base with compatible TOPO input data format. Such integrated ATMS system will provide the large test archives necessary for a quick signature comparison. This study will provide timely assessment of SSME component operational status, identify probable causes of malfunction, and indicate

  7. Analysis of acetylcholine receptor phosphorylation sites using antibodies to synthetic peptides and monoclonal antibodies.

    PubMed Central

    Safran, A; Neumann, D; Fuchs, S

    1986-01-01

    Three peptides corresponding to residues 354-367, 364-374, 373-387 of the acetylcholine receptor (AChR) delta subunit were synthesized. These peptides represent the proposed phosphorylation sites of the cAMP-dependent protein kinase, the tyrosine-specific protein kinase and the calcium/phospholipid-dependent protein kinase respectively. Using these peptides as substrates for phosphorylation by the catalytic subunit of cAMP-dependent protein kinase it was shown that only peptides 354-367 was phosphorylated whereas the other two were not. These results verify the location of the cAMP-dependent protein kinase phosphorylation site within the AChR delta subunit. Antibodies elicited against these peptides reacted with the delta subunit. The antipeptide antibodies and two monoclonal antibodies (7F2, 5.46) specific for the delta subunit were tested for their binding to non-phosphorylated receptor and to receptor phosphorylated by the catalytic subunit of cAMP-dependent protein kinase. Antibodies to peptide 354-367 were found to react preferentially with non-phosphorylated receptor whereas the two other anti-peptide antibodies bound equally to phosphorylated and non-phosphorylated receptors. Monoclonal antibody 7F2 reacted preferentially with the phosphorylated form of the receptor whereas monoclonal antibody 5.46 did not distinguish between the two forms. Images Fig. 2. Fig. 4. Fig. 5. PMID:3816758

  8. A Systematic Analysis of Drosophila Regulatory Peptide Expression in Enteroendocrine Cells

    PubMed Central

    Chen, Ji; Kim, Seol-min; Kwon, Jae Young

    2016-01-01

    The digestive system is gaining interest as a major regulator of various functions including immune defense, nutrient accumulation, and regulation of feeding behavior, aside from its conventional function as a digestive organ. The Drosophila midgut epithelium is completely renewed every 1–2 weeks due to differentiation of pluripotent intestinal stem cells in the midgut. Intestinal stem cells constantly divide and differentiate into enterocytes that secrete digestive enzymes and absorb nutrients, or enteroendocrine cells that secrete regulatory peptides. Regulatory peptides have important roles in development and metabolism, but study has mainly focused on expression and functions in the nervous system, and not much is known about the roles in endocrine functions of enteroendocrine cells. We systemically examined the expression of 45 regulatory peptide genes in the Drosophila midgut, and verified that at least 10 genes are expressed in the midgut enteroendocrine cells through RT-PCR, in situ hybridization, antisera, and 25 regulatory peptide-GAL transgenes. The Drosophila midgut is highly compartmentalized, and individual peptides in enteroendocrine cells were observed to express in specific regions of the midgut. We also confirmed that some peptides expressed in the same region of the midgut are expressed in mutually exclusive enteroendocrine cells. These results indicate that the midgut enteroendocrine cells are functionally differentiated into different subgroups. Through this study, we have established a basis to study regulatory peptide functions in enteroendocrine cells as well as the complex organization of enteroendocrine cells in the Drosophila midgut. PMID:27025390

  9. Photo-crosslinking analysis of preferential interactions between a transmembrane peptide and matching lipids.

    PubMed

    Ridder, Anja N J A; Spelbrink, Robin E J; Demmers, Jeroen A A; Rijkers, Dirk T S; Liskamp, Rob M J; Brunner, Josef; Heck, Albert J R; de Kruijff, Ben; Killian, J Antoinette

    2004-04-20

    In this study, a novel method is presented by which the molecular environment of a transmembrane peptide can be investigated directly. This was achieved by incorporating a photoactivatable crosslinking probe in the hydrophobic segment of a model transmembrane peptide. When this peptide was incorporated into lipid bilayers and irradiated with UV light, a covalent bond was formed between the crosslinking probe and a lipid. This crosslinking reaction could be visualized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and the resulting product could be characterized by mass spectrometry. By use of phospholipases, it was demonstrated that the peptide crosslinks to both acyl chains of the lipids. The peptide showed a clear preference to partition into fluid lipids and was excluded from lipids in the gel phase. However, when the peptide was incorporated into bilayers containing two lipid species with different acyl chain lengths, molecular sorting of the lipids around the peptide based on hydrophobic matching was not observed. It is proposed that the size of the transmembrane part plays an important role in the dynamic interactions of membrane proteins with the surrounding lipids and hence in determining whether molecular sorting can occur. PMID:15078094

  10. Analysis of relationships between peptide/MHC structural features and naive T cell frequency in humans.

    PubMed

    Reiser, Jean-Baptiste; Legoux, François; Gras, Stéphanie; Trudel, Eric; Chouquet, Anne; Léger, Alexandra; Le Gorrec, Madalen; Machillot, Paul; Bonneville, Marc; Saulquin, Xavier; Housset, Dominique

    2014-12-15

    The structural rules governing peptide/MHC (pMHC) recognition by T cells remain unclear. To address this question, we performed a structural characterization of several HLA-A2/peptide complexes and assessed in parallel their antigenicity, by analyzing the frequency of the corresponding Ag-specific naive T cells in A2(+) and A2(-) individuals, as well as within CD4(+) and CD8(+) subsets. We were able to find a correlation between specific naive T cell frequency and peptide solvent accessibility and/or mobility for a subset of moderately prominent peptides. However, one single structural parameter of the pMHC complexes could not be identified to explain each peptide antigenicity. Enhanced pMHC antigenicity was associated with both highly biased TRAV usage, possibly reflecting favored interaction between particular pMHC complexes and germline TRAV loops, and peptide structural features allowing interactions with a broad range of permissive CDR3 loops. In this context of constrained TCR docking mode, an optimal peptide solvent exposed surface leading to an optimal complementarity with TCR interface may constitute one of the key features leading to high frequency of specific T cells. Altogether our results suggest that frequency of specific T cells depends on the fine-tuning of several parameters, the structural determinants governing TCR-pMHC interaction being just one of them. PMID:25392532

  11. Isolation and structural analysis of antihypertensive peptides that exist naturally in Gouda cheese.

    PubMed

    Saito, T; Nakamura, T; Kitazawa, H; Kawai, Y; Itoh, T

    2000-07-01

    Seven kinds of ripened cheeses (8-mo-aged and 24-mo-aged Gouda, Emmental, Blue, Camembert, Edam, and Havarti) were homogenized with distilled water, and water-soluble peptides were prepared by C-18 hydrophobic chromatography. The inhibitory activity to angiotensin I-converting enzyme and decrease in the systolic blood pressure in spontaneously hypertensive rats were measured before and after oral administration of each peptide sample. The strongest depressive effect in the systolic blood pressure (-24.7 mm Hg) and intensive inhibitory activity to angiotensin I-converting enzyme (75.7%) were detected in the peptides from 8-mo-aged Gouda cheese. Four peptides were isolated by HPLC with reverse-phase and gel filtration modes. Their chemical structures and origins, clarified by combination analyses of protein sequencing, amino acid composition, and mass spectrometry, were as follows: peptide A, Arg-Pro-Lys-His-Pro-Ile-Lys-His-Gln [alpha(s1)-casein (CN), B-8P; f 1-9]; peptide B, Arg-Pro-Lys-His-Pro-Ile-Lys-His-Gln-Gly-Leu-Pro-Gln (alpha(s1)-CN, B-8P; f 1-13); peptide F, Tyr-Pro-Phe-Pro-Gly-Pro-Ile-Pro-Asn (beta-CN, A2-5P; f 60-68); and peptide G, Met-Pro-Phe-Pro-Lys-Tyr-Pro-Val-Gln-Pro-Phe (beta-CN, A2-5P; f 109-119). Peptides A and F, which were chemically synthesized, showed potent angiotensin I-converting enzyme inhibitory activity with little antihypertensive effects. PMID:10908049

  12. Analysis of Endogenous D-Amino Acid-Containing Peptides in Metazoa

    PubMed Central

    Bai, Lu; Sheeley, Sarah; Sweedler, Jonathan V.

    2010-01-01

    Peptides are chiral molecules with their structure determined by the composition and configuration of their amino acid building blocks. The naturally occurring amino acids, except glycine, possess two chiral forms. This allows the formation of multiple peptide diastereomers that have the same sequence. Although living organisms use L-amino acids to make proteins, a group of D-amino acid-containing peptides (DAACPs) has been discovered in animals that have at least one of their residues isomerized to the D-form via an enzyme-catalyzed process. In many cases, the biological functions of these peptides are enhanced due to this structural conversion. These DAACPs are different from those known to occur in bacterial cell wall and antibiotic peptides, the latter of which are synthesized in a ribosome-independent manner. DAACPs have now also been identified in a number of distinct groups throughout the Metazoa. Their serendipitous discovery has often resulted from discrepancies observed in bioassays or in chromatographic behavior between natural peptide fractions and peptides synthesized according to a presumed all-L sequence. Because this L-to-D post-translational modification is subtle and not detectable by most sequence determination approaches, it is reasonable to suspect that many studies have overlooked this change; accordingly, DAACPs may be more prevalent than currently thought. Although diastereomer separation techniques developed with synthetic peptides in recent years have greatly aided in the discovery of natural DAACPs, there is a need for new, more robust methods for naturally complex samples. In this review, a brief history of DAACPs in animals is presented, followed by discussion of a variety of analytical methods that have been used for diastereomeric separation and detection of peptides. PMID:20490347

  13. Effectiveness of CID, HCD, and ETD with FT MS/MS for Degradomic-Peptidomic Analysis: Comparison of Peptide Identification Methods

    SciTech Connect

    Shen, Yufeng; Tolić, Nikola; Xie, Fang; Zhao, Rui; Purvine, Samuel O.; Schepmoes, Athena A.; Moore, Ronald, J.; Anderson, Gordon A.; Smith, Richard D.

    2011-09-02

    We report on use of an Orbitrap Velos mass spectrometer for comparison of fragmentation methods namely CID-, HCD-, and ETD for FT MS/MS analysis of human blood plasma peptidomic peptides. The peptidomic peptides were able to be identified from CID, HCD, and ETD spectra on specific confidence levels (e.g., 1% false discovery rate) with use of conventional SEQUEST database search software, and the number of identified peptides was increased by ~50% using accurate fragments (e.g., with mass tolerance of 0.05Da) in comparison with traditional moderate accuracy fragments (e.g., with 1 Da mass tolerance) for database search. However, the peptide datasets identified with such decoy search strategy were found to be varied by ~25% in the dataset size and ~20% in the dataset content with type of decoy database and precursor mass tolerances used for database search. CID was evaluated as the largest contributor to the identified peptide datasets, and HCD, and ETD provided ~20% and ~22% respectively additional peptides with accurate fragments for peptide identification, in contrast to ~25% and ~13% respectively with use of moderate accuracy fragments. When long (typically ≥7 amino acids) sequences were used for identification of peptides from the previously published UStags and de novo sequencing methods, HCD was evaluated as the largest contributor, and CID and ETD provided ~26% and ~8% respectively additional peptides from the UStags method and ~26% and ~6% respectively additional peptides from the de novo sequencing method. The peptide datasets identified with the UStags method were little influenced by the decoy database and mass tolerance and 98-99% peptide overlaps could be achieved between these datasets. CID, HCD, and ETD contributed their identifications of various charge state peptides in the m/z range highly overlapped and complementary implementation of CID, HCD, and ETD should be applied to maximize the number of peptides identified. Finally, the investigation

  14. Reducing spatial uncertainty in climatic maps through geostatistical analysis

    NASA Astrophysics Data System (ADS)

    Pesquer, Lluís; Ninyerola, Miquel; Pons, Xavier

    2014-05-01

    Climatic maps from meteorological stations and geographical co-variables can be obtained through correlative models (Ninyerola et al., 2000)*. Nevertheless, the spatial uncertainty of the resulting maps could be reduced. The present work is a new stage over those approaches aiming to study how to obtain better results while characterizing spatial uncertainty. The study area is Catalonia (32000 km2), a region with highly variable relief (0 to 3143 m). We have used 217 stations (321 to 1244 mm) to model the annual precipitation in two steps: 1/ multiple regression using geographical variables (elevation, distance to the coast, latitude, etc) and 2/ refinement of the results by adding the spatial interpolation of the regression residuals with inverse distance weighting (IDW), regularized splines with tension (SPT) or ordinary kriging (OK). Spatial uncertainty analysis is based on an independent subsample (test set), randomly selected in previous works. The main contribution of this work is the analysis of this test set as well as the search for an optimal process of division (split) of the stations in two sets, one used to perform the multiple regression and residuals interpolation (fit set), and another used to compute the quality (test set); optimal division should reduce spatial uncertainty and improve the overall quality. Two methods have been evaluated against classical methods: (random selection RS and leave-one-out cross-validation LOOCV): selection by Euclidian 2D-distance, and selection by anisotropic 2D-distance combined with a 3D-contribution (suitable weighted) from the most representative independent variable. Both methods define a minimum threshold distance, obtained by variogram analysis, between samples. Main preliminary results for LOOCV, RS (average from 10 executions), Euclidian criterion (EU), and for anisotropic criterion (with 1.1 value, UTMY coordinate has a bit more weight than UTMX) combined with 3D criteria (A3D) (1000 factor for elevation

  15. CloudMap: a cloud-based pipeline for analysis of mutant genome sequences.

    PubMed

    Minevich, Gregory; Park, Danny S; Blankenberg, Daniel; Poole, Richard J; Hobert, Oliver

    2012-12-01

    Whole genome sequencing (WGS) allows researchers to pinpoint genetic differences between individuals and significantly shortcuts the costly and time-consuming part of forward genetic analysis in model organism systems. Currently, the most effort-intensive part of WGS is the bioinformatic analysis of the relatively short reads generated by second generation sequencing platforms. We describe here a novel, easily accessible and cloud-based pipeline, called CloudMap, which greatly simplifies the analysis of mutant genome sequences. Available on the Galaxy web platform, CloudMap requires no software installation when run on the cloud, but it can also be run locally or via Amazon's Elastic Compute Cloud (EC2) service. CloudMap uses a series of predefined workflows to pinpoint sequence variations in animal genomes, such as those of premutagenized and mutagenized Caenorhabditis elegans strains. In combination with a variant-based mapping procedure, CloudMap allows users to sharply define genetic map intervals graphically and to retrieve very short lists of candidate variants with a few simple clicks. Automated workflows and extensive video user guides are available to detail the individual analysis steps performed (http://usegalaxy.org/cloudmap). We demonstrate the utility of CloudMap for WGS analysis of C. elegans and Arabidopsis genomes and describe how other organisms (e.g., Zebrafish and Drosophila) can easily be accommodated by this software platform. To accommodate rapid analysis of many mutants from large-scale genetic screens, CloudMap contains an in silico complementation testing tool that allows users to rapidly identify instances where multiple alleles of the same gene are present in the mutant collection. Lastly, we describe the application of a novel mapping/WGS method ("Variant Discovery Mapping") that does not rely on a defined polymorphic mapping strain, and we integrate the application of this method into CloudMap. CloudMap tools and documentation are

  16. Automated tryptic digestion procedure for HPLC/MS/MS peptide mapping of immunoglobulin gamma antibodies in pharmaceutics.

    PubMed

    Chelius, Dirk; Xiao, Gang; Nichols, Andrew C; Vizel, Alona; He, Bing; Dillon, Thomas M; Rehder, Douglas S; Pipes, Gary D; Kraft, Edmund; Oroska, Asha; Treuheit, Michael J; Bondarenko, Pavel V

    2008-06-01

    The rapid growth of antibody drugs and drug candidates in the biopharmaceutical industry has created a demand for automated proteolytic digestion to assist in pharmaceutical stability studies, identity assays and quality control of these therapeutic proteins. Here, we describe the development of a fully automated proteolytic digestion procedure for monoclonal antibodies in solution, which requires a high concentration of denaturants for unfolding. The antibody samples were placed in a 96-well plate or in 0.5-mL Eppendorf tubes. The proteins were then reduced and alkylated in a denaturing solution of 6M guanidine HCl. The denaturing solution was replaced with a digestion buffer using a custom-designed 96-well size-exclusion plate for desalting. The sample was digested for 5 h with two additions of trypsin. The completeness and reproducibility of digestion were verified by reversed-phase high-performance liquid chromatography tandem mass spectrometry (HPLC/MS) analysis of the digestion products. The performance of the automatic digestion was comparable to the currently used manual digestion procedure, but saved time, reduced manual labor, and increased the reproducibility of the tryptic digests. Our method should be useful not only for high-throughput analysis of antibodies, but for other therapeutic protein samples as well. Other applications like gel-free proteomics, where the analysis of a large number of samples is often needed and the completeness of the liquid digestion is critical for the identification of a large number of different proteins, should also benefit from this fully automated liquid proteolytic digestion procedure. PMID:18313251

  17. Expression and purification of isotopically labeled peptide inhibitors and substrates of cAMP-dependant protein kinase A for NMR analysis.

    PubMed

    Masterson, Larry R; Bortone, Nadia; Yu, Tao; Ha, Kim N; Gaffarogullari, Ece C; Nguyen, Oanh; Veglia, Gianluigi

    2009-04-01

    Extensive X-ray crystallographic studies carried out on the catalytic-subunit of protein kinase A (PKA-C) enabled the atomic characterization of inhibitor and/or substrate peptide analogues trapped at its active site. Yet, the structural and dynamic transitions of these peptides from the free to the bound state are missing. These conformational transitions are central to understanding molecular recognition and the enzymatic cycle. NMR spectroscopy allows one to study these phenomena under functionally relevant conditions. However, the amounts of isotopically labeled peptides required for this technique present prohibitive costs for solid-phase peptide synthesis. To enable NMR studies, we have optimized both expression and purification of isotopically enriched substrate/inhibitor peptides using a recombinant fusion protein system. Three of these peptides correspond to the cytoplasmic regions of the wild-type and lethal mutants of the membrane protein phospholamban, while the fourth peptide correspond to the binding epitope of the heat-stable protein kinase inhibitor (PKI(5-24)). The target peptides were fused to the maltose binding protein (MBP), which is further purified using a His(6) tag approach. This convenient protocol allows for the purification of milligram amounts of peptides necessary for NMR analysis. PMID:19027069

  18. Analysis of peptide-protein binding using amino acid descriptors: prediction and experimental verification for human histocompatibility complex HLA-A0201.

    PubMed

    Guan, Pingping; Doytchinova, Irini A; Walshe, Valerie A; Borrow, Persephone; Flower, Darren R

    2005-11-17

    Amino acid descriptors are often used in quantitative structure-activity relationship (QSAR) analysis of proteins and peptides. In the present study, descriptors were used to characterize peptides binding to the human MHC allele HLA-A0201. Two sets of amino acid descriptors were chosen: 93 descriptors taken from the amino acid descriptor database AAindex and the z descriptors defined by Wold and Sandberg. Variable selection techniques (SIMCA, genetic algorithm, and GOLPE) were applied to remove redundant descriptors. Our results indicate that QSAR models generated using five z descriptors had the highest predictivity and explained variance (q2 between 0.6 and 0.7 and r2 between 0.6 and 0.9). Further to the QSAR analysis, 15 peptides were synthesized and tested using a T2 stabilization assay. All peptides bound to HLA-A0201 well, and four peptides were identified as high-affinity binders. PMID:16279801

  19. Ga + TOF-SIMS lineshape analysis for resolution enhancement of MALDI MS spectra of a peptide mixture

    NASA Astrophysics Data System (ADS)

    Malyarenko, D. I.; Chen, H.; Wilkerson, A. L.; Tracy, E. R.; Cooke, W. E.; Manos, D. M.; Sasinowski, M.; Semmes, O. J.

    2004-06-01

    The use of mass spectrometry to obtain molecular profiles indicative of alteration of concentrations of peptides in body fluids is currently the subject of intense investigation. For surface-based time-of-flight mass spectrometry the reliability and specificity of such profiling methods depend both on the resolution of the measuring instrument and on the preparation of samples. The present work is a part of a program to use Ga + beam TOF-SIMS alone, and as an adjunct to MALDI, in the development of reliable protein and peptide markers for diseases. Here, we describe techniques to prepare samples of relatively high-mass peptides, which serve as calibration standards and proxies for biomarkers. These are: Arg8-vasopressin, human angiotensin II, and somatostatin. Their TOF-SIMS spectra show repeatable characteristic features, with mass resolution exceeding 2000, including parent peaks and chemical adducts. The lineshape analysis for high-resolution parent peaks is shown to be useful for filter construction and deconvolution of inferior resolution SELDI-TOF spectra of calibration peptide mixture.

  20. Quantitative Architectural Analysis: A New Approach to Cortical Mapping

    ERIC Educational Resources Information Center

    Schleicher, Axel; Morosan, Patricia; Amunts, Katrin; Zilles, Karl

    2009-01-01

    Results from functional imaging studies are often still interpreted using the classical architectonic brain maps of Brodmann and his successors. One obvious weakness in traditional, architectural mapping is the subjective nature of localizing borders between cortical areas by means of a purely visual, microscopical examination of histological…

  1. In silico analysis and experimental validation of lipoprotein and novel Tat signal peptides processing in Anabaena sp. PCC7120.

    PubMed

    Kumari, Sonika; Chaurasia, Akhilesh Kumar

    2015-12-01

    Signal peptide (SP) plays a pivotal role in protein translocation. Lipoprotein- and twin arginine translocase (Tat) dependent signal peptides were studied in All3087, a homolog of competence protein of Synechocystis PCC6803 and in two putative alkaline phosphatases (ALPs, Alr2234 and Alr4976), respectively. In silico analysis of All3087 is shown to possess the characteristics feature of competence proteins such as helix-hairpin-helix, N and C-terminal HKD endonuclease domain, calcium binding domain and N-terminal lipoprotein signal peptide. The SP recognition-cleavage site in All3087 was predicted (AIA-AC) using SignalP while further in-depth analysis using Pred-Lipo and WebLogo analysis for consensus sequence showed it as IAA-C. Activities of putative ALPs were confirmed by heterologous overexpression, activity assessment and zymogram analysis. ALP activity in Anabaena remains cell bound in log-phase, but during late log/stationary phase, an enhanced ALP activity was detected in extracellular milieu. The enhancement of ALP activity during stationary phase was not only due to inorganic phosphate limitation but also contributed by the presence of novel bipartite Tat-SP. The Tat signal transported the folded active ALPs to the membrane, followed by anchoring into the membrane and successive cleavage enabling transportation of the ALPs to the extracellular milieu, because of bipartite architecture and processing of transit Tat-SP. PMID:26626354

  2. Genetic analysis of arsenic accumulation in maize using QTL mapping

    PubMed Central

    Fu, Zhongjun; Li, Weihua; Xing, Xiaolong; Xu, Mengmeng; Liu, Xiaoyang; Li, Haochuan; Xue, Yadong; Liu, Zonghua; Tang, Jihua

    2016-01-01

    Arsenic (As) is a toxic heavy metal that can accumulate in crops and poses a threat to human health. The genetic mechanism of As accumulation is unclear. Herein, we used quantitative trait locus (QTL) mapping to unravel the genetic basis of As accumulation in a maize recombinant inbred line population derived from the Chinese crossbred variety Yuyu22. The kernels had the lowest As content among the different maize tissues, followed by the axes, stems, bracts and leaves. Fourteen QTLs were identified at each location. Some of these QTLs were identified in different environments and were also detected by joint analysis. Compared with the B73 RefGen v2 reference genome, the distributions and effects of some QTLs were closely linked to those of QTLs detected in a previous study; the QTLs were likely in strong linkage disequilibrium. Our findings could be used to help maintain maize production to satisfy the demand for edible corn and to decrease the As content in As-contaminated soil through the selection and breeding of As pollution-safe cultivars. PMID:26880701

  3. Classification Algorithms for Big Data Analysis, a Map Reduce Approach

    NASA Astrophysics Data System (ADS)

    Ayma, V. A.; Ferreira, R. S.; Happ, P.; Oliveira, D.; Feitosa, R.; Costa, G.; Plaza, A.; Gamba, P.

    2015-03-01

    Since many years ago, the scientific community is concerned about how to increase the accuracy of different classification methods, and major achievements have been made so far. Besides this issue, the increasing amount of data that is being generated every day by remote sensors raises more challenges to be overcome. In this work, a tool within the scope of InterIMAGE Cloud Platform (ICP), which is an open-source, distributed framework for automatic image interpretation, is presented. The tool, named ICP: Data Mining Package, is able to perform supervised classification procedures on huge amounts of data, usually referred as big data, on a distributed infrastructure using Hadoop MapReduce. The tool has four classification algorithms implemented, taken from WEKA's machine learning library, namely: Decision Trees, Naïve Bayes, Random Forest and Support Vector Machines (SVM). The results of an experimental analysis using a SVM classifier on data sets of different sizes for different cluster configurations demonstrates the potential of the tool, as well as aspects that affect its performance.

  4. Genetic analysis of arsenic accumulation in maize using QTL mapping.

    PubMed

    Fu, Zhongjun; Li, Weihua; Xing, Xiaolong; Xu, Mengmeng; Liu, Xiaoyang; Li, Haochuan; Xue, Yadong; Liu, Zonghua; Tang, Jihua

    2016-01-01

    Arsenic (As) is a toxic heavy metal that can accumulate in crops and poses a threat to human health. The genetic mechanism of As accumulation is unclear. Herein, we used quantitative trait locus (QTL) mapping to unravel the genetic basis of As accumulation in a maize recombinant inbred line population derived from the Chinese crossbred variety Yuyu22. The kernels had the lowest As content among the different maize tissues, followed by the axes, stems, bracts and leaves. Fourteen QTLs were identified at each location. Some of these QTLs were identified in different environments and were also detected by joint analysis. Compared with the B73 RefGen v2 reference genome, the distributions and effects of some QTLs were closely linked to those of QTLs detected in a previous study; the QTLs were likely in strong linkage disequilibrium. Our findings could be used to help maintain maize production to satisfy the demand for edible corn and to decrease the As content in As-contaminated soil through the selection and breeding of As pollution-safe cultivars. PMID:26880701

  5. Operational mode analysis of the maps NTP system

    SciTech Connect

    Linet, F.L.; Bernard, S.; Carruge, D.; Poitevin, Y.; Raepsaet, X.

    1996-03-01

    Within the framework of the french NTP program MAPS, the analysis of the (start-up/shut-down) transient sequences whose negative impact on the specific impulsion Isp is important, requires the evaluation of the hydrogen system performance and consequently the development of a simulation computer program. This work induces a preliminary evaluation of the hydrogen system performance under nominal operating conditions. A first approach of the transient operating mode has been simultaneously performed; more specifically the evolution of the core during a shut-down sequence has been studied in order to improve the residual power evacuation and optimize necessary hydrogen amounts for cooling. Furthermore the {open_quote}{open_quote}SIMAPS{close_quote}{close_quote} computer program based on the 3D thermohydraulic code {open_quote}{open_quote}FLICA 4{close_quote}{close_quote} is being developed to analyze transient process and its benchmarking under nominal conditions is under way. Its summary presentation is given in conclusion. {copyright} {ital 1996 American Institute of Physics.}

  6. Transcriptome analysis of Streptococcus pneumoniae treated with the designed antimicrobial peptides, DM3.

    PubMed

    Le, Cheng-Foh; Gudimella, Ranganath; Razali, Rozaimi; Manikam, Rishya; Sekaran, Shamala Devi

    2016-01-01

    In our previous studies, we generated a short 13 amino acid antimicrobial peptide (AMP), DM3, showing potent antipneumococcal activity in vitro and in vivo. Here we analyse the underlying mechanisms of action using Next-Generation transcriptome sequencing of penicillin (PEN)-resistant and PEN-susceptible pneumococci treated with DM3, PEN, and combination of DM3 and PEN (DM3PEN). DM3 induced differential expression in cell wall and cell membrane structural and transmembrane processes. Notably, DM3 altered the expression of competence-induction pathways by upregulating CelA, CelB, and CglA while downregulating Ccs16, ComF, and Ccs4 proteins. Capsular polysaccharide subunits were downregulated in DM3-treated cells, however, it was upregulated in PEN- and DM3PEN-treated groups. Additionally, DM3 altered the amino acids biosynthesis pathways, particularly targeting ribosomal rRNA subunits. Downregulation of cationic AMPs resistance pathway suggests that DM3 treatment could autoenhance pneumococci susceptibility to DM3. Gene enrichment analysis showed that unlike PEN and DM3PEN, DM3 treatment exerted no effect on DNA-binding RNA polymerase activity but observed downregulation of RpoD and RNA polymerase sigma factor. In contrast to DM3, DM3PEN altered the regulation of multiple purine/pyrimidine biosynthesis and metabolic pathways. Future studies based on in vitro experiments are proposed to investigate the key pathways leading to pneumococcal cell death caused by DM3. PMID:27225022

  7. Evolution of Conus Peptide Toxins: Analysis of Conus californicus Reeve, 1844

    PubMed Central

    Biggs, Jason S.; Watkins, Maren; Puillandre, Nicolas; Ownby, John-Paul; Lopez-Vera, Estuardo; Christensen, Sean; Moreno, Karla Juarez; Navarro, Alexei Licea; Corneli, Patrice Showers; Olivera, Baldomero M.

    2010-01-01

    Conus species are characterized by their hyperdiverse toxins, encoded by a few gene superfamilies. Our phylogenies of the genus, based on mitochondrial genes, confirm previous results that C. californicus is highly divergent from all other species. Genetic and biochemical analysis of their venom peptides comprise the fifteen most abundant conopeptides and over 50 mature cDNA transcripts from the venom duct. Although C. californicus venom retains many of the general properties of other Conus species, they share only half of the toxin gene superfamilies found in other Conus species. Thus, in these two lineages, approximately half of the rapidly diversifying gene superfamilies originated after an early Tertiary split. Such results demonstrate that, unlike endogenously acting gene families, these genes are likely to be significantly more restricted in their phylogenetic distribution. In concordance with the evolutionary duistance of C. californicus from other species, there are aspects of prey-capture behavior and prey preferences of this species that diverges significantly from all other Conus. PMID:20363338

  8. Higher efficiency soluble prokaryotic expression, purification, and structural analysis of antimicrobial peptide G13.

    PubMed

    Che, Yuanyuan; Lu, Yinghu; Zha, Xiangdong; Huang, Huoqing; Yang, Peilong; Ma, Lijuan; Xu, Xuejiao

    2016-03-01

    G13 is a 19-residue cationic antimicrobial peptide derived from granulysin. In order to achieve high-level expression of G13 in Escherichia coli cells, and to reduce downstream processing costs, we introduced an Asp-Pro acid labile bond between the His-Patch thioredoxin and G13 and constructed the recombinant plasmid pThiohisA-DP-G13. The plasmid was transformed into E. coli BL21 (DE3). After induction with isopropyl-β-d-thiogalactopyranoside for 5 h, the fusion protein accumulated up to 200 mg/L in soluble form. The fusion protein was released by a high pressure homogenizer, cleaved using 13% acetic acid at 50 °C hydrolysis for 72 h. The recombinant G13 (r-G13) was then successively purified by fractional precipitation with ammonium sulfate and trichloroacetic acid, followed by one-step cation exchange chromatography. The purified r-G13 displayed a single band (about 2.2 kDa) as analyzed by Tris-Tricine buffered SDS-PAGE, and its precise molecular weight was confirmed using tandem mass spectrometry. Analysis of r-G13 by circular dichroism (CD) indicated that r-G13 contained predominantly β-sheet and random coil. Agar plate diffusion assay revealed that the r-G13 exhibited antibacterial activity against both Bacillus subtilis and E. coli. PMID:26581777

  9. Enrichment of Extracellular Matrix Proteins from Tissues and Digestion into Peptides for Mass Spectrometry Analysis.

    PubMed

    Naba, Alexandra; Clauser, Karl R; Hynes, Richard O

    2015-01-01

    The extracellular matrix (ECM) is a complex meshwork of cross-linked proteins that provides biophysical and biochemical cues that are major regulators of cell proliferation, survival, migration, etc. The ECM plays important roles in development and in diverse pathologies including cardio-vascular and musculo-skeletal diseases, fibrosis, and cancer. Thus, characterizing the composition of ECMs of normal and diseased tissues could lead to the identification of novel prognostic and diagnostic biomarkers and potential novel therapeutic targets. However, the very nature of ECM proteins (large in size, cross-linked and covalently bound, heavily glycosylated) has rendered biochemical analyses of ECMs challenging. To overcome this challenge, we developed a method to enrich ECMs from fresh or frozen tissues and tumors that takes advantage of the insolubility of ECM proteins. We describe here in detail the decellularization procedure that consists of sequential incubations in buffers of different pH and salt and detergent concentrations and that results in 1) the extraction of intracellular (cytosolic, nuclear, membrane and cytoskeletal) proteins and 2) the enrichment of ECM proteins. We then describe how to deglycosylate and digest ECM-enriched protein preparations into peptides for subsequent analysis by mass spectrometry. PMID:26273955

  10. Transcriptome analysis of Streptococcus pneumoniae treated with the designed antimicrobial peptides, DM3

    PubMed Central

    Le, Cheng-Foh; Gudimella, Ranganath; Razali, Rozaimi; Manikam, Rishya; Sekaran, Shamala Devi

    2016-01-01

    In our previous studies, we generated a short 13 amino acid antimicrobial peptide (AMP), DM3, showing potent antipneumococcal activity in vitro and in vivo. Here we analyse the underlying mechanisms of action using Next-Generation transcriptome sequencing of penicillin (PEN)-resistant and PEN-susceptible pneumococci treated with DM3, PEN, and combination of DM3 and PEN (DM3PEN). DM3 induced differential expression in cell wall and cell membrane structural and transmembrane processes. Notably, DM3 altered the expression of competence-induction pathways by upregulating CelA, CelB, and CglA while downregulating Ccs16, ComF, and Ccs4 proteins. Capsular polysaccharide subunits were downregulated in DM3-treated cells, however, it was upregulated in PEN- and DM3PEN-treated groups. Additionally, DM3 altered the amino acids biosynthesis pathways, particularly targeting ribosomal rRNA subunits. Downregulation of cationic AMPs resistance pathway suggests that DM3 treatment could autoenhance pneumococci susceptibility to DM3. Gene enrichment analysis showed that unlike PEN and DM3PEN, DM3 treatment exerted no effect on DNA-binding RNA polymerase activity but observed downregulation of RpoD and RNA polymerase sigma factor. In contrast to DM3, DM3PEN altered the regulation of multiple purine/pyrimidine biosynthesis and metabolic pathways. Future studies based on in vitro experiments are proposed to investigate the key pathways leading to pneumococcal cell death caused by DM3. PMID:27225022

  11. Genome-wide analysis of signal peptide functionality in Lactobacillus plantarum WCFS1

    PubMed Central

    Mathiesen, Geir; Sveen, Anita; Brurberg, May Bente; Fredriksen, Lasse; Axelsson, Lars; Eijsink, Vincent GH

    2009-01-01

    Background Lactobacillus plantarum is a normal, potentially probiotic, inhabitant of the human gastrointestinal (GI) tract. The bacterium has great potential as food-grade cell factory and for in situ delivery of biomolecules. Since protein secretion is important both for probiotic activity and in biotechnological applications, we have carried out a genome-wide experimental study of signal peptide (SP) functionality. Results We have constructed a library of 76 Sec-type signal peptides from L. plantarum WCFS1 that were predicted to be cleaved by signal peptidase I. SP functionality was studied using staphylococcal nuclease (NucA) as a reporter protein. 82% of the SPs gave significant extracellular NucA activity. Levels of secreted NucA varied by a dramatic 1800-fold and this variation was shown not to be the result of different mRNA levels. For the best-performing SPs all produced NucA was detected in the culture supernatant, but the secretion efficiency decreased for the less well performing SPs. Sequence analyses of the SPs and their cognate proteins revealed four properties that correlated positively with SP performance for NucA: high hydrophobicity, the presence of a transmembrane helix predicted by TMHMM, the absence of an anchoring motif in the cognate protein, and the length of the H+C domain. Analysis of a subset of SPs with a lactobacillal amylase (AmyA) showed large variation in production levels and secretion efficiencies. Importantly, there was no correlation between SP performance with NucA and the performance with AmyA. Conclusion This is the first comprehensive experimental study showing that predicted SPs in the L. plantarum genome actually are capable of driving protein secretion. The results reveal considerable variation between the SPs that is at least in part dependent on the protein that is secreted. Several SPs stand out as promising candidates for efficient secretion of heterologous proteins in L. plantarum. The results for NucA provide some

  12. A Mathematical Analysis of Semantic Maps, with Theoretical and Applied Implications for Blended Learning Software

    ERIC Educational Resources Information Center

    Tang, Michael; David, Hyerle; Byrne, Roxanne; Tran, John

    2012-01-01

    This paper is a mathematical (Boolean) analysis a set of cognitive maps called Thinking Maps[R], based on Albert Upton's semantic principles developed in his seminal works, Design for Thinking (1961) and Creative Analysis (1961). Albert Upton can be seen as a brilliant thinker who was before his time or after his time depending on the future of…

  13. Analysis of protamine peptides in insulin pharmaceutical formulations by capillary electrophoresis.

    PubMed

    Lamalle, Caroline; Servais, Anne-Catherine; Demelenne, Alice; Crommen, Jacques; Fillet, Marianne

    2016-03-01

    Protamines are a group of highly basic peptides that are sometimes added to insulin formulations to prolong the pharmacological action. In this study, different methods were investigated to identify protamine in insulin formulations. Capillary electrophoresis in aqueous and non-aqueous media was tested to separate these peptides with very close amino acid sequences. Different buffers (phosphate or formate, both acidified) and various additives (principally negatively charged and neutral surfactants) were investigated to optimize peptide separation. Finally, a micellar electrokinetic capillary chromatography method using a capillary of 120 cm effective length and an aqueous background electrolyte made up of 100 mM phosphate buffer (pH 2) and 50 mM Thesit® gave the best results, providing the separation of the four major protamine peptides within 25 min. PMID:26829340

  14. [The Qualitative Analysis of the Amide Derivative of HLDF-6 Peptide and Its Metabolites with the Use of Tritium- and Deuterium-Labeled Derivatives].

    PubMed

    Zolotarev, A; Dadayan, A K; Kost, N V; Voevodina, M E; Sokolov, O Y; Kozik, V S; Shram, S I; Azev, V N; Bocharov, E V; Bogachouk, A P; Lipkin, V M; Myasoedov, N F

    2015-01-01

    The goal of the study was to elaborate the pharmacokinetics methods of the amide derivative of peptide HLDF-6 (TGENHR-NH2) and its range of nootropic and neuroprotective activity is wide. The hexapeptide 41TGENHR46 is a fragment of the HDLF differentiation factor. It forms the basis for the development of preventive and therapeutic preparations for treating cerebrovascular and neurodegenerative conditions. Pharmacokinetic and molecular mechanisms of the action of the HLDF-6 peptide were studied using tritium- and deuterium-labeled derivatives of this peptide, produced with the use of the high-temperature solid-state catalytic isotope exchange reaction (HSCIE). This reaction was employed to produce the tritium-labeled peptide [3H]TGENHR-NH2 with a molar radioactivity of 230 Ci/mmol and the deuterium-labeled peptide [2H]TGENHR-NH2 with an average deuterium incorporation equal to 10.5 atoms. It was shown by the NMR spectroscopy that the isotope label distribution over the labeled peptide's molecule was uniform, which allowed qualitative analysis ofboth the peptide itself and its fragments in the organism's tissues to be conducted. The newly developed pharmacokinetics method makes it possible to avoid almost completely losses of the peptides under study due to biodegradation during the analysis of tissues. These labeled peptides were used in mice, rats and rabbits to study the pharmacokinetics of the peptide and to calculate the values of its principal pharmacokinetic parameters. Characteristics of its pharmacokinetic profile in the blood were obtained, the hypothesis of pharmacokinetics linearity tested, its metabolism analyzed and its bioavailability value, 34%, calculated. It has been shown that the studied TGENHR-NH2 peptide shows high resistance to hydrolysis in the blood plasma, with dipeptidyl aminopeptidases making the largest contribution to its hydrolysis. PMID:27125017

  15. Disposable pencil graphite electrode modified with peptide nanotubes for Vitamin B12 analysis

    NASA Astrophysics Data System (ADS)

    Pala, Betül Bozdoğan; Vural, Tayfun; Kuralay, Filiz; Çırak, Tamer; Bolat, Gülçin; Abacı, Serdar; Denkbaş, Emir Baki

    2014-06-01

    In this study, peptide nanostructures from diphenylalanine were synthesized in various solvents with various polarities and characterized with Scanning Electron Microscopy (SEM) and Powder X-ray Diffraction (PXRD) techniques. Formation of peptide nanofibrils, nanovesicles, nanoribbons, and nanotubes was observed in different solvent mediums. In order to investigate the effects of peptide nanotubes (PNT) on electrochemical behavior of disposable pencil graphite electrodes (PGE), electrode surfaces were modified with fabricated peptide nanotubes. Electrochemical activity of the pencil graphite electrode was increased with the deposition of PNTs on the surface. The effects of the solvent type, the peptide nanotube concentration, and the passive adsorption time of peptide nanotubes on pencil graphite electrode were studied. For further electrochemical studies, electrodes were modified for 30 min by immobilizing PNTs, which were prepared in water at 6 mg/mL concentration. Vitamin B12 analyses were performed by the Square Wave (SW) voltammetry method using modified PGEs. The obtained data showed linearity over the range of 0.2 μM and 9.50 μM Vitamin B12 concentration with high sensitivity. Results showed that PNT modified PGEs were highly simple, fast, cost effective, and feasible for the electro-analytical determination of Vitamin B12 in real samples.

  16. rMAPS: RNA map analysis and plotting server for alternative exon regulation

    PubMed Central

    Park, Juw Won; Jung, Sungbo; Rouchka, Eric C.; Tseng, Yu-Ting; Xing, Yi

    2016-01-01

    RNA-binding proteins (RBPs) play a critical role in the regulation of alternative splicing (AS), a prevalent mechanism for generating transcriptomic and proteomic diversity in eukaryotic cells. Studies have shown that AS can be regulated by RBPs in a binding-site-position dependent manner. Depending on where RBPs bind, splicing of an alternative exon can be enhanced or suppressed. Therefore, spatial analyses of RBP motifs and binding sites around alternative exons will help elucidate splicing regulation by RBPs. The development of high-throughput sequencing technologies has allowed transcriptome-wide analyses of AS and RBP–RNA interactions. Given a set of differentially regulated alternative exons obtained from RNA sequencing (RNA-seq) experiments, the rMAPS web server (http://rmaps.cecsresearch.org) performs motif analyses of RBPs in the vicinity of alternatively spliced exons and creates RNA maps that depict the spatial patterns of RBP motifs. Similarly, rMAPS can also perform spatial analyses of RBP–RNA binding sites identified by cross-linking immunoprecipitation sequencing (CLIP-seq) experiments. We anticipate rMAPS will be a useful tool for elucidating RBP regulation of alternative exon splicing using high-throughput sequencing data. PMID:27174931

  17. rMAPS: RNA map analysis and plotting server for alternative exon regulation.

    PubMed

    Park, Juw Won; Jung, Sungbo; Rouchka, Eric C; Tseng, Yu-Ting; Xing, Yi

    2016-07-01

    RNA-binding proteins (RBPs) play a critical role in the regulation of alternative splicing (AS), a prevalent mechanism for generating transcriptomic and proteomic diversity in eukaryotic cells. Studies have shown that AS can be regulated by RBPs in a binding-site-position dependent manner. Depending on where RBPs bind, splicing of an alternative exon can be enhanced or suppressed. Therefore, spatial analyses of RBP motifs and binding sites around alternative exons will help elucidate splicing regulation by RBPs. The development of high-throughput sequencing technologies has allowed transcriptome-wide analyses of AS and RBP-RNA interactions. Given a set of differentially regulated alternative exons obtained from RNA sequencing (RNA-seq) experiments, the rMAPS web server (http://rmaps.cecsresearch.org) performs motif analyses of RBPs in the vicinity of alternatively spliced exons and creates RNA maps that depict the spatial patterns of RBP motifs. Similarly, rMAPS can also perform spatial analyses of RBP-RNA binding sites identified by cross-linking immunoprecipitation sequencing (CLIP-seq) experiments. We anticipate rMAPS will be a useful tool for elucidating RBP regulation of alternative exon splicing using high-throughput sequencing data. PMID:27174931

  18. Association analysis of formyl peptide receptor 2 (FPR2) polymorphisms and aspirin exacerbated respiratory diseases.

    PubMed

    Kim, Hee-Jeong; Cho, Sung-Hwan; Park, Jong-Sook; Lee, Tae-Hyeong; Lee, Eun-Ju; Kim, Yong-Hoon; Uh, Soo-Taek; Chung, Il Yup; Kim, Mi-Kyeong; Choi, Inseon S; Park, Byung-Lae; Shin, Hyoung-Doo; Park, Choon-Sik

    2012-04-01

    Aspirin-exacerbated respiratory diseases (AERD) are associated with the metabolism of arachidonic acid. FPR2 (formyl peptide receptor2) is a high-affinity ligand receptor for potent anti-inflammatory lipid metabolites: lipoxins. Thus, functional alterations of the FPR2 may contribute to AERD. We investigated the relationship between single-nucleotide polymorphisms (SNPs) in the FPR2 and AERD. Asthmatics were categorized into AERD <15% decreases in forced expiratory volume in one second (FEV(1)), and/or naso-ocular reactions after oral aspirin challenge (n=170) and aspirin-tolerant asthma (ATA, n=268). In all, 11 SNPs were genotyped. FPR2 protein expressions on CD14-positive monocytes in peripheral blood were measured using flow cytometric analysis. We performed RT-PCR of the FPR2 mRNA expressed by peripheral blood mononuclear cells. Logistic regression analysis showed that the minor allele frequency of FPR2 -4209T>G (rs1769490) in intron 2 was significantly lower in the AERD group (n=170) than in the ATA group (n=268) (P=0.006, P(corr)=0.04, recessive model). The decline of FEV(1) after aspirin challenge was significantly lower in the subjects with GG homozygotes of FPR2 -4209T>G than those with the other genotypes (P=0.0002). Asthmatic homozygotes for FPR2 -4209T>G minor allele exhibited significantly higher FPR2 protein expression in CD14-positive monocytes than did those with the common allele of FPR2 -4209T>G allele (P=0.01). There was no difference in the expression of the wild form and the exon 2 deleted variant form of FPR2 gene according to the genotypes of FPR2 -4209T>G. The minor allele at FPR2 -4209T>G may have a protective role against the development of AERD, via increase of FPR2 protein expression in inflammatory cells. PMID:22377711

  19. Subpopulation-Specific Transcriptome Analysis of Competence-Stimulating-Peptide-Induced Streptococcus mutans▿†

    PubMed Central

    Lemme, André; Gröbe, Lothar; Reck, Michael; Tomasch, Jürgen; Wagner-Döbler, Irene

    2011-01-01

    Competence-stimulating-peptide (CSP)-mediated competence development in Streptococcus mutans is a transient and biphasic process, since only a subpopulation induces the expression of ComX in the presence of CSP, and the activation of the DNA uptake machinery in this fraction shuts down ∼3 to 4 h postinduction. Here, we combine for the first time, to our knowledge, the bacterial flow-cytometric sorting of cells and subpopulation-specific transcriptome analysis of both the competent and noncompetent fraction of CSP-treated S. mutans cells. Sorting was guided by a ComX-green fluorescent protein (ComX-GFP) reporter, and the transcriptome analysis demonstrated the successful combination of both methods, because a strong enrichment of transcripts for comX and its downstream genes was achieved. Three two-component systems were expressed in the competent fraction, and among them was ComDE. Moreover, the recently identified regulator system ComR/S was expressed exclusively in the competent fraction. In contrast, the expression of bacteriocin-related genes was at the same level in all cells. GFP reporter strains for ComE and CipB (mutacin V) confirmed this expression pattern on the single-cell level. Fluorescence microscopy revealed that some ComX-expressing cells committed autolysis in an early stage of competence initiation. In viable ComX-expressing cells, the uptake of DNA could be shown on the single-cell level. This study demonstrates that all cells in the population respond to CSP through the activation of bacteriocin-related genes. Some of these cells start to activate ComX expression but then segregate into two subpopulations, one becoming competent and another one that lyses, resulting in intrapopulation diversity. PMID:21317319

  20. Error analysis of deep sequencing of phage libraries: peptides censored in sequencing.

    PubMed

    Matochko, Wadim L; Derda, Ratmir

    2013-01-01

    Next-generation sequencing techniques empower selection of ligands from phage-display libraries because they can detect low abundant clones and quantify changes in the copy numbers of clones without excessive selection rounds. Identification of errors in deep sequencing data is the most critical step in this process because these techniques have error rates >1%. Mechanisms that yield errors in Illumina and other techniques have been proposed, but no reports to date describe error analysis in phage libraries. Our paper focuses on error analysis of 7-mer peptide libraries sequenced by Illumina method. Low theoretical complexity of this phage library, as compared to complexity of long genetic reads and genomes, allowed us to describe this library using convenient linear vector and operator framework. We describe a phage library as N × 1 frequency vector n = ||ni||, where ni is the copy number of the ith sequence and N is the theoretical diversity, that is, the total number of all possible sequences. Any manipulation to the library is an operator acting on n. Selection, amplification, or sequencing could be described as a product of a N × N matrix and a stochastic sampling operator (Sa). The latter is a random diagonal matrix that describes sampling of a library. In this paper, we focus on the properties of Sa and use them to define the sequencing operator (Seq). Sequencing without any bias and errors is Seq = Sa IN, where IN is a N × N unity matrix. Any bias in sequencing changes IN to a nonunity matrix. We identified a diagonal censorship matrix (CEN), which describes elimination or statistically significant downsampling, of specific reads during the sequencing process. PMID:24416071

  1. The delta EEG (sleep)-inducing peptide (DSIP). XI. Amino-acid analysis, sequence, synthesis and activity of the nonapeptide.

    PubMed

    Schoenenberger, G A; Maier, P F; Tobler, H J; Wilson, K; Monnier, M

    1978-09-01

    A peptide which induces slow-wave EEG (sleep) after intraventricular infusion into the brain has been isolated from the extracorporeal dialysate of cerebral venous blood in rabbits submitted to hypnogenic electrical stimulation of the intralaminar thalamic area. It was shown by amino-acid analysis and sequence determination to be Trp-Ala-Gly-Gly-Asp-Ala-Ser-Gly-Glu and named "Delta Sleep-Inducing Peptide" (DSIP). This compound was synthesized as well as 5 possible metabolic products (1--8, 2--9, 2--8, 1--4 and 5--9), 2 nonapeptide analogues (with one and two amino-acids exchanged) and a related tripeptide (Trp-Ser-Glu). All 9 synthetic peptides were infused intraventricularly in rabbits (6 nmol/kg in 0.05 ml of CSF-like solution over 3.5 min) and tested under double-blind conditions. A total of 61 rabbits including controls were used. The EEG from the frontal neocortex and the limbic archicortex were subjected to direct fast-Fourier transformation and analyzed by an 1108 computer system. A highly specific delta and spindle EEG-enhancing effect of the synthetic DSIP could be demonstrated. The mean increase of EEG delta activity reached 35% in the neocortex and limbic cortex as compared to control animals receiving CSF-like solution or any of the other 8 peptides. The final chemical characterization of the synthetic DSIP revealed that only the pure alpha-aspartyl peptide is highly active in contrast to its beta-Asp isomer. A neurohumoral modulating and programming activity was suggested. PMID:568769

  2. SNP and haplotype mapping for genetic analysis in the rat.

    PubMed

    Saar, Kathrin; Beck, Alfred; Bihoreau, Marie-Thérèse; Birney, Ewan; Brocklebank, Denise; Chen, Yuan; Cuppen, Edwin; Demonchy, Stephanie; Dopazo, Joaquin; Flicek, Paul; Foglio, Mario; Fujiyama, Asao; Gut, Ivo G; Gauguier, Dominique; Guigo, Roderic; Guryev, Victor; Heinig, Matthias; Hummel, Oliver; Jahn, Niels; Klages, Sven; Kren, Vladimir; Kube, Michael; Kuhl, Heiner; Kuramoto, Takashi; Kuroki, Yoko; Lechner, Doris; Lee, Young-Ae; Lopez-Bigas, Nuria; Lathrop, G Mark; Mashimo, Tomoji; Medina, Ignacio; Mott, Richard; Patone, Giannino; Perrier-Cornet, Jeanne-Antide; Platzer, Matthias; Pravenec, Michal; Reinhardt, Richard; Sakaki, Yoshiyuki; Schilhabel, Markus; Schulz, Herbert; Serikawa, Tadao; Shikhagaie, Medya; Tatsumoto, Shouji; Taudien, Stefan; Toyoda, Atsushi; Voigt, Birger; Zelenika, Diana; Zimdahl, Heike; Hubner, Norbert

    2008-05-01

    The laboratory rat is one of the most extensively studied model organisms. Inbred laboratory rat strains originated from limited Rattus norvegicus founder populations, and the inherited genetic variation provides an excellent resource for the correlation of genotype to phenotype. Here, we report a survey of genetic variation based on almost 3 million newly identified SNPs. We obtained accurate and complete genotypes for a subset of 20,238 SNPs across 167 distinct inbred rat strains, two rat recombinant inbred panels and an F2 intercross. Using 81% of these SNPs, we constructed high-density genetic maps, creating a large dataset of fully characterized SNPs for disease gene mapping. Our data characterize the population structure and illustrate the degree of linkage disequilibrium. We provide a detailed SNP map and demonstrate its utility for mapping of quantitative trait loci. This community resource is openly available and augments the genetic tools for this workhorse of physiological studies. PMID:18443594

  3. Purification, structure-function analysis, and molecular characterization of novel linear peptides from scorpion Opisthacanthus madagascariensis.

    PubMed

    Dai, Li; Corzo, Gerardo; Naoki, Hideo; Andriantsiferana, Marta; Nakajima, Terumi

    2002-05-24

    In the previous report [Biochem. Biophys. Res. Commun. 286 (2001) 820], we described a novel short linear peptide, IsCT, with cytolytic activity isolated from the venom of scorpion Opisthacanthus madagascariensis. From the same scorpion venom, we further purified and characterized three short linear peptides named IsCT2, IsCTf, and IsCT2f that shared high homology with IsCT, while with different C-terminal areas between IsCT/IsCT2 and IsCTf/IsCT2f. Structure-activity relationship was analyzed by performing vivo and vitro assays and circular dichroism spectroscopy. Like IsCT, IsCT2 showed broad activity spectra against microbes (Gram positive and negative bacteria as well as fungi) and relatively weak hemolytic activity against sheep red blood cells. It adopts an amphipathic alpha-helical structure in aqueous TFE and is able to disrupt the artificial membrane. However, the other two peptides IsCTf and IsCT2f showed no activity in antimicrobial or hemolytic assay. Furthermore, IsCTf and IsCT2f cannot form amphipathic alpha-helix while demonstrating random coil structure in aqueous TFE, which might result in their lost cytolytic activity. IsCTf and IsCT2f both exist in the crude venom and are proved to be enzymatic products from IsCT and IsCT2. Whether they have some other biological activity is still unclear. In addition, we got the cDNAs encoding the precursors of IsCT and IsCT2. Besides the signal peptide, they still contain an unusual acidic pro-peptide at the C-terminal that was quite different from other known precursors of scorpion venom peptides. The novel structure and biological activity of these peptides proposed them to be a new class in scorpion venom. PMID:12054688

  4. The analysis of three typical tropospheric mapping functions

    NASA Astrophysics Data System (ADS)

    Xie, Shaofeng; Jin, Liyang; Zhang, Pengfei

    2015-12-01

    Processing the tropospheric data provided by IGS stations of china with the NMF function,VMF1 function and GMF function. comparing the baseline repetition rate. If the change of IGS station latitude and the cutoff elevation angles can make the height correction become more precision when using this three mapping function. And whether the dynamic mapping function can meet the accuracy requirement with the highly temporal.

  5. SUBMILLIMETER NUMBER COUNTS FROM STATISTICAL ANALYSIS OF BLAST MAPS

    SciTech Connect

    Patanchon, Guillaume; Ade, Peter A. R.; Griffin, Matthew; Hargrave, Peter C.; Mauskopf, Philip; Moncelsi, Lorenzo; Pascale, Enzo; Bock, James J.; Chapin, Edward L.; Halpern, Mark; Marsden, Gaelen; Scott, Douglas; Devlin, Mark J.; Dicker, Simon R.; Klein, Jeff; Rex, Marie; Gundersen, Joshua O.; Hughes, David H.; Netterfield, Calvin B.; Olmi, Luca

    2009-12-20

    We describe the application of a statistical method to estimate submillimeter galaxy number counts from confusion-limited observations by the Balloon-borne Large Aperture Submillimeter Telescope (BLAST). Our method is based on a maximum likelihood fit to the pixel histogram, sometimes called 'P(D)', an approach which has been used before to probe faint counts, the difference being that here we advocate its use even for sources with relatively high signal-to-noise ratios. This method has an advantage over standard techniques of source extraction in providing an unbiased estimate of the counts from the bright end down to flux densities well below the confusion limit. We specifically analyze BLAST observations of a roughly 10 deg{sup 2} map centered on the Great Observatories Origins Deep Survey South field. We provide estimates of number counts at the three BLAST wavelengths 250, 350, and 500 mum; instead of counting sources in flux bins we estimate the counts at several flux density nodes connected with power laws. We observe a generally very steep slope for the counts of about -3.7 at 250 mum, and -4.5 at 350 and 500 mum, over the range approx0.02-0.5 Jy, breaking to a shallower slope below about 0.015 Jy at all three wavelengths. We also describe how to estimate the uncertainties and correlations in this method so that the results can be used for model-fitting. This method should be well suited for analysis of data from the Herschel satellite.

  6. CapsidMaps: Protein-protein interaction pattern discovery platform for the structural analysis of virus capsids using Google Maps

    PubMed Central

    Carrillo-Tripp, Mauricio; Montiel-García, Daniel Jorge; Brooks, Charles L.; Reddy, Vijay

    2016-01-01

    Structural analysis and visualization of protein-protein interactions is a challenging task since it is difficult to appreciate easily the extent of all contacts made by the residues forming the interfaces. In the case of viruses, structural analysis becomes even more demanding because several interfaces coexist and, in most cases, these are formed by hundreds of contacting residues that belong to multiple interacting coat proteins. CapsidMaps is an interactive analysis and visualization tool that is designed to benefit the structural virology community. Developed as an improved extension of the φ-ψ Explorer, here we describe the details of its design and implementation. We present results of analysis of a spherical virus to showcase the features and utility of the new tool. CapsidMaps also facilitates the comparison of quaternary interactions between two spherical virus particles by computing a similarity (S)-score. The tool can also be used to identify residues that are solvent exposed and in the process of locating antigenic epitope regions as well as residues forming the inside surface of the capsid that interact with the nucleic acid genome. CapsidMaps is part of the VIPERdb Science Gateway, and is freely available as a web-based and cross-browser compliant application at http://viperdb.scripps.edu. PMID:25697908

  7. Antimicrobial Peptides in Reptiles

    PubMed Central

    van Hoek, Monique L.

    2014-01-01

    Reptiles are among the oldest known amniotes and are highly diverse in their morphology and ecological niches. These animals have an evolutionarily ancient innate-immune system that is of great interest to scientists trying to identify new and useful antimicrobial peptides. Significant work in the last decade in the fields of biochemistry, proteomics and genomics has begun to reveal the complexity of reptilian antimicrobial peptides. Here, the current knowledge about antimicrobial peptides in reptiles is reviewed, with specific examples in each of the four orders: Testudines (turtles and tortosises), Sphenodontia (tuataras), Squamata (snakes and lizards), and Crocodilia (crocodilans). Examples are presented of the major classes of antimicrobial peptides expressed by reptiles including defensins, cathelicidins, liver-expressed peptides (hepcidin and LEAP-2), lysozyme, crotamine, and others. Some of these peptides have been identified and tested for their antibacterial or antiviral activity; others are only predicted as possible genes from genomic sequencing. Bioinformatic analysis of the reptile genomes is presented, revealing many predicted candidate antimicrobial peptides genes across this diverse class. The study of how these ancient creatures use antimicrobial peptides within their innate immune systems may reveal new understandings of our mammalian innate immune system and may also provide new and powerful antimicrobial peptides as scaffolds for potential therapeutic development. PMID:24918867

  8. Structure Analysis and Conformational Transitions of the Cell Penetrating Peptide Transportan 10 in the Membrane-Bound State

    PubMed Central

    Strandberg, Erik; Verdurmen, Wouter P. R.; Bürck, Jochen; Ehni, Sebastian; Mykhailiuk, Pavel K.; Afonin, Sergii; Gerthsen, Dagmar; Komarov, Igor V.; Brock, Roland; Ulrich, Anne S.

    2014-01-01

    Structure analysis of the cell-penetrating peptide transportan 10 (TP10) revealed an exemplary range of different conformations in the membrane-bound state. The bipartite peptide (derived N-terminally from galanin and C-terminally from mastoparan) was found to exhibit prominent characteristics of (i) amphiphilic α-helices, (ii) intrinsically disordered peptides, as well as (iii) β-pleated amyloid fibrils, and these conformational states become interconverted as a function of concentration. We used a complementary approach of solid-state 19F-NMR and circular dichroism in oriented membrane samples to characterize the structural and dynamical behaviour of TP10 in its monomeric and aggregated forms. Nine different positions in the peptide were selectively substituted with either the L- or D-enantiomer of 3-(trifluoromethyl)-bicyclopent-[1.1.1]-1-ylglycine (CF3-Bpg) as a reporter group for 19F-NMR. Using the L-epimeric analogs, a comprehensive three-dimensional structure analysis was carried out in lipid bilayers at low peptide concentration, where TP10 is monomeric. While the N-terminal region is flexible and intrinsically unstructured within the plane of the lipid bilayer, the C-terminal α-helix is embedded in the membrane with an oblique tilt angle of ∼55° and in accordance with its amphiphilic profile. Incorporation of the sterically obstructive D-CF3-Bpg reporter group into the helical region leads to a local unfolding of the membrane-bound peptide. At high concentration, these helix-destabilizing C-terminal substitutions promote aggregation into immobile β-sheets, which resemble amyloid fibrils. On the other hand, the obstructive D-CF3-Bpg substitutions can be accommodated in the flexible N-terminus of TP10 where they do not promote aggregation at high concentration. The cross-talk between the two regions of TP10 thus exerts a delicate balance on its conformational switch, as the presence of the α-helix counteracts the tendency of the unfolded N

  9. Analysis of the proteolysis of bioactive peptides using a peptidomics approach

    PubMed Central

    Kim, Yun-Gon; Lone, Anna Mari; Saghatelian, Alan

    2014-01-01

    Identifying the peptidases that inactivate bioactive peptides (e.g. peptide hormones and neuropeptides) in mammals is an important unmet challenge. This protocol describes a recent approach that combines liquid chromatography-mass spectrometry peptidomics to identify endogenous cleavage sites of a bioactive peptide, the subsequent biochemical purification of a candidate peptidase based on these cleavage sites, and validation of the candidate peptidase’s role in the physiological regulation of the bioactive peptide by examining a peptidase knockout mouse. We highlight successful application of this protocol to discover that insulin-degrading enzyme (IDE) regulates physiological calcitonin gene-related peptide (CGRP) levels and detail the key stages and steps in this approach. This protocol requires 7 days of work; however, the total time for this protocol is highly variable because of its dependence on the availability of biological reagents, namely purified enzymes and knockout mice. The protocol is valuable because it expedites the characterization of mammalian peptidases, such as IDE, which in certain instances can be used to develop novel therapeutics. PMID:23949379

  10. Optimization of Glutamine Peptide Production from Soybean Meal and Analysis of Molecular Weight Distribution of Hydrolysates

    PubMed Central

    Xie, Yanli; Liang, Xinhong; Wei, Min; Zhao, Wenhong; He, Baoshan; Lu, Qiyu; Huo, Quangong; Ma, Chengye

    2012-01-01

    The process parameters of enzymatic hydrolysis and molecular weight distribution of glutamine (Gln) peptides from soybean meal were investigated. The Protamex® hydrolysis pH of 6.10, temperature of 56.78 °C, enzyme to substrate ratio (E/S) of 1.90 and hydrolysis time of 10.72 h were found to be the optimal conditions by response surface methodology (RSM) for a maximal degree of hydrolysis (DH) value of 16.63% and Gln peptides content at 5.95 mmol/L. The soybean meal was hydrolyzed by a combination of Protamex® and trypsinase so that DH and Gln peptides would reach 22.02% and 6.05 mmol/mL, respectively. The results of size exclusion chromatography indicated that the relative proportion of the molecular weight <1000 Da fraction increased with DH values from 6.76%, 11.13%, 17.89% to 22.02%, most notably the 132–500 Da fractions of hydrolysates were 42.14%, 46.57%, 58.44% and 69.65%. High DH values did not lead to high Gln peptides content of the hydrolysate but to the low molecular weight Gln peptides. PMID:22837706

  11. Identification and quantitation of MHC class II-bound peptides from mouse spleen dendritic cells by immunoprecipitation and mass spectrometry analysis

    PubMed Central

    Bozzacco, Leonia; Yu, Haiqiang

    2014-01-01

    Summary Advances in immunology and immune therapies require knowledge of antigenic peptide sequences that are presented on MHC class II and class I molecules of antigen presenting cells. The most specialized antigen presenting cells are dendritic cells (DCs). In the past, the small number of DCs that can be isolated from mouse spleen prevented direct analysis of the MHC II peptide repertoire presented by DCs. Here we describe a protocol that integrates immunological methods (in vivo enrichment of mouse spleen DCs by Flt3L treatment and immunoprecipation of MHC II-peptide complexes), mass spectrometry analysis and peptide synthesis (LC-MS/MS and quantitation analysis for non tryptic peptides) to identify and quantitate the endogenous peptides that are bound to MHC II molecules on DCs. The described method produces quantitative data that are reproducible and reliable enough to cover a wide range of peptide copy numbers. We propose the application of this method in future studies to quantitatively investigate the MHC II repertoire on DCs presented during viral infections or different immunizations in vaccine development research. PMID:23963941

  12. Sensitive electrospray mass spectrometry analysis of one-bead-one-compound peptide libraries labeled by quaternary ammonium salts.

    PubMed

    Bąchor, Remigiusz; Cydzik, Marzena; Rudowska, Magdalena; Kluczyk, Alicja; Stefanowicz, Piotr; Szewczuk, Zbigniew

    2012-08-01

    A rapid and straightforward method for high-throughput analysis of single resin beads from one-bead-one-compound combinatorial libraries with high resolution electrospray ionization tandem mass spectrometry (HR ESI-MS/MS) is presented. The application of an efficient method of peptide derivatization by quaternary ammonium salts (QAS) formation increases ionization efficiency and reduces the detection limit, allowing analysis of trace amounts of compounds by ESI-MS. Peptides, synthesized on solid support, contain a new cleavable linker composed of a Peg spacer (9-aza-3,6,12,15-tetraoxa-10-on-heptadecanoic acid), lysine with ɛ-amino group marked by the N,N,N-triethylglycine salt, and methionine, which makes possible the selective cleavage by cyanogen bromide. Even a small portion of peptides derivatized by QAS cleaved from a single resin bead is sufficient for sequencing by HR ESI-MS/MS experiments. The developed strategy was applied to a small training library of α chymotrypsin substrates. The obtained results confirm the applicability of the proposed method in combinatorial chemistry. PMID:22740104

  13. Identification and expression analysis of a novel stylicin antimicrobial peptide from Kuruma shrimp (Marsupenaeus japonicus).

    PubMed

    Liu, Hong-tao; Wang, Jun; Mao, Yong; Liu, Min; Niu, Su-fang; Qiao, Ying; Su, Yong-quan; Wang, Chun-zhong; Zheng, Zhi-peng

    2015-12-01

    Antimicrobial peptides (AMPs) are important components of the innate immune system and function as the first line of defense against invading pathogens. In current study we identified, cloned and characterized a novel stylicin AMP from Kuruma shrimp Marsupenaeus japonicus (Mj-sty). The full-length cDNA of Mj-sty was 428 bp with an open reading frame of 315 bp that encoded 104 amino acids. The theoretical molecular mass of mature Mj-sty was 8.693 kDa with an isoelectric point (pI) of 4.79. A proline-rich N-terminal region and a C-terminal region contained 13 cysteine residues were identified. Genomic sequence analysis with respect to its cDNA showed that Mj-sty was organized into two exons interrupted by one intron. Tissue-specific expression revealed that Mj-sty was mainly transcribed in gills and hemocytes. Expression of Mj-sty in early developmental stages demonstrated that Mj-sty mRNA were present from fertilized eggs to post-larvae of 17 days (PL17), and the expression levels showed a significant variation in different developmental stages. After challenge of white spot syndrome virus (WSSV), the time-dependent expression pattern of Mj-sty in both gills and hepatopancrease showed down-regulation at the early hours of infection, subsequently up-regulation and down-regulation, and then up-regulation at the end hours to almost the half of the controls. The results indicate that Mj-sty is potentially involved in the ontogenesis and immune responses against WSSV. PMID:26439413

  14. Synthesis of polydopamine-coated magnetic graphene for Cu(2+) immobilization and application to the enrichment of low-concentration peptides for mass spectrometry analysis.

    PubMed

    Zhao, Man; Deng, Chunhui; Zhang, Xiangmin

    2013-12-26

    In this work, Cu(2+)-immobilized magnetic graphene@polydopamine (magG@PDA@Cu(2+)) composites were synthesized for the first time. Magnetic graphene prepared via a hydrothermal reaction were easily encapsulated by a layer of polydopamine through the oxidative polymerization of dopamine in alkaline buffer, and it was conveniently modified with Cu(2+) ions afterward. The as-prepared magG@PDA@Cu(2+) composites were endowed with strong magnetic responsivness, excellent dispersibility and biological compatibility. We applied the novel nanocomposites to the enrichment and identification of low-concentration standard peptides, peptides in standard protein digestions, endogenous peptides in human urine and serum. The enriched peptides were eluted and analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The magG@PDA@Cu(2+) composites were proved to exhibit great affinity to both hydrophobic and hydrophilic peptides, thus providing a rapid and facile approach to the extraction of low-concentration peptides. Notably, peptides at an extremely low concentration of 10 pM could be detected by MALDI-TOF MS after enrichment with magG@PDA@Cu(2+) composites. The results demonstrated that the magG@PDA@Cu(2+) composite is a promising candidate for the enrichment of low-abundance peptides for mass spectrometry analysis. PMID:24281731

  15. Accurate Structure Prediction and Conformational Analysis of Cyclic Peptides with Residue-Specific Force Fields.

    PubMed

    Geng, Hao; Jiang, Fan; Wu, Yun-Dong

    2016-05-19

    Cyclic peptides (CPs) are promising candidates for drugs, chemical biology tools, and self-assembling nanomaterials. However, the development of reliable and accurate computational methods for their structure prediction has been challenging. Here, 20 all-trans CPs of 5-12 residues selected from Cambridge Structure Database have been simulated using replica-exchange molecular dynamics with four different force fields. Our recently developed residue-specific force fields RSFF1 and RSFF2 can correctly identify the crystal-like conformations of more than half CPs as the most populated conformation. The RSFF2 performs the best, which consistently predicts the crystal structures of 17 out of 20 CPs with rmsd < 1.1 Å. We also compared the backbone (ϕ, ψ) sampling of residues in CPs with those in short linear peptides and in globular proteins. In general, unlike linear peptides, CPs have local conformational free energies and entropies quite similar to globular proteins. PMID:27128113

  16. Analysis of the antimicrobial activities of a chemokine-derived peptide (CDAP-4) on Pseudomonas aeruginosa

    SciTech Connect

    Martinez-Becerra, Francisco; Dominguez-Ramirez, Lenin; Mendoza-Hernandez, Guillermo; Lopez-Vidal, Yolanda; Soldevila, Gloria . E-mail: garciaze@servidor.unam.mx

    2007-04-06

    Chemokines are key molecules involved in the control of leukocyte trafficking. Recently, a novel function as antimicrobial proteins has been described. CCL13 is the only member of the MCP chemokine subfamily displaying antimicrobial activity. To determine Key residues involved in its antimicrobial activity, CCL13 derived peptides were synthesized and tested against several bacterial strains, including Pseudomonas aeruginosa. One of these peptides, corresponding to the C-terminal region of CCL13 (CDAP-4) displayed good antimicrobial activity. Electron microscopy studies revealed remarkable morphological changes after CDAP-4 treatment. By computer modeling, CDAP-4 in {alpha} helical configuration generated a positive electrostatic potential that extended beyond the surface of the molecule. This feature is similar to other antimicrobial peptides. Altogether, these findings indicate that the antimicrobial activity was displayed by CCL13 resides to some extent at the C-terminal region. Furthermore, CDAP-4 could be considered a good antimicrobial candidate with a potential use against pathogens including P. aeruginosa.

  17. [Peptides analysis in digested edible bird's nest by HPLC-MS].

    PubMed

    Liu, Lin; Li, Xiu-Le; Gao, Jian-Ping; Kong, Ying-Jun; Wang, Ming-Lin; Zhang, Gui-Feng; Su, Zhi-Guo

    2013-03-01

    Edible bird's nest contains lots of glycoproteins. The glycosylation inhomogeneity for glycoprotein often results in wide range of molecular weight and the difficulty for protein separation and charaterization. In this paper, proteins in the edible bird's nest were extracted using multiple extractions, and then digested by PNgase F and trypsin. The digest mixture was separated with HPLC, and peptides were identified based on MS/MS data searching. The results indicated that the extracted proteins were amount to 79.7% of total protein in the edible bird's nest. More than 20 species of peptides in the digested mixture were identified. The sequences of these peptides showed similarity with some proteins from Swiss-prot. The research indicated that deglycosylation, tryptic digestion coupled with HPLC-MS/MS is a proper strategy for characterization of proteins in the edible bird's nest. PMID:23724682

  18. Multiplexed Analysis of Peptide Functionality Using Lanthanide-based Structural Shift Reagents

    PubMed Central

    Kerr, Thomas J.; Gant-Branum, Randi L.; McLean, John A.

    2011-01-01

    Functionally selective lanthanide-based ion mobility shift reagents are presented as a method to elucidate protein or peptide structural information as well as relative quantitation of protein expression profiles. Sequence information and site localization of primary amines (n-terminus and lysine), phosphorylation sites, and cysteine residues can be obtained in a data dependent manner using ion mobility-mass spectrometry (IM-MS). The high mass of the incorporated lanthanide ensures a significant shift of where the signal occurs in IM-MS conformation space. Peptide sequence information provided by the use of IM-MS shift reagents allows for both a more confident identification of peptides from complex mixtures and site localization following tandem MS experiments. Stable isotopes of the lanthanide series may also be used as relative quantitation labels since several lanthanides can be utilized in differential sample analyses. PMID:21966243

  19. Peptide-MHC Cellular Microarray with Innovative Data Analysis System for Simultaneously Detecting Multiple CD4 T-Cell Responses

    PubMed Central

    Ge, Xinhui; Gebe, John A.; Bollyky, Paul L.; James, Eddie A.; Yang, Junbao; Stern, Lawrence J.; Kwok, William W.

    2010-01-01

    Background Peptide:MHC cellular microarrays have been proposed to simultaneously characterize multiple Ag-specific populations of T cells. The practice of studying immune responses to complicated pathogens with this tool demands extensive knowledge of T cell epitopes and the availability of peptide:MHC complexes for array fabrication as well as a specialized data analysis approach for result interpretation. Methodology/Principal Findings We co-immobilized peptide:DR0401 complexes, anti-CD28, anti-CD11a and cytokine capture antibodies on the surface of chamber slides to generate a functional array that was able to detect rare Ag-specific T cell populations from previously primed in vitro T cell cultures. A novel statistical methodology was also developed to facilitate batch processing of raw array-like data into standardized endpoint scores, which linearly correlated with total Ag-specific T cell inputs. Applying these methods to analyze Influenza A viral antigen-specific T cell responses, we not only revealed the most prominent viral epitopes, but also demonstrated the heterogeneity of anti-viral cellular responses in healthy individuals. Applying these methods to examine the insulin producing beta-cell autoantigen specific T cell responses, we observed little difference between autoimmune diabetic patients and healthy individuals, suggesting a more subtle association between diabetes status and peripheral autoreactive T cells. Conclusions/Significance The data analysis system is reliable for T cell specificity and functional testing. Peptide:MHC cellular microarrays can be used to obtain multi-parametric results using limited blood samples in a variety of translational settings. PMID:20634998

  20. Genome mapping by random anchoring: A discrete theoretical analysis

    NASA Astrophysics Data System (ADS)

    Zhang, M. Q.; Marr, T. G.

    1993-11-01

    As a part of the international human genome project, large-scale genomic maps of human and other model organisms are being generated. More recently, mapping using various anchoring (as opposed to the traditional "fingerprinting") strategies have been proposed based largely on mathematical models. In all of the theoretical work dealing with anchoring, an anchor has been idealized as a point on a continuous, infinite-length genome. In general, it is not desirable to make these assumptions, since in practice they may be violated under a variety of actual biological situations. Here we analyze a discrete model that can be used to predict the expected progress made when mapping by random anchoring. By virtue of keeping all three length scales (genome length, clone length, and probe length) finite, our results for the random anchoring strategy are derived in full generality, which contain previous results as special cases and hence can have broad application for planning mapping experiments or assessing the accuracy of the continuum models. Finally, we pose a challenging nonrandom anchoring model corresponding to a more efficient mapping scheme.

  1. Cubic map algebra functions for spatio-temporal analysis

    USGS Publications Warehouse

    Mennis, J.; Viger, R.; Tomlin, C.D.

    2005-01-01

    We propose an extension of map algebra to three dimensions for spatio-temporal data handling. This approach yields a new class of map algebra functions that we call "cube functions." Whereas conventional map algebra functions operate on data layers representing two-dimensional space, cube functions operate on data cubes representing two-dimensional space over a third-dimensional period of time. We describe the prototype implementation of a spatio-temporal data structure and selected cube function versions of conventional local, focal, and zonal map algebra functions. The utility of cube functions is demonstrated through a case study analyzing the spatio-temporal variability of remotely sensed, southeastern U.S. vegetation character over various land covers and during different El Nin??o/Southern Oscillation (ENSO) phases. Like conventional map algebra, the application of cube functions may demand significant data preprocessing when integrating diverse data sets, and are subject to limitations related to data storage and algorithm performance. Solutions to these issues include extending data compression and computing strategies for calculations on very large data volumes to spatio-temporal data handling.

  2. Analysis of RapidEye imagery for agricultural land mapping

    NASA Astrophysics Data System (ADS)

    Sang, Huiyong; Zhang, Jixian; Zhai, Liang; Xie, Wenhan; Sun, Xiaoxia

    2015-12-01

    With the improvement of remote sensing technology, the spatial, structural and texture information of land covers are present clearly in high resolution imagery, which enhances the ability of crop mapping. Since the satellite RapidEye was launched in 2009, high resolution multispectral imagery together with wide red edge band has been utilized in vegetation monitoring. Broad red edge band related vegetation indices improved land use classification and vegetation studies. RapidEye high resolution imagery was used in this study to evaluate the potential of red edge band in agricultural land cover/use mapping using an objected-oriented classification approach. A new object-oriented decision tree classifier was introduced in this study to map agricultural lands in the study area. Besides the five bands of RapidEye image, the vegetation indexes derived from spectral bands and the structural and texture features are utilized as inputs for agricultural land cover/use mapping in the study. The optimization of input features for classification by reducing redundant information improves the mapping precision about 18% for AdaTree. WL decision tree, and 5% for SVM, the accuracy is over 90% for both classifiers.

  3. Antimicrobial peptides

    PubMed Central

    2014-01-01

    With increasing antibiotics resistance, there is an urgent need for novel infection therapeutics. Since antimicrobial peptides provide opportunities for this, identification and optimization of such peptides have attracted much interest during recent years. Here, a brief overview of antimicrobial peptides is provided, with focus placed on how selected hydrophobic modifications of antimicrobial peptides can be employed to combat also more demanding pathogens, including multi-resistant strains, without conferring unacceptable toxicity. PMID:24758244

  4. Lunar terrain mapping and relative-roughness analysis

    NASA Technical Reports Server (NTRS)

    Rowan, L. C.; Mccauley, J. F.; Holm, E. A.

    1971-01-01

    Terrain maps of the equatorial zone were prepared at scales of 1:2,000,000 and 1:1,000,000 to classify lunar terrain with respect to roughness and to provide a basis for selecting sites for Surveyor and Apollo landings, as well as for Ranger and Lunar Orbiter photographs. Lunar terrain was described by qualitative and quantitative methods and divided into four fundamental classes: maria, terrae, craters, and linear features. Some 35 subdivisions were defined and mapped throughout the equatorial zone, and, in addition, most of the map units were illustrated by photographs. The terrain types were analyzed quantitatively to characterize and order their relative roughness characteristics. For some morphologically homogeneous mare areas, relative roughness can be extrapolated to the large scales from measurements at small scales.

  5. Assessing the Health Impacts of Air Pollution Regulations Using BenMAP, the Environmental Benefits Mapping and Analysis Program

    NASA Astrophysics Data System (ADS)

    Hubbell, B.; McCubbin, D.; Hallberg, A.

    2003-12-01

    The U.S. EPA Office of Air and Radiation has developed BenMAP, the environmental Benefits Mapping and Analysis Program, a new software tool for estimating the health and environmental impacts of environmental regulations. BenMAP is the US EPA's premier tool for estimating benefits associated with air pollution reduction strategies, and has recently been used in evaluating US EPA's Proposed Non-Road Diesel Vehicle Standards and the proposed Clear Skies Act legislation. BenMAP is a geographic information system (GIS) that uses modeled and monitored air quality data combined with population forecasts to develop estimates of changes in community level exposure to ambient environmental pollution (currently ambient air pollution, e.g. ozone and PM). These estimated changes in exposure to ambient pollution are used as inputs to concentration-response functions derived from the epidemiological literature, along with data on baseline incidence of health effects, i.e. county level age and cause specific mortality rates. The resulting point estimates of changes in incidence of health effects, along with their associated uncertainty distributions (currently based on reported standard errors in the literature), are then multiplied by economic unit values (represented by distributions), i.e. the cost of a hospital admission, to derive dollar estimates of health benefits. BenMAP is unique in that it uses highly detailed census and health data matched with spatially detailed environmental quality data to estimate health benefits. The program can also provide estimates of the uncertainty associated with the estimated benefits. Other features of the program include the ability to pool results from multiple studies of the same endpoint, using fixed or random effects weights, or user supplied weights. BenMAP also incorporates functions to manipulate and combine information on environmental quality from many different sources. For the current version focusing on air pollution, these

  6. Issues in analysis of soil-landscape effects in a large regional yield map collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Yield maps are commonly collected by producers and precision agriculture service providers and are accumulating in warehouse scale data-stores. A key goal in analysis of yield maps is to understand how climate interacts with soil landscapes to cause spatial and temporal variability in grain yield. H...

  7. RT-SVR+q: A Strategy for Post-Mascot Analysis Using Retention Time and q Value Metric to Improve Peptide and Protein Identifications

    PubMed Central

    Cao, Weifeng; Ma, Di; Kapur, Arvinder; Patankar, Manish S; Ma, Yadi; Li, Lingjun

    2011-01-01

    Shotgun proteomics commonly utilizes database search like Mascot to identify proteins from tandem MS/MS spectra. False discovery rate (FDR) is often used to assess the confidence of peptide identifications. However, a widely accepted FDR of 1% sacrifices the sensitivity of peptide identification while improving the accuracy. This article details a machine learning approach combining retention time based support vector regressor (RT-SVR) with q value based statistical analysis to improve peptide and protein identifications with high sensitivity and accuracy. The use of confident peptide identifications as training examples and careful feature selection ensures high R values (>0.900) for all models. The application of RT-SVR model on Mascot results (p=0.10) increases the sensitivity of peptide identifications. q value, as a function of deviation between predicted and experimental RTs(Δ RT), is used to assess the significance of peptide identifications. We demonstrate that the peptide and protein identifications increase by up to 89.4% and 83.5%, respectively, for a specified q value of 0.01 when applying the method to proteomic analysis of the natural killer leukemia cell line (NKL). This study establishes an effective methodology and provides a platform for profiling confident proteomes in more relevant species as well as a future investigation of accurate protein quantification. PMID:21888997

  8. Transcription-inhibition and RNA-binding domains of influenza A virus matrix protein mapped with anti-idiotypic antibodies and synthetic peptides.

    PubMed Central

    Ye, Z P; Baylor, N W; Wagner, R R

    1989-01-01

    We have undertaken by biochemical and immunological experiments to locate the region of the matrix (M1) protein responsible for down-regulating endogenous transcription of A/WSN/33 influenza virus. A more refined map of the antigenic determinants of the M1 protein was obtained by binding of epitope-specific monoclonal antibodies (MAbs) to chemically cleaved fragments. Epitope 2-specific MAb 289/4 and MAb 7E5 reverse transcription inhibition by M1 protein and react with a 4-kilodalton cyanogen bromide fragment extending from amino acid Gly-129 to Gln-164. Anti-idiotype serum immunoglobulin G prepared in rabbits immunized with MAb 289/4 or MAb 7E5 mimicked the action of M1 protein by inhibiting transcription in vitro of influenza virus ribonucleoprotein cores. This transcription-inhibition activity of anti-MAb 7E5 immunoglobulin G and anti-MAb 289/4 immunoglobulin G could be reversed by MAb 7E5 and MAb 289/4 or could be removed by MAb 7E5-Sepharose affinity chromatography. Transcription of influenza virus ribonucleoprotein was inhibited by one of three synthetic oligopeptides, a nonodecapeptide SP3 with an amino acid sequence corresponding to Pro-90 through Thr-108 of the M1 protein. Of all the structural proteins of influenza virus, only NP and M1 showed strong affinity for binding viral RNA or other extraneous RNAs. The 4-kilodalton cyanogen bromide peptide (Gly-129 to Gln-164), exhibited marked affinity for viral RNA, the binding of which was blocked by epitope 2-specific MAb 7E5 but not by MAbs directed to three other epitopes. Viral RNA also bound strongly to the nonodecapeptide SP3 and rather less well to anti-idiotype anti-MAb 7E5; these latter viral RNA-binding reactions were only slightly blocked by preincubation of anti-MAb 7E5 or SP3 with MAb 7E5. These experiments suggest the presence of at least two RNA-binding sites, which also serve as transcription-inhibition sites, centered around amino acid sequences 80 through 109 (epitope 4?) and 129 through 164

  9. Summarization vs Peptide-Based Models in Label-Free Quantitative Proteomics: Performance, Pitfalls, and Data Analysis Guidelines.

    PubMed

    Goeminne, Ludger J E; Argentini, Andrea; Martens, Lennart; Clement, Lieven

    2015-06-01

    Quantitative label-free mass spectrometry is increasingly used to analyze the proteomes of complex biological samples. However, the choice of appropriate data analysis methods remains a major challenge. We therefore provide a rigorous comparison between peptide-based models and peptide-summarization-based pipelines. We show that peptide-based models outperform summarization-based pipelines in terms of sensitivity, specificity, accuracy, and precision. We also demonstrate that the predefined FDR cutoffs for the detection of differentially regulated proteins can become problematic when differentially expressed (DE) proteins are highly abundant in one or more samples. Care should therefore be taken when data are interpreted from samples with spiked-in internal controls and from samples that contain a few very highly abundant proteins. We do, however, show that specific diagnostic plots can be used for assessing differentially expressed proteins and the overall quality of the obtained fold change estimates. Finally, our study also illustrates that imputation under the "missing by low abundance" assumption is beneficial for the detection of differential expression in proteins with low abundance, but it negatively affects moderately to highly abundant proteins. Hence, imputation strategies that are commonly implemented in standard proteomics software should be used with care. PMID:25827922

  10. Analysis of the Linker Region Joining the Adenylation and Carrier Protein Domains of the Modular Non-Ribosomal Peptide Synthetases

    PubMed Central

    Miller, Bradley R.; Sundlov, Jesse A.; Drake, Eric J.; Makin, Thomas A.; Gulick, Andrew M.

    2014-01-01

    Non-Ribosomal Peptide Synthetases (NRPSs) are multi-modular proteins capable of producing important peptide natural products. Using an assembly-line process the amino acid substrate and peptide intermediates are passed between the active sites of different catalytic domains of the NRPS while bound covalently to a peptidyl carrier protein (PCP) domain. Examination of the linker sequences that join the NRPS adenylation and PCP domains identified several conserved proline residues that are not found in standalone adenylation domains. We examined the roles of these proline residues and neighboring conserved sequences through mutagenesis and biochemical analysis of the reaction catalyzed by the adenylation domain and the fully reconstituted NRPS pathway. In particular, we identified a conserved LPxP motif at the start of the adenylation-PCP linker. The LPxP motif interacts with a region on the adenylation domain to stabilize a critical catalytic lysine residue belonging to the A10 motif that immediately precedes the linker. Further, this interaction with the C-terminal sub-domain of the adenylation domain may coordinate movement of the PCP with the conformational change of the adenylation domain. Through this work, we extend the conserved A10 motif of the adenylation domain and identify residues that enable proper adenylation domain function. PMID:24975514

  11. Photocross-Linked Peptide-Protein Complexes Analysis: A Comparative Study of CID and ETD Fragmentation Modes

    NASA Astrophysics Data System (ADS)

    Clavier, Séverine; Bolbach, Gérard; Sachon, Emmanuelle

    2015-06-01

    Protein-protein interactions are among the keys to organizing cellular processes in space and time. One of the only direct ways to identify such interactions in their cellular environment is to covalently bond the interacting partners to fix the interaction. Photocross-linking in living cells is thus a very promising technique. The feasibility of in cellulo photocross-linking reactions has been shown and mass spectrometry is a tool of choice to analyze photocross-linked proteins. However, the interpretation of the MS and MS/MS spectra of photocross-linked peptides remains one of the most important bottlenecks of the method and still limits its potential for large-scale applications (interactomics). Fundamental studies are still necessary to understand and characterize the fragmentation behavior of photocross-linked peptides. Here, we report the successful identification of the interaction sites in a well-characterized model of in vitro interaction between a protein and a peptide. We describe in detail the fragmentation pattern of these photocross-linked species in order to identify trends that could be generalized. In particular, we compare CID and ETD fragmentation modes (and HCD in a lesser extent), demonstrating the complementarity of both methods and the advantage of ETD for the analysis of photocross-linked species. The information should help further development of dedicated software to properly score MS/MS spectra of photocross-linked species.

  12. Nonlinear neural mapping analysis of the adverse effects of drugs.

    PubMed

    Domine, D; Guillon, C; Devillers, J; Lacroix, R; Lacroix, J; Doré, J C

    1998-01-01

    Numerous drugs have been identified as presenting adverse effects towards the driving of vehicles. A large set of these drugs was compiled and classified into ten categories. Nonlinear neural mapping (N2M) was used to derive a typology of these molecules and also to link their adverse effects to therapeutic categories and structural information. PMID:9517012

  13. Using Concept Maps to Engage Adult Learners in Critical Analysis

    ERIC Educational Resources Information Center

    Yelich Biniecki, Susan M.; Conceição, Simone C. O.

    2016-01-01

    An understanding of learning theories can help adult educators become more effective practitioners and meet the needs of the learners they serve. Adult educators who understand how individuals learn can be better prepared to use effective strategies during the learning process. This article addresses the use of concept maps as a strategy to engage…

  14. MAPS - a computerized management analysis and planning system

    NASA Technical Reports Server (NTRS)

    Packe, D. R.; Raffaeli, G. A.

    1971-01-01

    Program lists work structure of projects at all levels. System integrates work item, its schedule, its status against the schedule, responsible personnel, and explanatory comments. structure of MAPS promotes natural organization of project work elements, project features and uses are given.

  15. DESIGNA ND ANALYSIS FOR THEMATIC MAP ACCURACY ASSESSMENT: FUNDAMENTAL PRINCIPLES

    EPA Science Inventory

    Before being used in scientific investigations and policy decisions, thematic maps constructed from remotely sensed data should be subjected to a statistically rigorous accuracy assessment. The three basic components of an accuracy assessment are: 1) the sampling design used to s...

  16. Porcine major histocompatibility complex (MHC) class I molecules and analysis of their peptide-binding specificities

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In all vertebrate animals, CD8+ cytotoxic T lymphocytes (CTLs) are controlled by major histocompatibility complex class I (MHC-I) molecules, which are highly polymorphic peptide receptors selecting and presenting endogenously derived epitopes to circulating cytotoxic lymphocytes (CTLs). The polymorp...

  17. Evidence for N-Terminal Myristoylation of Tetrahymena Arginine Kinase Using Peptide Mass Fingerprinting Analysis.

    PubMed

    Motomura, Shou; Suzuki, Tomohiko

    2016-06-01

    In this study, we confirmed N-terminal myristoylation of Tetrahymena pyriformis arginine kinase (AK1) by identifying a myristoylation signal sequence at the N-terminus. A sufficient amount of modified enzyme was synthesized using an insect cell-free protein synthesis system that contains all of the elements necessary for post-transcriptional modification by fatty acids. Subsequent peptide mass fingerprinting (PMF) analyses were performed after digestion with trypsin. The PMF data covered 39 % (143 residues) of internal peptides. The target N-myristoylated peptide had a theoretical mass of 832.4477 and was clearly observed with an experimental mass (m/z-H(+)) of 832.4747. The difference between the two masses was 0.0271, supporting the accuracy of identification and indicating that the synthesized T. pyriformis AK1 is myristoylated. The fixed specimens of T. pyriformis were reacted with an anti-AK1 peptide antibody followed by a secondary antibody with a fluorescent chromophore and were observed using immunofluorescence microscope. In agreement with previous western blotting analyses, microscopic observations suggested that AK1 is localized in the cilia. The present PMF and microscopic analyses indicate that T. pyriformis AK1 may be localized and anchored to ciliary membranes via N-terminal myristoyl groups. PMID:27129461

  18. Functional analysis of nematode secreted CLAVATA3/ESR (CLE)-like peptides of the genus Heterodera

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cyst nematodes of the genus Heterodera are obligate, sedentary endoparasites that have developed highly evolved relationships with specific host plant species. We have identified two H. glycines CLAVATA3/ESR(CLE)-like genes, HgCLEA and HgCLEB, that encode secreted peptides with similarity to plant ...

  19. XMAn: a Homo sapiens mutated-peptide database for the MS analysis of cancerous cell states.

    PubMed

    Yang, Xu; Lazar, Iulia M

    2014-12-01

    To enable the identification of mutated peptide sequences in complex biological samples, in this work, two novel cancer- and disease-related protein databases with mutation information collected from several public resources such as COSMIC, IARC P53, OMIM, and UniProtKB were developed. In-house developed Perl scripts were used to search and process the data and to translate each gene-level mutation into a mutated peptide sequence. The cancer and disease mutation databases comprise a total of 872,125 and 27,148 peptide entries from 25 642 and 2913 proteins, respectively. A description line for each entry provides the parent protein ID and name, the cDNA- and protein-level mutation site and type, the originating database, and the disease or cancer tissue type and corresponding hits. The two databases are FASTA-formatted to enable data retrieval by commonly used tandem MS search engines. While the largest number of mutations were encountered for the amino acids A/D/E/G/L/P/R/S, the global mutation profiles replicate closely the outcome of the 1000 Genomes Project aimed at cataloguing natural mutations in the human population. The affected proteins were primarily involved in transcription regulation, splicing, protein synthesis/folding/binding, redox/energy production, adhesion/motility, and to some extent in DNA damage repair and signaling. The applicability of the database to identifying the presence of mutated peptides was investigated with MCF-7 breast cancer cell extracts. PMID:25211293

  20. High-performance computational analysis and peptide screening from databases of cyclotides from poaceae.

    PubMed

    Porto, William F; Miranda, Vivian J; Pinto, Michelle F S; Dohms, Stephan M; Franco, Octavio L

    2016-01-01

    Cyclotides are a family of head-to-tail cyclized peptides containing three conserved disulfide bonds, in a structural scaffold also known as a cyclic cysteine knot. Due to the high degree of cysteine conservation, novel members from this peptide family can be identified in protein databases through a search through regular expression (REGEX). In this work, six novel cyclotide-like precursors from the Poaceae were identified from NCBI's non-redundant protein database by the use of REGEX. Two out of six sequences (named Zea mays L and M) showed an Asp residue in the C-terminal, which indicated that they could be cyclic. Gene expression in maize tissues was investigated, showing that the previously described cyclotide-like Z. mays J is expressed in the roots. According to molecular dynamics, the structure of Z. mays J seems to be stable, despite the putative absence of cyclization. As regards cyclotide evolution, it was hypothesized that this is an outcome from convergent evolution and/or horizontal gene transfer. The results showed that peptide screening from databases should be performed periodically in order to include novel sequences, which are deposited as the databases grow. Indeed, the advances in computational and experimental methods will together help to answer key questions and reach new horizons in defense-related peptide identification. PMID:26572696

  1. Intracellular trafficking of superparamagnetic iron oxide nanoparticles conjugated with TAT peptide: 3-dimensional electron tomography analysis

    SciTech Connect

    Nair, Baiju G.; Fukuda, Takahiro; Mizuki, Toru; Hanajiri, Tatsuro; Maekawa, Toru

    2012-05-18

    Highlights: Black-Right-Pointing-Pointer We study the intracellular localisation of TAT-SPIONs using 3-D electron tomography. Black-Right-Pointing-Pointer 3-D images of TAT-SPIONs in a cell are clearly shown. Black-Right-Pointing-Pointer Release of TAT-SPIONs from endocytic vesicles into the cytoplasm is clearly shown. -- Abstract: Internalisation of nanoparticles conjugated with cell penetrating peptides is a promising approach to various drug delivery applications. Cell penetrating peptides such as transactivating transcriptional activator (TAT) peptides derived from HIV-1 proteins are effective intracellular delivery vectors for a wide range of nanoparticles and pharmaceutical agents thanks to their amicable ability to enter cells and minimum cytotoxicity. Although different mechanisms of intracellular uptake and localisation have been proposed for TAT conjugated nanoparticles, it is necessary to visualise the particles on a 3-D plane in order to investigate the actual intracellular uptake and localisation. Here, we study the intracellular localisation and trafficking of TAT peptide conjugated superparamagnetic ion oxide nanoparticles (TAT-SPIONs) using 3-D electron tomography. 3-D tomograms clearly show the location of TAT-SPIONs in a cell and their slow release from the endocytic vesicles into the cytoplasm. The present methodology may well be utilised for further investigations of the behaviours of nanoparticles in cells and eventually for the development of nano drug delivery systems.

  2. Quantum Chemical Analysis of MHC-Peptide Interactions for Vaccine Design

    PubMed Central

    Agudelo, W.A; Patarroyo, M.E

    2010-01-01

    The development of an adequate immune response against pathogens is mediated by molecular interactions between different cell types. Among them, binding of antigenic peptides to the Major Histocompatibility Complex (MHC) molecule expressed on the membrane of antigen presenting cells (APCs), and their subsequent recognition by the T cell receptor have been demonstrated to be crucial for developing an adequate immune response. The present review compiles computational quantum chemistry studies about the electrostatic potential variations induced on the MHC binding region by peptide’s amino acids, carried out with the aim of describing MHC–peptide binding interactions. The global idea is that the electrostatic potential can be represented in terms of a series expansion (charge, dipole, quadrupole, hexadecapole, etc.) whose three first terms provide a good local approximation to the molecular electrostatic ‘landscape’ and to the variations induced on such landscape by targeted modifications on the residues of the antigenic peptide. Studies carried out in four MHC class II human allele molecules, which are the most representative alleles of their corresponding haplotypes, showed that each of these molecules have conserved as well as specific electrostatic characteristics, which can be correlated at a good extent with the peptide binding profiles reported experimentally for these molecules. The information provided by such characteristics would help increase our knowledge about antigen binding and presentation, and could ultimately contribute to developing a logical and rational methodology for designing chemically synthesized, multi-antigenic, subunit-based vaccines, through the application of quantum chemistry methods. PMID:20394575

  3. Cleavage Specificity Analysis of Six Type II Transmembrane Serine Proteases (TTSPs) Using PICS with Proteome-Derived Peptide Libraries

    PubMed Central

    Béliveau, François; Leduc, Richard; Overall, Christopher M.

    2014-01-01

    Background Type II transmembrane serine proteases (TTSPs) are a family of cell membrane tethered serine proteases with unclear roles as their cleavage site specificities and substrate degradomes have not been fully elucidated. Indeed just 52 cleavage sites are annotated in MEROPS, the database of proteases, their substrates and inhibitors. Methodology/Principal Finding To profile the active site specificities of the TTSPs, we applied Proteomic Identification of protease Cleavage Sites (PICS). Human proteome-derived database searchable peptide libraries were assayed with six human TTSPs (matriptase, matriptase-2, matriptase-3, HAT, DESC and hepsin) to simultaneously determine sequence preferences on the N-terminal non-prime (P) and C-terminal prime (P’) sides of the scissile bond. Prime-side cleavage products were isolated following biotinylation and identified by tandem mass spectrometry. The corresponding non-prime side sequences were derived from human proteome databases using bioinformatics. Sequencing of 2,405 individual cleaved peptides allowed for the development of the family consensus protease cleavage site specificity revealing a strong specificity for arginine in the P1 position and surprisingly a lysine in P1′ position. TTSP cleavage between R↓K was confirmed using synthetic peptides. By parsing through known substrates and known structures of TTSP catalytic domains, and by modeling the remainder, structural explanations for this strong specificity were derived. Conclusions Degradomics analysis of 2,405 cleavage sites revealed a similar and characteristic TTSP family specificity at the P1 and P1′ positions for arginine and lysine in unfolded peptides. The prime side is important for cleavage specificity, thus making these proteases unusual within the tryptic-enzyme class that generally has overriding non-prime side specificity. PMID:25211023

  4. Mapping Quantitative Trait Loci Underlying Function-Valued Traits Using Functional Principal Component Analysis and Multi-Trait Mapping

    PubMed Central

    Kwak, Il-Youp; Moore, Candace R.; Spalding, Edgar P.; Broman, Karl W.

    2015-01-01

    We previously proposed a simple regression-based method to map quantitative trait loci underlying function-valued phenotypes. In order to better handle the case of noisy phenotype measurements and accommodate the correlation structure among time points, we propose an alternative approach that maintains much of the simplicity and speed of the regression-based method. We overcome noisy measurements by replacing the observed data with a smooth approximation. We then apply functional principal component analysis, replacing the smoothed phenotype data with a small number of principal components. Quantitative trait locus mapping is applied to these dimension-reduced data, either with a multi-trait method or by considering the traits individually and then taking the average or maximum LOD score across traits. We apply these approaches to root gravitropism data on Arabidopsis recombinant inbred lines and further investigate their performance in computer simulations. Our methods have been implemented in the R package, funqtl. PMID:26530421

  5. Bovine serum albumin as a universal suppressor of non-specific peptide binding in vials prior to nano-chromatography coupled mass-spectrometry analysis.

    PubMed

    Kovalchuk, Sergey I; Anikanov, Nikolay A; Ivanova, Olga M; Ziganshin, Rustam H; Govorun, Vadim M

    2015-09-17

    Non-specific binding (NSB) is a well-known problem for any application that deals with ultralow analyte quantities. The modern nano-flow chromatography coupled tandem mass-spectrometry (nanoLC-MS/MS) works with the lowest conceivable analyte concentrations. However, while the NSB problem is widely accepted and investigated for metabolomics and single-peptide medicine-related assays, its impact is not studied for complex peptide mixtures in proteomic applications. In this work peptide NSB to a common plastic autosampler vial was studied for a model mixture of 46 synthetic peptides. A significant NSB level was demonstrated for total peptide concentrations of up to 1 mg mL(-1). Different agents were tried for NSB suppression and compatibility with nanoLC-MS/MS analysis: a chaotropic agent, an amino acid mixture, a peptide mixture and a protein solution. The first two were inefficacious. The peptide matrix blocked NSB, however, it also led to analyte ionization suppression in nanoLC-MS/MS. The protein solution (0.1% BSA) efficiently eliminated NSB, while a trap-elute nanoHPLC configuration together with a small-pore reverse-phased sorbent effectively and quantitatively extracted the model peptides and depleted protein material from the sample. Higher protein concentration partially impeded peptide extraction. Thus, the 0.1% BSA solution might be regarded as an effective non-interfering blockader of NSB for sample resuspension and storage in an autosampler prior to LC-MS/MS analysis. PMID:26398423

  6. Current peptidomics: applications, purification, identification, quantification, and functional analysis.

    PubMed

    Dallas, David C; Guerrero, Andres; Parker, Evan A; Robinson, Randall C; Gan, Junai; German, J Bruce; Barile, Daniela; Lebrilla, Carlito B

    2015-03-01

    Peptidomics is an emerging field branching from proteomics that targets endogenously produced protein fragments. Endogenous peptides are often functional within the body-and can be both beneficial and detrimental. This review covers the use of peptidomics in understanding digestion, and identifying functional peptides and biomarkers. Various techniques for peptide and glycopeptide extraction, both at analytical and preparative scales, and available options for peptide detection with MS are discussed. Current algorithms for peptide sequence determination, and both analytical and computational techniques for quantification are compared. Techniques for statistical analysis, sequence mapping, enzyme prediction, and peptide function, and structure prediction are explored. PMID:25429922

  7. Current peptidomics: Applications, purification, identification, quantification, and functional analysis

    PubMed Central

    Dallas, David C.; Guerrero, Andres; Parker, Evan A.; Robinson, Randall C.; Gan, Junai; German, J. Bruce; Barile, Daniela; Lebrilla, Carlito B.

    2015-01-01

    Peptidomics is an emerging field branching from proteomics that targets endogenously produced protein fragments. Endogenous peptides are often functional within the body—and can be both beneficial and detrimental. This review covers the use of peptidomics in understanding digestion, and identifying functional peptides and biomarkers. Various techniques for peptide and glycopeptide extraction, both at analytical and preparative scales, and available options for peptide detection with MS are discussed. Current algorithms for peptide sequence determination, and both analytical and computational techniques for quantification are compared. Techniques for statistical analysis, sequence mapping, enzyme prediction, and peptide function, and structure prediction are explored. PMID:25429922

  8. Highly sensitive and ultrafast read mapping for RNA-seq analysis.

    PubMed

    Medina, I; Tárraga, J; Martínez, H; Barrachina, S; Castillo, M I; Paschall, J; Salavert-Torres, J; Blanquer-Espert, I; Hernández-García, V; Quintana-Ortí, E S; Dopazo, J

    2016-04-01

    As sequencing technologies progress, the amount of data produced grows exponentially, shifting the bottleneck of discovery towards the data analysis phase. In particular, currently available mapping solutions for RNA-seq leave room for improvement in terms of sensitivity and performance, hindering an efficient analysis of transcriptomes by massive sequencing. Here, we present an innovative approach that combines re-engineering, optimization and parallelization. This solution results in a significant increase of mapping sensitivity over a wide range of read lengths and substantial shorter runtimes when compared with current RNA-seq mapping methods available. PMID:26740642

  9. Highly sensitive and ultrafast read mapping for RNA-seq analysis

    PubMed Central

    Medina, I.; Tárraga, J.; Martínez, H.; Barrachina, S.; Castillo, M. I.; Paschall, J.; Salavert-Torres, J.; Blanquer-Espert, I.; Hernández-García, V.; Quintana-Ortí, E. S.; Dopazo, J.

    2016-01-01

    As sequencing technologies progress, the amount of data produced grows exponentially, shifting the bottleneck of discovery towards the data analysis phase. In particular, currently available mapping solutions for RNA-seq leave room for improvement in terms of sensitivity and performance, hindering an efficient analysis of transcriptomes by massive sequencing. Here, we present an innovative approach that combines re-engineering, optimization and parallelization. This solution results in a significant increase of mapping sensitivity over a wide range of read lengths and substantial shorter runtimes when compared with current RNA-seq mapping methods available. PMID:26740642

  10. Comprehensive objective maps of macromolecular conformations by quantitative SAXS analysis

    PubMed Central

    Hura, Greg L.; Budworth, Helen; Dyer, Kevin N.; Rambo, Robert P.; Hammel, Michal

    2013-01-01

    Comprehensive perspectives of macromolecular conformations are required to connect structure to biology. Here we present a small angle X-ray scattering (SAXS) Structural Similarity Map (SSM) and Volatility of Ratio (VR) metric providing comprehensive, quantitative and objective (superposition-independent) perspectives on solution state conformations. We validate VR and SSM utility on human MutSβ, a key ABC ATPase and chemotherapeutic target, by revealing MutSβ DNA sculpting and identifying multiple conformational states for biological activity. PMID:23624664

  11. Uncertainty Analysis in Large Area Aboveground Biomass Mapping

    NASA Astrophysics Data System (ADS)

    Baccini, A.; Carvalho, L.; Dubayah, R.; Goetz, S. J.; Friedl, M. A.

    2011-12-01

    Satellite and aircraft-based remote sensing observations are being more frequently used to generate spatially explicit estimates of aboveground carbon stock of forest ecosystems. Because deforestation and forest degradation account for circa 10% of anthropogenic carbon emissions to the atmosphere, policy mechanisms are increasingly recognized as a low-cost mitigation option to reduce carbon emission. They are, however, contingent upon the capacity to accurately measures carbon stored in the forests. Here we examine the sources of uncertainty and error propagation in generating maps of aboveground biomass. We focus on characterizing uncertainties associated with maps at the pixel and spatially aggregated national scales. We pursue three strategies to describe the error and uncertainty properties of aboveground biomass maps, including: (1) model-based assessment using confidence intervals derived from linear regression methods; (2) data-mining algorithms such as regression trees and ensembles of these; (3) empirical assessments using independently collected data sets.. The latter effort explores error propagation using field data acquired within satellite-based lidar (GLAS) acquisitions versus alternative in situ methods that rely upon field measurements that have not been systematically collected for this purpose (e.g. from forest inventory data sets). A key goal of our effort is to provide multi-level characterizations that provide both pixel and biome-level estimates of uncertainties at different scales.

  12. Self-Organized Maps in Scientific Data Analysis

    NASA Astrophysics Data System (ADS)

    Soo Hoo, J.; Pollock, C. J.; Jahn, J.; Lim, D.; Weatherwax, A. T.

    2008-12-01

    The Thermal Ion Dynamics Experiment (TIDE) investigates low energy (0.1 - 450 eV) plasma in the Earth's magnetosphere, especially in the polar regions. It is part of NASA's larger Polar mission. After six months in orbit it became necessary for TIDE to operate in a mode that did not directly provide mass discrimination. However, in this mode, energy-time and spin-time spectrograms of differential ion flux were routinely available. The number of peaks in the energy-time spectrograms relates to the composition of the plasma. Kohonen self-organized maps (SOMs,) a type of neural network, are particularly suited to this problem due to the amount of data that needs to be analyzed and the algorithm's ability to find patterns within data. The algorithm leads to clustering of similar data points on the map. Ultimately, the location of the input data point on the map allows for determination of how many peaks the data point contains, and thus the composition of the plasma at that time. The SOM correctly classified 99% of the input data, making it a viable solution to the problem. Further research is planned, namely the possibility of extending this concept to investigate energetic neural atom (ENA) images in order to determine the source of these atoms.

  13. Synthesis and ESI mass spectrometric analysis of the association of mercury(II) with multi-cysteinyl peptides.

    PubMed

    Ngu-Schwemlein, Maria; Lin, Xiuli; Rudd, Brent; Bronson, Matthew

    2014-04-01

    In order to gain more insight into the associations of mercury(II) with cysteinyl peptides, we investigated the effect of increasing cysteinyl residues on complex type formations. Three series of di-, tri-, and tetra-cysteinyl peptides, D[CGD]nCG (CP 2A, CP 3A, and CP 4A), E[CEG]nCG (CP 2B, CP 3B, and CP 4B) and E[CDG]nCG (CP 2C, CP 3C, and CP 4C), where n=1, 2, or 3, were prepared by microwave-assisted solid phase peptide synthesis. Complexes formed in different relative ratios of mercury(II) to cysteinyl peptides were characterized by electrospray orbitrap mass spectrometry utilizing complex specific mercury isotopic patterns. In equimolar mercury(II) to peptide ratio, all three series of di-, tri-, and tetra-cysteinyl peptides form predominantly the 1:1Hg(peptide) complex type, indicating that the intervening amino acid residues do not elicit preferential complex type formation. However, in non-equivalent mercury(II) to peptide ratio, the number of cysteinyl residues has a significant effect on the Hg:peptide stoichiometry in the complex formed. For example, in four times excess peptide, the 1:2Hg(peptide)2 and 1:1Hg(peptide) complexes are formed for di-cysteinyl peptides but not for the tri- and tetra-cysteinyl peptides. In contrast, the 2:1Hg2(peptide) and 1:1Hg(peptide) complexes are formed for the tri- and tetra-cysteinyl peptides. In excess mercury(II), CP 4C formed exclusively the 2:1Hg2(peptide) complex. The exact number of deprotonations observed for each complex could be derived from its signature mercury isotope pattern and monoisotopic peak mass. These multi-cysteinyl peptides present an attractive option for mercury chelation or environmental heavy metal remediation. PMID:24413258

  14. Reversible Major Histocompatibility Complex I-Peptide Multimers Containing Ni2+-Nitrilotriacetic Acid Peptides and Histidine Tags Improve Analysis and Sorting of CD8+ T Cells*

    PubMed Central

    Schmidt, Julien; Guillaume, Philippe; Irving, Melita; Baumgaertner, Petra; Speiser, Daniel; Luescher, Immanuel F.

    2011-01-01

    MHC-peptide multimers containing biotinylated MHC-peptide complexes bound to phycoerythrin (PE) streptavidin (SA) are widely used for analyzing and sorting antigen-specific T cells. Here we describe alternative T cell-staining reagents that are superior to conventional reagents. They are built on reversible chelate complexes of Ni2+-nitrilotriacetic acid (NTA) with oligohistidines. We synthesized biotinylated linear mono-, di-, and tetra-NTA compounds using conventional solid phase peptide chemistry and studied their interaction with HLA-A*0201-peptide complexes containing a His6, His12, or 2×His6 tag by surface plasmon resonance on SA-coated sensor chips and equilibrium dialysis. The binding avidity increased in the order His6 < His12 < 2×His6 and NTA1 < NTA2 < NTA4, respectively, depending on the configuration of the NTA moieties and increased to picomolar KD for the combination of a 2×His6 tag and a 2×Ni2+-NTA2. We demonstrate that HLA-A2–2×His6-peptide multimers containing either Ni2+-NTA4-biotin and PE-SA- or PE-NTA4-stained influenza and Melan A-specific CD8+ T cells equal or better than conventional multimers. Although these complexes were highly stable, they very rapidly dissociated in the presence of imidazole, which allowed sorting of bona fide antigen-specific CD8+ T cells without inducing T cell death as well as assessment of HLA-A2-peptide monomer dissociation kinetics on CD8+ T cells. PMID:21990358

  15. Vibrational analysis of amino acids and short peptides in aqueous media. V. The effect of the disulfide bridge on the structural features of the peptide hormone somatostatin-14.

    PubMed

    Hernández, Belén; Carelli, Claude; Coïc, Yves-Marie; De Coninck, Joël; Ghomi, Mahmoud

    2009-09-24

    To emphasize the role played by the S-S bridge in the structural features of somatostatin-14 (SST-14), newly recorded CD and Raman spectra of this cyclic peptide and its open analogue obtained by Cys-->Ser substitution are presented. CD spectra of both peptides recorded in aqueous solutions in the 100-500 microM concentration range are strikingly similar. They reveal principally that random conformers constitute the major population in both peptides. Consequently, the S-S bridge has no structuring effect at submillimolar concentrations. In methanol, the CD spectrum of somatostatin-14 keeps globally the same spectral shape as that observed in water, whereas its open analogue presents a major population of helical conformers. Raman spectra recorded as a function of peptide concentration (5-20 mM) and also in the presence of 150 mM NaCl provide valuable conformational information. All Raman spectra present a mixture of random and beta-hairpin structures for both cyclic and open peptides. More importantly, the presence or the absence of the disulfide bridge does not seem to influence considerably different populations of secondary structures within this range of concentrations. CD and Raman data obtained in the submillimolar and millimolar ranges of concentrations, respectively, lead us to accept the idea that SST-14 monomers aggregate upon increasing concentration, thus stabilizing beta-hairpin conformations in solution. However, even at high concentrations, random conformers do not disappear. Raman spectra of SST-14 also reveal a concentration effect on the flexibility of the S-S linkage and consequently on that of its cyclic part. In conclusion, although the disulfide linkage does not seem to markedly influence the SST-14 conformational features in aqueous solutions, its presence seems to be necessary to ensure the flexibility of the cyclic part of this peptide and to maintain its closed structure in lower dielectric constant environments. PMID:19708669

  16. Vibrational analysis of amino acids and short peptides in hydrated media. II. Role of KLLL repeats to induce helical conformations in minimalist LK-peptides.

    PubMed

    Guiffo-Soh, Guy; Hernandez, Belén; Coïc, Yves-Marie; Boukhalfa-Heniche, Fatima-Zohra; Ghomi, Mahmoud

    2007-11-01

    Aqueous solution secondary structures of minimalist LK-peptides, with the generic sequence defined as KLL(KLLL)nKLLK, have been analyzed by means of circular dichroism (CD) and Raman scattering techniques. Our discussion in the present paper is mainly focused on four synthetic peptides (from 5 to 19 amino acids), KLLLK, KLLKLLLKLLK, KLLKLLLKLLLKLLK, and KLLKLLLKLLLKLLLKLLK, corresponding to the repeat unit, and to the peptide chains with the values of n = 1-3, respectively. CD and Raman spectra were analyzed in order to study both structural features of the peptide chains and their capability to form aggregates. On the basis of the obtained results it was concluded that the conformational flexibility of the shortest peptides (5-mer and 11-mer) is high enough to adopt random, beta-type, and helical chains in aqueous solution. However, the 11-mer shows a clear tendency to form beta-strands in phosphate buffer. The conformational equilibrium can be completely shifted to beta-type structures upon increasing ionic strength, i.e., in PBS and tris buffers. This equilibrium can also be shifted toward helical chains in the presence of methanol. Finally, the longest peptides (15-mer and 19-mer) are shown to form alpha-helical chains with an amphipathic character in aqueous solution. The possibility of bundle formation between helical chains is discussed over the temperature-dependent H-D exchange on labile hydrogens and particularly by considering the particular behavior of an intense Raman mode at 1127 cm-1 originating from the leucine residue side chain. The conformational dependence of this mode observed upon selective deuteration has never been documented up to now. PMID:17918991

  17. Conformationally restricted C-terminal peptides of substance P. Synthesis, mass spectral analysis and pharmacological properties.

    PubMed

    Theodoropoulos, D; Poulos, C; Gatos, D; Cordopatis, P; Escher, E; Mizrahi, J; Regoli, D; Dalietos, D; Furst, A; Lee, T D

    1985-10-01

    Four cyclic analogues of the C-terminal hepta- or hexapeptide of substance P were prepared by the solution method. The cyclizations were obtained by substituting with cysteine the residues normally present in positions 5 or 6 or 11 of substance P and by subsequent disulfide bond formation. The final products were identified by ordinary analytical procedures and advanced mass spectroscopy. The biological activities were determined on three bioassays: the guinea pig ileum, the guinea pig trachea and the rabbit mesenteric vein. Results obtained with these assays indicate that all peptides with a disulfide bridgehead in position 11 are inactive and that a cycle between positions 5 and 6 already strongly reduces the biological activity. The acyclic precursors containing thiol protection groups display weak biological activities. These results further underline the importance of the side chain in position 11 of substance P and suggest that optimal biological activities may require a linear peptide sequence. PMID:2413208

  18. A molecular cytogenetic map of sorghum chromosome 1. Fluorescence in situ hybridization analysis with mapped bacterial artificial chromosomes.

    PubMed Central

    Islam-Faridi, M N; Childs, K L; Klein, P E; Hodnett, G; Menz, M A; Klein, R R; Rooney, W L; Mullet, J E; Stelly, D M; Price, H J

    2002-01-01

    We used structural genomic resources for Sorghum bicolor (L.) Moench to target and develop multiple molecular cytogenetic probes that would provide extensive coverage for a specific chromosome of sorghum. Bacterial artificial chromosome (BAC) clones containing molecular markers mapped across sorghum linkage group A were labeled as probes for fluorescence in situ hybridization (FISH). Signals from single-, dual-, and multiprobe BAC-FISH to spreads of mitotic chromosomes and pachytene bivalents were associated with the largest sorghum chromosome, which bears the nucleolus organizing region (NOR). The order of individual BAC-FISH loci along the chromosome was fully concordant to that of marker loci along the linkage map. In addition, the order of several tightly linked molecular markers was clarified by FISH analysis. The FISH results indicate that markers from the linkage map positions 0.0-81.8 cM reside in the short arm of chromosome 1 whereas markers from 81.8-242.9 cM are located in the long arm of chromosome 1. The centromere and NOR were located in a large heterochromatic region that spans approximately 60% of chromosome 1. In contrast, this region represents only 0.7% of the total genetic map distance of this chromosome. Variation in recombination frequency among euchromatic chromosomal regions also was apparent. The integrated data underscore the value of cytological data, because minor errors and uncertainties in linkage maps can involve huge physical regions. The successful development of multiprobe FISH cocktails suggests that it is feasible to develop chromosome-specific "paints" from genomic resources rather than flow sorting or microdissection and that when applied to pachytene chromatin, such cocktails provide an especially powerful framework for mapping. Such a molecular cytogenetic infrastructure would be inherently cross-linked with other genomic tools and thereby establish a cytogenomics system with extensive utility in development and application

  19. Mutational analysis of hepatitis B virus pre-S1 (9-24) fusogenic peptide.

    PubMed

    Liu, Qiushi; Somiya, Masaharu; Shimada, Naohiko; Sakamoto, Wakako; Yoshimoto, Nobuo; Iijima, Masumi; Tatematsu, Kenji; Nakai, Tadashi; Okajima, Toshihide; Maruyama, Atsushi; Kuroda, Shuńichi

    2016-05-27

    A hollow nanoparticle known as a bio-nanocapsule (BNC) consisting of hepatitis B virus (HBV) envelope L protein and liposome (LP) can encapsulate drugs and genes and thereby deliver them in vitro and in vivo to human hepatic tissues, specifically by utilizing the HBV-derived infection machinery. Recently, we identified a low pH-dependent fusogenic domain at the N-terminal part of the pre-S1 region of the HBV L protein (amino acid residues 9 to 24; NPLGFFPDHQLDPAFG), which shows membrane destabilizing activity (i.e., membrane fusion, membrane disruption, and payload release) upon interaction with target LPs. In this study, instead of BNC and HBV, we generated LPs displaying a mutated form of the pre-S1 (9-24) peptide, and performed a membrane disruption assay using target LPs containing pyranine (fluorophore) and p-xylene-bis (N-pyridinium bromide) (DPX) as a quencher. The membrane disruption activity was found to correlate with the hydrophobicity of the whole structure, while the peptide retained a random-coil structure even under low pH condition. One large hydrophobic cluster (I) and one small hydrophobic cluster (II) residing in the peptide would be connected by the protonation of residues D16 and D20, and thereby exhibit strong membrane disruption activity in a low pH-dependent manner. Furthermore, the introduction of a positively charged residue enhanced the activity significantly, suggesting that a sole positively charged residue (H17) may be important for the interaction with target LPs by electrostatic interaction. Collectively, these results suggest that the pre-S1 (9-24) peptide may be involved in the endosomal escape of the BNC's payloads, as well as in the HBV uncoating process. PMID:27120459

  20. Peptide motif analysis predicts lymphocytic choriomeningitis virus as trigger for multiple sclerosis.

    PubMed

    Hogeboom, Charissa

    2015-10-01

    The etiology of multiple sclerosis (MS) involves both genetic and environmental factors. Genetically, the strongest link is with HLA DRB1*1501, but the environmental trigger, probably a virus, remains uncertain. This investigation scans a panel of proteins from encephalitogenic viruses for peptides homologous to the primary autoantigen from myelin basic protein (MBP), then evaluates candidate peptides against a motif required for T cell cross-reactivity and compares viral prevalence patterns to epidemiological characteristics of MS. The only peptide meeting criteria for cross-reactivity with MBP was one from lymphocytic choriomeningitis virus (LCMV), a zoonotic agent. In contrast to current candidates such as Epstein-Barr virus, the distribution of LCMV is consistent with epidemiological features of MS, including concentration in the temperate zone, higher prevalence farther from the equator, and increased prevalence in proximity to regions of peak MS incidence, while lack of person-to-person transmission is consistent with low MS concordance across monozygotic twins. Further, LCMV blocks induction of type I interferon (IFN). Hypothetically this would dysregulate immune processes in favor of proinflammatory pathways as well as upregulating HLA class II and providing more binding sites for autoantigen. The combination of molecular mimicry with virally-induced immune dysregulation has the potential to explain aspects of autoimmunity not addressed by either mechanism alone. PMID:26319106

  1. Dynamic Light Scattering Analysis of the Effect of Phosphorylated Osteopontin Peptides on Mineral Formation

    NASA Astrophysics Data System (ADS)

    Mozaffari, Maryam; Goiko, Maria; de Bruyn, John; Goldberg, Harvey

    2015-03-01

    Biomineralization is the process by which living organisms synthesize minerals. Osteopontin (OPN), a mineral-associated protein, has been shown to be a potent inhibitor of mineral formation, a process that is dependent on phosphorylation. To gain a better understanding of the mechanism of inhibition, dynamic light scattering (DLS) was used to monitor the initial stages of nucleation, providing information about the size and relative concentration of the growing crystals as a function of time. DLS was used to investigate the effect of phosphorylated (P3, pOPAR) and non-phosphorylated (P0, OPAR) OPN peptides on the formation and growth of hydroxyapatite (HA) crystals from supersaturated solutions of calcium and phosphate ions. The non-phosphorylated P0 had a limited effect on HA nucleation and growth, while its thrice-phosphorylated isoform, P3, was a potent inhibitor of HA nucleation. The aspartic acid-rich OPAR was found to moderately inhibit nucleation but not growth, while its singly-phosphorylated isoform, pOPAR, inhibited HA nucleation more effectively, with some effect on HA crystal growth. The order of the inhibitory potential of these peptides was pOPAR>OPAR>P3>P0. This work confirms that highly acidic and phosphorylated peptides can inhibit the nucleation of HA more effectively.

  2. Gold nanoparticle-coated capillaries for protein and peptide analysis on open-tubular capillary electrochromatography.

    PubMed

    Hamer, Mariana; Yone, Angel; Rezzano, Irene

    2012-01-01

    We report a new method of immobilization of gold nanoparticles (AuNPs) on a fused-silica capillary through covalent binding. The resulting modified capillary was applied to electrophoretic systems to improve the efficiency of separation and the selectivity of selected solutes. The immobilization of AuNPs on the capillary wall was performed in a very simple and fast way without requiring heating. The surface features of an AuNP-coated capillary column were determined using the scanning electron microscopy. The chromatographic properties of AuNP-coated capillaries were investigated through variation of the buffer pH and separation voltage. Effective separations of synthetic peptides mixture were obtained on the AuNP-coated capillaries. The method shows a remarkable stability since it was reused about 900 times. The capacity factor was duplicated. Therefore, this modification is stable and can be applied to different separation purposes. A complex mixture of tryptic peptide fragments of HSA was analyzed in both the bare- and the AuNP-coated capillaries. Better electrophoretic peptide profile was observed when using the AuNP-coated capillary. PMID:22222978

  3. Mutational and structural analysis of KIR3DL1 reveals a lineage-defining allotypic dimorphism that impacts both HLA and peptide sensitivity.

    PubMed

    O'Connor, Geraldine M; Vivian, Julian P; Widjaja, Jacqueline M; Bridgeman, John S; Gostick, Emma; Lafont, Bernard A P; Anderson, Stephen K; Price, David A; Brooks, Andrew G; Rossjohn, Jamie; McVicar, Daniel W

    2014-03-15

    Killer Ig-like receptors (KIRs) control the activation of human NK cells via interactions with peptide-laden HLAs. KIR3DL1 is a highly polymorphic inhibitory receptor that recognizes a diverse array of HLA molecules expressing the Bw4 epitope, a group with multiple polymorphisms incorporating variants within the Bw4 motif. Genetic studies suggest that KIR3DL1 variation has functional significance in several disease states, including HIV infection. However, owing to differences across KIR3DL1 allotypes, HLA-Bw4, and associated peptides, the mechanistic link with biological outcome remains unclear. In this study, we elucidated the impact of KIR3DL1 polymorphism on peptide-laden HLA recognition. Mutational analysis revealed that KIR residues involved in water-mediated contacts with the HLA-presented peptide influence peptide binding specificity. In particular, residue 282 (glutamate) in the D2 domain underpins the lack of tolerance of negatively charged C-terminal peptide residues. Allotypic KIR3DL1 variants, defined by neighboring residue 283, displayed differential sensitivities to HLA-bound peptide, including the variable HLA-B*57:01-restricted HIV-1 Gag-derived epitope TW10. Residue 283, which has undergone positive selection during the evolution of human KIRs, also played a central role in Bw4 subtype recognition by KIR3DL1. Collectively, our findings uncover a common molecular regulator that controls HLA and peptide discrimination without participating directly in peptide-laden HLA interactions. Furthermore, they provide insight into the mechanics of interaction and generate simple, easily assessed criteria for the definition of KIR3DL1 functional groupings that will be relevant in many clinical applications, including bone marrow transplantation. PMID:24563253

  4. Multichannel analysis of surface waves to map bedrock

    USGS Publications Warehouse

    Miller, Richard D.; Xia, Jianghai; Park, Choon B.; Ivanov, Julian M.

    1999-01-01

    High velocity gradients within the shear wave velocity field consistent with drill confirmed bedrock are considered diagnostic of the bedrock surface and were used to map the top of bedrock on all four lines connected at this site. Calculating the shear wave velocity field from surface wave arrivals was accomplished with a high degree of accuracy regardless of cultural noise. Improved resolution on the surface of the bedrock provides insight into the texture of bedrock and permits identification and appraisal of short wavelength variations in the bedrock surface.

  5. Tularosa Basin Play Fairway Analysis: Hydrothermal Alteration Map

    DOE Data Explorer

    Adam Brandt

    2015-11-15

    This is a hydrothermal alteration map of the Tularosa Basin area, New Mexico and Texas that was created using Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) multispectral data band ratios based upon diagnostic features of clay, calcite, silica, gypsum, ferric iron, and ferrous iron. Mesoproterozoic granite in the San Andreas Range often appeared altered, but this may be from clays produced by weathering or, locally, by hydrothermal alteration. However, no field checking was done. This work was done under U.S. D.O.E. Contract #DE-EE0006730

  6. A Molecular Dynamics Study and Free Energy Analysis of Complexes between the Mlc1p Protein and Two IQ Motif Peptides

    PubMed Central

    Ganoth, Assaf; Friedman, Ran; Nachliel, Esther; Gutman, Menachem

    2006-01-01

    The Mlc1p protein from the budding yeast Saccharomyces cerevisiae is a Calmodulin-like protein, which interacts with IQ-motif peptides located at the yeast's myosin neck. In this study, we report a molecular dynamics study of the Mlc1p-IQ2 protein-peptide complex, starting with its crystal structure, and investigate its dynamics in an aqueous solution. The results are compared with those obtained by a previous study, where we followed the solution structure of the Mlc1p-IQ4 protein-peptide complex by molecular dynamics simulations. After the simulations, we performed an interaction free-energy analysis using the molecular mechanics Poisson-Boltzmann surface area approach. Based on the dynamics of the Mlc1p-IQ protein-peptide complexes, the structure of the light-chain-binding domain of myosin V from the yeast S. cerevisiae is discussed. PMID:16844751

  7. Structure-Function Analysis of the Two-Peptide Bacteriocin Plantaricin EF.

    PubMed

    Ekblad, Bie; Kyriakou, Panagiota K; Oppegård, Camilla; Nissen-Meyer, Jon; Kaznessis, Yiannis N; Kristiansen, Per Eugen

    2016-09-13

    Plantaricin EF is a two-peptide bacteriocin that depends on the complementary action of two different peptides (PlnE and PlnF) to function. The structures of the individual peptides have previously been analyzed by nuclear magnetic resonance spectroscopy ( Fimland, N. et al. ( 2008 ) , Biochim. Biophys. Acta 1784 , 1711 - 1719 ), but the bacteriocin structure and how the two peptides interact have not been determined. All two-peptide bacteriocins identified so far contain GxxxG motifs. These motifs, together with GxxxG-like motifs, are known to mediate helix-helix interactions in membrane proteins. We have mutated all GxxxG and GxxxG-like motifs in PlnE and PlnF in order to determine if any of these motifs are important for antimicrobial activity and thus possibly for interactions between PlnE and PlnF. Moreover, the aromatic amino acids Tyr and Trp in PlnE and PlnF were substituted, and four fusion polypeptides were constructed in order to investigate the relative orientation of PlnE and PlnF in target cell membranes. The results obtained with the fusion polypeptides indicate that PlnE and PlnF interact in an antiparallel manner and that the C-terminus of PlnE and N-terminus of PlnF are on the outer part of target cell membranes and the N-terminus of PlnE and C-terminus of PlnF are on the inner part. The preference for an aromatic residue at position 6 in PlnE suggests a positioning of this residue in or near the membrane interface on the cells inside. Mutations in the GxxxG motifs indicate that the G5xxxG9 motif in PlnE and the S26xxxG30 motif in PlnF are involved in helix-helix interactions. Atomistic molecular dynamics simulation of a structural model consistent with the results confirmed the stability of the structure and its orientation in membranes. The simulation approved the anticipated interactions and revealed additional interactions that further increase the stability of the proposed structure. PMID:27538436

  8. Epitope mapping and functional analysis of sigma A and sigma NS proteins of avian reovirus

    SciTech Connect

    Huang, Pi H.; Li, Ying J.; Su, Yu P.; Lee, Long H.; Liu, Hung J. . E-mail: hjliu@mail.npust.edu.tw

    2005-02-20

    We have previously shown that avian reovirus (ARV) {sigma}A and {sigma}NS proteins possess dsRNA and ssRNA binding activity and suggested that there are two epitopes on {sigma}A (I and II) and three epitopes (A, B, and C) on {sigma}NS. To further define the location of epitopes on {sigma}A and {sigma}NS proteins and to further elucidate the biological functions of these epitopes by using monoclonal antibodies (MAbs) 62, 1F9, H1E1, and 4A123 against the ARV S1133 strain, the full-length and deletion fragments of S2 and S4 genes of ARV generated by polymerase chain reaction (PCR) were cloned into pET32 expression vectors and the fusion proteins were overexpressed in Escherichia coli BL21 strain. Epitope mapping using MAbs and E. coli-expressed deletion fragments of {sigma}A and {sigma}NS of the ARV S1133 strain, synthetic peptides, and the cross reactivity of MAbs to heterologous ARV strains demonstrated that epitope II on {sigma}A was located at amino acid residues {sup 340}QWVMAGLVSAA{sup 350} and epitope B on {sigma}NS at amino acid residues {sup 180}MLDMVDGRP{sup 188}. The MAbs (62, 1F9, and H1E1) directed against epitopes II and B did not require the native conformation of {sigma}A and {sigma}NS, suggesting that their binding activities were conformation-independent. On the other hand, MAb 4A123 only reacted with complete {sigma}NS but not with truncated {sigma}NS fusion proteins in Western blot, suggesting that the binding activity of MAb to epitope A on {sigma}NS was conformation-dependent. Amino acid sequence analysis and the binding assays of MAb 62 to heterologous ARV strains suggested that epitope II on {sigma}A was highly conserved among ARV strains and that this epitope is suitable as a serological marker for the detection of ARV antibodies following natural infection in chickens. On the contrary, an amino acid substitution at position 183 (M to V) in epitope B of ARV could hinder the reactivity of the {sigma}NS with MAb 1F9. The {sigma}NS of ARV with ss

  9. Validation analysis of OpenStreetMap data in some areas of China

    NASA Astrophysics Data System (ADS)

    Zhou, P.; Huang, W.; Jiang, J.

    2014-04-01

    The rapid development of computer technologies has given rise to the increase of open source web-based map services such as OpenStreetMap, a global vector data created by volunteers for free use. There is a concern about the quality and usability of the OpenStreetMap data because the volunteers that contribute the data generally lack the sufficient cartographic training. This paper focuses on the data quality analysis method for OpenStreetMap. A model for usability evaluation has been proposed. A benchmark between OpenStreetMap data and the 1:10 000 topographic data in some areas of China has been done to verify the proposed model, and the method proves to be effective.

  10. Mapping and Initial Analysis of Human Subtelomeric Sequence Assemblies

    PubMed Central

    Riethman, Harold; Ambrosini, Anthony; Castaneda, Carlos; Finklestein, Jeffrey; Hu, Xue-Lan; Mudunuri, Uma; Paul, Sheila; Wei, Jun

    2004-01-01

    Physical mapping data were combined with public draft and finished sequences to derive subtelomeric sequence assemblies for each of the 41 genetically distinct human telomere regions. Sequence gaps that remain on the reference telomeres are generally small,well-defined,and for the most part,restricted to regions directly adjacent to the terminal (TTAGGG)n tract. Of the 20.66 Mb of subtelomeric DNA analyzed, 3.01 Mb are subtelomeric repeat sequences (Srpt),and an additional 2.11 Mb are segmental duplications. The subtelomeric sequence assemblies are enriched >25-fold in short,internal (TTAGGG)n-like sequences relative to the rest of the genome; a total of 114 (TTAGGG)n-like islands were found,55 within Srpt regions,35 within one-copy regions,11 at one-copy/Srpt or Srpt/segmental duplication boundaries,and 13 at the telomeric ends of assemblies. Transcripts were annotated in each assembly,noting their mapping coordinates relative to their respective telomere and whether they originate in duplicated DNA or single-copy DNA. A total of 697 transcripts were found in 15.53 Mb of one-copy DNA,76 transcripts in 2.11 Mb of segmentally duplicated DNA,and 168 transcripts in 3.01 Mb of Srpt sequence. This overall transcript density is similar (within ∼10%) to that found genome-wide. Zinc finger-containing genes and olfactory receptor genes are duplicated within and between multiple telomere regions. PMID:14707167

  11. Definition and characterization of a "trypsinosome" from specific peptide characteristics by nano-HPLC-MS/MS and in silico analysis of complex protein mixtures.

    PubMed

    Le Bihan, Thierry; Robinson, Mark D; Stewart, Ian I; Figeys, Daniel

    2004-01-01

    Although HPLC-ESI-MS/MS is rapidly becoming an indispensable tool for the analysis of peptides in complex mixtures, the sequence coverage it affords is often quite poor. Low protein expression resulting in peptide signal intensities that fall below the limit of detection of the MS system in combination with differences in peptide ionization efficiency plays a significant role in this. A second important factor stems from differences in physicochemical properties of each peptide and how these properties relate to chromatographic retention and ultimate detection. To identify and understand those properties, we compared data from experimentally identified peptides with data from peptides predicted by in silico digest of all corresponding proteins in the experimental set. Three different complex protein mixtures extracted were used to define a training set to evaluate the amino acid retention coefficients based on linear regression analysis. The retention coefficients were also compared with other previous hydrophobic and retention scale. From this, we have constructed an empirical model that can be readily used to predict peptides that are likely to be observed on our HPLC-ESI-MS/MS system based on their physicochemical properties. Finally, we demonstrated that in silico prediction of peptides and their retention coefficients can be used to generate an inclusion list for a targeted mass spectrometric identification of low abundance proteins in complex protein samples. This approach is based on experimentally derived data to calibrate the method and therefore may theoretically be applied to any HPLC-MS/MS system on which data are being generated. PMID:15595722

  12. High-throughput identification of putative receptors for cancer-binding peptides using biopanning and microarray analysis

    PubMed Central

    Ferraro, Daniel J; Bhave, Sandeep R; Kotipatruni, Rama P; Hunn, Jeremy C; Wildman, Scott A; Hong, Charles; Dadey, David Y. A.; Muhoro, Lincoln K.; Jaboin, Jerry J; Thotala, Dinesh; Hallahan, Dennis E

    2013-01-01

    Phage-display peptide biopanning has been successfully used to identify cancer-targeting peptides in multiple models. For cancer-binding peptides, identification of the peptide receptor is necessary to demonstrate mechanism of action and to further optimize specificity and target binding. The process of receptor identification can be slow and some peptides may turn out to bind ubiquitous proteins not suitable for further drug development. In this report, we describe a high-throughput method for screening a large number of peptides in parallel to identify peptide receptors, which we have termed “reverse biopanning,” which can then be selected for further development based on their peptide receptor. To demonstrate this method, we screened a library of 39 peptides previously identified in our laboratory to bind specifically cancers after irradiation. The reverse biopanning process identified 2 peptides, RKFLMTTRYSRV and KTAKKNVFFCSV, as candidate ligands for the protein tax interacting protein 1 (TIP-1), a protein previously identified in our laboratory to be expressed in the cell surface in tumors and upregulated after exposure to ionizing radiation. We used computational modeling as the initial method for rapid validation of peptide-TIP-1 binding. Pseudo-binding energies were calculated to be −360.645 kcal/mol, −487.239 kcal/mol, and −595.328 kcal/mol for HVGGSSV, TTRYSRV, and NVFFCSV respectively, suggesting that the peptides would have at least similar, if not stronger, binding to TIP-1 compared to the known TIP-1 binding peptide HVGGSSV. We validated peptide in vitro via electrophoretic mobility shift assay, which showed strong binding of RKFLMTTRYSRV and the truncated form TTRYSRV. This method allows for the identification of many peptide receptors and subsequent selection of peptides for further drug development based on the peptide receptor. PMID:23147990

  13. Top-Down Analysis of Highly Post-Translationally Modified Peptides by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Guerrero, Andres; Lerno, Larry; Barile, Daniela; Lebrilla, Carlito B.

    2015-03-01

    Bovine κ-caseinoglycomacropeptide (GMP) is a highly modified peptide from κ-casein produced during the cheese making process. The chemical nature of GMP makes analysis by traditional proteomic approaches difficult, as the peptide bears a strong net negative charge and a variety of post-translational modifications. In this work, we describe the use of electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS) for the top-down analysis of GMP. The method allows the simultaneous detection of different GMP forms that result from the combination of amino acid genetic variations and post-translational modifications, specifically phosphorylation and O-glycosylation. The different GMP forms were identified by high resolution mass spectrometry in both negative and positive mode and confirmation was achieved by tandem MS. The results showed the predominance of two genetic variants of GMP that occur as either mono- or bi-phosphorylated species. Additionally, these four forms can be modified with up to two O-glycans generally sialylated. The results demonstrate the presence of glycosylated, bi-phosphorylated forms of GMP never described before.

  14. Comprehensive Evaluation and Analysis of China's Mainstream Online Map Service Websites

    NASA Astrophysics Data System (ADS)

    Zhang, H.; Jiang, J.; Huang, W.; Wang, Q.; Gu, X.

    2012-08-01

    With the flourish development of China's Internet market, all kinds of users for map service demand is rising continually, within it contains tremendous commercial interests. Many internet giants have got involved in the field of online map service, and defined it as an important strategic product of the company. The main purpose of this research is to evaluate these online map service websites comprehensively with a model, and analyse the problems according to the evaluation results. Then some corresponding solving measures are proposed, which provides a theoretical and application guidance for the future development of fiercely competitive online map websites. The research consists of three stages: (a) the mainstream online map service websites in China are introduced and the present situation of them is analysed through visit, investigation, consultant, analysis and research. (b) a whole comprehensive evaluation quota system of online map service websites from the view of functions, layout, interaction design color position and so on, combining with the data indexes such as time efficiency, accuracy, objectivity and authority. (c) a comprehensive evaluation to these online map service websites is proceeded based on the fuzzy evaluation mathematical model, and the difficulty that measure the map websites quantitatively is solved.

  15. Rapid multipoint linkage analysis of recessive traits in nuclear families, including homozygosity mapping

    SciTech Connect

    Kruglyak, L.; Daly, M.J.; Lander, E.S. |

    1995-02-01

    Homozygosity mapping is a powerful strategy for mapping rare recessive traits in children of consanguineous marriages. Practical applications of this strategy are currently limited by the inability of conventional linkage analysis software to compute, in reasonable time, multipoint LOD scores for pedigrees with inbreeding loops. We have developed a new algorithm for rapid multipoint likelihood calculations in small pedigrees, including those with inbreeding loops. The running time of the algorithm grows, at most, linearly with the number of loci considered simultaneously. The running time is not sensitive to the presence of inbreeding loops, missing genotype information, and highly polymorphic loci. We have incorporated this algorithm into a software package, MAPMAKER/HOMOZ, that allows very rapid multipoint mapping of disease genes in nuclear families, including homozygosity mapping. Multipoint analysis with dozens of markers can be carried out in minutes on a personal workstation. 23 refs., 4 figs., 1 tab.

  16. The BrainMap strategy for standardization, sharing, and meta-analysis of neuroimaging data

    PubMed Central

    2011-01-01

    Background Neuroimaging researchers have developed rigorous community data and metadata standards that encourage meta-analysis as a method for establishing robust and meaningful convergence of knowledge of human brain structure and function. Capitalizing on these standards, the BrainMap project offers databases, software applications, and other associated tools for supporting and promoting quantitative coordinate-based meta-analysis of the structural and functional neuroimaging literature. Findings In this report, we describe recent technical updates to the project and provide an educational description for performing meta-analyses in the BrainMap environment. Conclusions The BrainMap project will continue to evolve in response to the meta-analytic needs of biomedical researchers in the structural and functional neuroimaging communities. Future work on the BrainMap project regarding software and hardware advances are also discussed. PMID:21906305

  17. Recent developments in capillary and microchip electroseparations of peptides (2013-middle 2015).

    PubMed

    Kašička, Václav

    2016-01-01

    The review brings a comprehensive survey of recent developments and applications of high performance capillary and microchip electroseparation methods (zone electrophoresis, isotachophoresis, isoelectric focusing, affinity electrophoresis, electrokinetic chromatography, and electrochromatography) to analysis, micropreparation, purification, and physicochemical and biochemical characterization of peptides in the years 2013, 2014, and ca. up to the middle of 2015. Advances in the investigation of electromigration properties of peptides, in the methodology of their analysis, including sample preseparation, preconcentration and derivatization, adsorption suppression and EOF control, as well as in detection of peptides, are described. New developments in particular CE and CEC modes are presented and several types of their applications to peptide analysis are reported: conventional qualitative and quantitative analysis, determination in complex (bio)matrices, monitoring of chemical and enzymatical reactions and physical changes, amino acid, sequence, and chiral analysis, and peptide mapping of proteins. Some micropreparative peptide separations are shown and capabilities of CE and CEC techniques to provide important physicochemical characteristics of peptides are demonstrated. PMID:26332110

  18. Global Mapping Analysis: Stochastic Gradient Algorithm in Multidimensional Scaling

    NASA Astrophysics Data System (ADS)

    Matsuda, Yoshitatsu; Yamaguchi, Kazunori

    In order to implement multidimensional scaling (MDS) efficiently, we propose a new method named “global mapping analysis” (GMA), which applies stochastic approximation to minimizing MDS criteria. GMA can solve MDS more efficiently in both the linear case (classical MDS) and non-linear one (e.g., ALSCAL) if only the MDS criteria are polynomial. GMA separates the polynomial criteria into the local factors and the global ones. Because the global factors need to be calculated only once in each iteration, GMA is of linear order in the number of objects. Numerical experiments on artificial data verify the efficiency of GMA. It is also shown that GMA can find out various interesting structures from massive document collections.

  19. Analysis and machine mapping of the distribution of band recoveries

    USGS Publications Warehouse

    Cowardin, L.M.

    1977-01-01

    A method of calculating distance and bearing from banding site to recovery location based on the solution of a spherical triangle is presented. X and Y distances on an ordinate grid were applied to computer plotting of recoveries on a map. The advantages and disadvantages of tables of recoveries by State or degree block, axial lines, and distance of recovery from banding site for presentation and comparison of the spatial distribution of band recoveries are discussed. A special web-shaped partition formed by concentric circles about the point of banding and great circles at 30-degree intervals through the point of banding has certain advantages over other methods. Comparison of distributions by means of a X? contingency test is illustrated. The statistic V = X?/N can be used as a measure of difference between two distributions of band recoveries and its possible use is illustrated as a measure of the degree of migrational homing.

  20. Structure analysis of an amyloid-forming model peptide by a systematic glycine and proline scan.

    PubMed

    Gerling, Ulla I M; Brandenburg, Enrico; von Berlepsch, Hans; Pagel, Kevin; Koksch, Beate

    2011-08-01

    The ability to adopt at least two different stable conformations is a common feature of proteins involved in many neurodegenerative diseases. The involved molecules undergo a conformational transition from native, mainly helical states to insoluble amyloid structures that have high β-sheet content. A detailed characterization of the molecular architecture of highly ordered amyloid structures, however, is still challenging. Their intrinsically low solubility and high tendency to aggregate often considerably limits the application of established high-resolution techniques such as NMR and X-ray crystallography. An alternative approach to elucidating the tertiary and quaternary organization within an amyloid fibril is the systematic replacement of residues with amino acids that exhibit special conformational characteristics, such as glycine and proline. Substitutions within the β-sheet-prone sequences of the molecules usually severely affect their ability to form fibrils, whereas incorporation at external loop- and bend-like positions often has only marginal effects. Here we present the characterization of the internal architecture of a de novo designed coiled-coil-based amyloid-forming model peptide by means of a series of systematic single glycine and proline replacements in combination with a set of simple low-resolution methods. The folding and assembly behavior of the substituted peptides was monitored simultaneously using circular dichroism spectroscopy, Thioflavin T fluorescence staining, and transmission electron microscopy. On the basis of the obtained data, we successfully identify characteristic bend and core positions within the peptide sequence and propose a detailed structural model of the internal fibrillar arrangement. PMID:21726080

  1. Radial distribution function imaging by STEM diffraction: Phase mapping and analysis of heterogeneous nanostructured glasses.

    PubMed

    Mu, Xiaoke; Wang, Di; Feng, Tao; Kübel, Christian

    2016-09-01

    Characterizing heterogeneous nanostructured amorphous materials is a challenging topic, because of difficulty to solve disordered atomic arrangement in nanometer scale. We developed a new transmission electron microscopy (TEM) method to enable phase analysis and mapping of heterogeneous amorphous structures. That is to combine scanning TEM (STEM) diffraction mapping, radial distribution function (RDF) analysis, and hyperspectral analysis. This method was applied to an amorphous zirconium oxide and zirconium iron multilayer system, and showed extreme sensitivity to small atomic packing variations. This approach helps to understand local structure variations in glassy composite materials and provides new insights to correlate structure and properties of glasses. PMID:27236215

  2. Analysis of Intrinsic Peptide Detectability via Integrated Label-Free and SRM-Based Absolute Quantitative Proteomics.

    PubMed

    Jarnuczak, Andrew F; Lee, Dave C H; Lawless, Craig; Holman, Stephen W; Eyers, Claire E; Hubbard, Simon J

    2016-09-01

    Quantitative mass spectrometry-based proteomics of complex biological samples remains challenging in part due to the variability and charge competition arising during electrospray ionization (ESI) of peptides and the subsequent transfer and detection of ions. These issues preclude direct quantification from signal intensity alone in the absence of a standard. A deeper understanding of the governing principles of peptide ionization and exploitation of the inherent ionization and detection parameters of individual peptides is thus of great value. Here, using the yeast proteome as a model system, we establish the concept of peptide F-factor as a measure of detectability, closely related to ionization efficiency. F-factor is calculated by normalizing peptide precursor ion intensity by absolute abundance of the parent protein. We investigated F-factor characteristics in different shotgun proteomics experiments, including across multiple ESI-based LC-MS platforms. We show that F-factors mirror previously observed physicochemical predictors as peptide detectability but demonstrate a nonlinear relationship between hydrophobicity and peptide detectability. Similarly, we use F-factors to show how peptide ion coelution adversely affects detectability and ionization. We suggest that F-factors have great utility for understanding peptide detectability and gas-phase ion chemistry in complex peptide mixtures, selection of surrogate peptides in targeted MS studies, and for calibration of peptide ion signal in label-free workflows. Data are available via ProteomeXchange with identifier PXD003472. PMID:27454336

  3. 1,2,3-Triazole Bridge as Conformational Constrain in β-Hairpin Peptides: Analysis of Hydrogen-Bonded Positions.

    PubMed

    Celentano, V; Diana, D; Di Salvo, C; De Rosa, L; Romanelli, A; Fattorusso, R; D'Andrea, L D

    2016-04-11

    Conformational constrained β-hairpin peptides are useful tool to modulate protein-protein interactions. A triazole bridge in hydrogen-bonded positions between two antiparallel strands induces a conformational stabilization of the β-hairpin peptide. The entity of the stability of the β-hairpin peptide depends on the length of the bridge. PMID:26938670

  4. Depletion of internal peptides by site-selective blocking, phosphate labeling, and TiO2 adsorption for in-depth analysis of C-terminome.

    PubMed

    Chen, Lingfan; Shan, Yichu; Weng, Yejing; Yuan, Huiming; Zhang, Shen; Fan, Runlong; Sui, Zhigang; Zhang, Xiaodan; Zhang, Lihua; Zhang, Yukui

    2016-05-01

    The analysis of protein C-termini is of great importance, because it not only provides valuable information about protein function, but also facilitates the elucidation of proteolytic processing. However, even with the recent methods for the global profiling of protein C-termini, the identification of C-termini is still far behind that of N-termini due to the lack of basic residue and low reactive carboxyl group. Therefore, an unbiased and complementary method for C-termini profiling is imperative. In this work, we developed a negative enrichment strategy to achieve the in-depth analysis of C-terminome. Proteins were firstly amidated to block carboxyl groups, followed by lysyl endoproteinase (LysC) digestion to generate C-terminal peptides with α-amines and internal peptides bearing both α- and ε-amines. After the α-amines were blocked by site-selective dimethylation or succinylation, the remaining ε-amines on internal peptides were labeled with phosphate groups. Finally, internal peptides were depleted by TiO2, leaving exclusively the fraction of C-terminal peptides for LC-MS/MS analysis. With Escherichia coli (E. coli) digests as the sample, the efficiency of amidation, dimethylation/succinylation, phosphate labeling and TiO2 depletion was proved high. With the combination of dimethyl and succinic blocking strategy, our method enabled the identification of 477 unique C-terminal peptides in E. coli. In comparison with the C-terminal amine-based isotope labeling of substrates (C-TAILS) method, 83 C-termini were identified by both methods, whereas 369 C-termini were unique to C-TAILS and 394 to our dataset. The method proposed is therefore efficient and possibly promotes the comprehensive profiling of C-termini. Graphical Abstract Negative isolation of C-terminal peptides with combination of site-selective blocking, phosphate labeling, and TiO2 adsorption. PMID:27071760

  5. Bioinformatic and phylogenetic analysis of the CLAVATA3/EMBRYO-SURROUNDING REGION (CLE) and the CLE-LIKE signal peptide genes in the Pinophyta

    PubMed Central

    2014-01-01

    Background There is a rapidly growing awareness that plant peptide signalling molecules are numerous and varied and they are known to play fundamental roles in angiosperm plant growth and development. Two closely related peptide signalling molecule families are the CLAVATA3-EMBRYO-SURROUNDING REGION (CLE) and CLE-LIKE (CLEL) genes, which encode precursors of secreted peptide ligands that have roles in meristem maintenance and root gravitropism. Progress in peptide signalling molecule research in gymnosperms has lagged behind that of angiosperms. We therefore sought to identify CLE and CLEL genes in gymnosperms and conduct a comparative analysis of these gene families with angiosperms. Results We undertook a meta-analysis of the GenBank/EMBL/DDBJ gymnosperm EST database and the Picea abies and P. glauca genomes and identified 93 putative CLE genes and 11 CLEL genes among eight Pinophyta species, in the genera Cryptomeria, Pinus and Picea. The predicted conifer CLE and CLEL protein sequences had close phylogenetic relationships with their homologues in Arabidopsis. Notably, perfect conservation of the active CLE dodecapeptide in presumed orthologues of the Arabidopsis CLE41/44-TRACHEARY ELEMENT DIFFERENTIATION (TDIF) protein, an inhibitor of tracheary element (xylem) differentiation, was seen in all eight conifer species. We cloned the Pinus radiata CLE41/44-TDIF orthologues. These genes were preferentially expressed in phloem in planta as expected, but unexpectedly, also in differentiating tracheary element (TE) cultures. Surprisingly, transcript abundances of these TE differentiation-inhibitors sharply increased during early TE differentiation, suggesting that some cells differentiate into phloem cells in addition to TEs in these cultures. Applied CLE13 and CLE41/44 peptides inhibited root elongation in Pinus radiata seedlings. We show evidence that two CLEL genes are alternatively spliced via 3′-terminal acceptor exons encoding separate CLEL peptides

  6. Structure-based characterization of the binding of peptide to the human endophilin-1 Src homology 3 domain using position-dependent noncovalent potential analysis.

    PubMed

    Fu, Chunjiang; Wu, Gang; Lv, Fenglin; Tian, Feifei

    2012-05-01

    Many protein-protein interactions are mediated by a peptide-recognizing domain, such as WW, PDZ, or SH3. In the present study, we describe a new method called position-dependent noncovalent potential analysis (PDNPA), which can accurately characterize the nonbonding profile between the human endophilin-1 Src homology 3 (hEndo1 SH3) domain and its peptide ligands and quantitatively predict the binding affinity of peptide to hEndo1 SH3. In this procedure, structure models of diverse peptides in complex with the hEndo1 SH3 domain are constructed by molecular dynamics simulation and a virtual mutagenesis protocol. Subsequently, three noncovalent interactions associated with each position of the peptide ligand in the complexed state are analyzed using empirical potential functions, and the resulting potential descriptors are then correlated with the experimentally measured affinity on the basis of 1997 hEndo1 SH3-binding peptides with known activities, using linear partial least squares regression (PLS) and the nonlinear support vector machine (SVM). The results suggest that: (i) the electrostatics appears to be more important than steric properties and hydrophobicity in the formation of the hEndo1 SH3-peptide complex; (ii) P(-4) of the core decapeptide ligand with the sequence pattern P(-6)P(-5)P(-4)P(-3)P(-2)P(-1)P(0)P(1)P(2)P(3) is the most important position in terms of determining both the stability and specificity of the architecture of the complex, and; (iii) nonlinear SVM appears to be more effective than linear PLS for accurately predicting the binding affinity of a peptide ligand to hEndo1 SH3, whereas PLS models are straightforward and easy to interpret as compared to those built by SVM. PMID:21947444

  7. High-Density Peptide Microarray Analysis of IgG Autoantibody Reactivities in Serum and Cerebrospinal Fluid of Multiple Sclerosis Patients.

    PubMed

    Hecker, Michael; Fitzner, Brit; Wendt, Matthias; Lorenz, Peter; Flechtner, Kristin; Steinbeck, Felix; Schröder, Ina; Thiesen, Hans-Jürgen; Zettl, Uwe Klaus

    2016-04-01

    Intrathecal immunoglobulin G (IgG) synthesis and oligoclonal IgG bands in cerebrospinal fluid (CSF) are hallmarks of multiple sclerosis (MS), but the antigen specificities remain enigmatic. Our study is the first investigating the autoantibody repertoire in paired serum and CSF samples from patients with relapsing-remitting MS (RRMS), primary progressive MS (PPMS), and other neurological diseases by the use of high-density peptide microarrays. Protein sequences of 45 presumed MS autoantigens (e.g.MOG, MBP, and MAG) were represented on the microarrays by overlapping 15mer peptides. IgG reactivities were screened against a total of 3991 peptides, including also selected viral epitopes. The measured antibody reactivities were highly individual but correlated for matched serum and CSF samples. We found 54 peptides to be recognized significantly more often by serum or CSF antibodies from MS patients compared with controls (pvalues <0.05). The results for RRMS and PPMS clearly overlapped. However, PPMS patients presented a broader peptide-antibody signature. The highest signals were detected for a peptide mapping to a region of the Epstein-Barr virus protein EBNA1 (amino acids 392-411), which is homologous to the N-terminal part of human crystallin alpha-B. Our data confirmed several known MS-associated antigens and epitopes, and they delivered additional potential linear epitopes, which await further validation. The peripheral and intrathecal humoral immune response in MS is polyspecific and includes antibodies that are also found in serum of patients with other diseases. Further studies are required to assess the pathogenic relevance of autoreactive and anti-EBNA1 antibodies as well as their combinatorial value as biomarkers for MS. PMID:26831522

  8. Analysis of the brain ACTH-immunoreactive peptide spectrum in inbred mice

    SciTech Connect

    Fedoseev, Yu.L.; Blednov, Yu.A.; Seredenin, S.B.

    1987-01-01

    Mice of the BALB/c (C) and C57BL/6 (B6) strains, characterized by high and low emotionality respectively in open field tests, have been shown to differ considerably in both the initial level and the time course of changes in the plasma ACTH concentration after exposure to stress in an open field and after administration of a benzodiazepine tranquilizer. The ACTH concentration in the pituitary gland of animals of these lines also differs. The ACTH molecule is known to contain regions with neurotropic activity. It can therefore be postulated that differences in the level of this hormone and the products of its bioconversion in the brain are an essential factor in the mechanisms of formation of the hereditary features of emotional behavior. In this first stage of this investigation, represented in this paper and undertaken to test this hypothesis, spectra of ACTH-immunoreactive peptides were studied in chromatographic fractions of an acid brain extract as well as in the blood plasma of mice belonging to B6 and C lines and their hybrids. The peptides were determined by radioimmunoassay.

  9. Analysis of an insect neuropeptide, Schistocerca gregaria ion transport peptide (ITP), expressed in insect cell systems.

    PubMed

    Pfeifer, T A; Hegedus, D; Wang, Y J; Zhao, Y; Meredith, J; Brock, H W; Phillips, J E; Grigliatti, T A; Theilmann, D A

    1999-12-01

    We have produced an active form of Schistocerca gregaria ion transport peptide (ITP) in an insect cell expression system. Transformed Drosophila Kc1 cells secreted a form of ITP into the cell culture medium that was proteolytically cleaved correctly at the amino (N)-terminus. Concentrated culture supernatant from transformed Kc1 and Hi5 cells had high biological activity when tested on isolated locust ilea. Conversely, ITP expressed by baculovirus-infected Sf9 cells was larger in size and had decreased specific activity compared to ITP produced by Kc1 cells due to incorrect cleavage of the peptide at the N-terminus in the baculovirus system. This demonstrates how processing of the secreted foreign protein (ITP) expressed under the late polyhedrin promoter is compromised in a baculovirus-infected cell. Transient transformation of Kc1 cells results in supernatants containing two forms of ITP; one form (A) co-elutes with synthetic ITP and the other form (B) has reduced electrophoretic mobility. In contrast, in stably transformed Kc1 cell supernatant, ITP is expressed in a single form, which has the same electrophoretic mobility and specific biological activity as form A produced by transiently transformed Kc1 cells. Arch. PMID:10578114

  10. In-depth proteomic analysis of banana (Musa spp.) fruit with combinatorial peptide ligand libraries.

    PubMed

    Esteve, Clara; D'Amato, Alfonsina; Marina, María Luisa; García, María Concepción; Righetti, Pier Giorgio

    2013-01-01

    Musa ssp. is among the world's leading fruit crops. Although a strong interest on banana biochemistry exists in the scientific community, focused on metabolite composition, proteins have been scarcely investigated even if they play an important role in food allergy and stability, are a source of biologically active peptides, and can provide information about nutritional aspects of this fruit. In this work we have employed the combinatorial peptide ligand libraries after different types of protein extractions, for searching the very low-abundance proteins in banana. The use of advanced MS techniques and Musa ssp. mRNAs database in combination with the Uniprot_viridiplantae database allowed us to identify 1131 proteins. Among this huge amount of proteins we found several already known allergens such as Mus a 1, pectinesterase, superoxide dismutase, and potentially new allergens. Additionally several enzymes involved in degradation of starch granules and strictly correlated to ripening stage were identified. This is the first in-depth exploration of the banana fruit proteome and one of the largest descriptions of the proteome of any vegetable system. PMID:23161558

  11. Structural analysis of a signal peptide inside the ribosome tunnel by DNP MAS NMR.

    PubMed

    Lange, Sascha; Franks, W Trent; Rajagopalan, Nandhakishore; Döring, Kristina; Geiger, Michel A; Linden, Arne; van Rossum, Barth-Jan; Kramer, Günter; Bukau, Bernd; Oschkinat, Hartmut

    2016-08-01

    Proteins are synthesized in cells by ribosomes and, in parallel, prepared for folding or targeting. While ribosomal protein synthesis is progressing, the nascent chain exposes amino-terminal signal sequences or transmembrane domains that mediate interactions with specific interaction partners, such as the signal recognition particle (SRP), the SecA-adenosine triphosphatase, or the trigger factor. These binding events can set the course for folding in the cytoplasm and translocation across or insertion into membranes. A distinction of the respective pathways depends largely on the hydrophobicity of the recognition sequence. Hydrophobic transmembrane domains stabilize SRP binding, whereas less hydrophobic signal sequences, typical for periplasmic and outer membrane proteins, stimulate SecA binding and disfavor SRP interactions. In this context, the formation of helical structures of signal peptides within the ribosome was considered to be an important factor. We applied dynamic nuclear polarization magic-angle spinning nuclear magnetic resonance to investigate the conformational states of the disulfide oxidoreductase A (DsbA) signal peptide stalled within the exit tunnel of the ribosome. Our results suggest that the nascent chain comprising the DsbA signal sequence adopts an extended structure in the ribosome with only minor populations of helical structure. PMID:27551685

  12. Biophysical analysis of the interaction of granulysin-derived peptides with enterobacterial endotoxins

    PubMed Central

    Chen, Xi; Howe, Jörg; Andrä, Jörg; Rössle, Manfred; Richter, Walter; Silva, Ana Paula Galvão da; Krensky, Alan M.; Clayberger, Carol; Brandenburg, Klaus

    2009-01-01

    To combat infections by Gram-negative bacteria, it is not only necessary to kill the bacteria but also to neutralize pathogenicity factors such as endotoxin (lipopolysaccharide, LPS). The development of antimicrobial peptides based on mammalian endotoxin-binding proteins is a promising tool in the fight against bacterial infections, and septic shock syndrome. Here, synthetic peptides derived from granulysin (Gra-pep) were investigated in microbiological and biophysical assays to understand their interaction with LPS. We analyzed the influence of the binding of Gra-pep on (1) the acyl chain melting of the hydrophobic moiety of LPS, lipid A, by Fourier-transform spectroscopy, (2) the aggregate structure of LPS by small-angle X-ray scattering and cryo-transmission electron microscopy, and 3) the enthalpy change by isothermal titration calorimetry. In addition, the influence of Gra-pep on the incorporation of LPS and LPS-LBP (lipopolysaccharide-binding protein) complexes into negatively charged liposomes was monitored. Our findings demonstrate a characteristic change in the aggregate structure of LPS into multilamellar stacks in the presence of Gra-pep, but little or no change of acyl chain fluidity. Neutralization of LPS by Gra-pep is not due to a scavenging effect in solution, but rather proceeds after incorporation into target membranes, suggesting a requisite membrane-bound step. PMID:17555705

  13. Structural analysis of a signal peptide inside the ribosome tunnel by DNP MAS NMR

    PubMed Central

    Lange, Sascha; Franks, W. Trent; Rajagopalan, Nandhakishore; Döring, Kristina; Geiger, Michel A.; Linden, Arne; van Rossum, Barth-Jan; Kramer, Günter; Bukau, Bernd; Oschkinat, Hartmut

    2016-01-01

    Proteins are synthesized in cells by ribosomes and, in parallel, prepared for folding or targeting. While ribosomal protein synthesis is progressing, the nascent chain exposes amino-terminal signal sequences or transmembrane domains that mediate interactions with specific interaction partners, such as the signal recognition particle (SRP), the SecA–adenosine triphosphatase, or the trigger factor. These binding events can set the course for folding in the cytoplasm and translocation across or insertion into membranes. A distinction of the respective pathways depends largely on the hydrophobicity of the recognition sequence. Hydrophobic transmembrane domains stabilize SRP binding, whereas less hydrophobic signal sequences, typical for periplasmic and outer membrane proteins, stimulate SecA binding and disfavor SRP interactions. In this context, the formation of helical structures of signal peptides within the ribosome was considered to be an important factor. We applied dynamic nuclear polarization magic-angle spinning nuclear magnetic resonance to investigate the conformational states of the disulfide oxidoreductase A (DsbA) signal peptide stalled within the exit tunnel of the ribosome. Our results suggest that the nascent chain comprising the DsbA signal sequence adopts an extended structure in the ribosome with only minor populations of helical structure. PMID:27551685

  14. Structure-Activity Analysis of the Dermcidin-derived Peptide DCD-1L, an Anionic Antimicrobial Peptide Present in Human Sweat*

    PubMed Central

    Paulmann, Maren; Arnold, Thomas; Linke, Dirk; Özdirekcan, Suat; Kopp, Annika; Gutsmann, Thomas; Kalbacher, Hubert; Wanke, Ines; Schuenemann, Verena J.; Habeck, Michael; Bürck, Jochen; Ulrich, Anne S.; Schittek, Birgit

    2012-01-01

    Dermcidin encodes the anionic amphiphilic peptide DCD-1L, which displays a broad spectrum of antimicrobial activity under conditions resembling those in human sweat. Here, we have investigated its mode of antimicrobial activity. We found that DCD-1L interacts preferentially with negatively charged bacterial phospholipids with a helix axis that is aligned flat on a lipid bilayer surface. Upon interaction with lipid bilayers DCD-1L forms oligomeric complexes that are stabilized by Zn2+. DCD-1L is able to form ion channels in the bacterial membrane, and we propose that Zn2+-induced self-assembly of DCD-1L upon interaction with bacterial lipid bilayers is a prerequisite for ion channel formation. These data allow us for the first time to propose a molecular model for the antimicrobial mechanism of a naturally processed human anionic peptide that is active under the harsh conditions present in human sweat. PMID:22262861

  15. Cluster analysis of Wisconsin Breast Cancer dataset using self-organizing maps.

    PubMed

    Pantazi, Stefan; Kagolovsky, Yuri; Moehr, Jochen R

    2002-01-01

    This work deals with multidimensional data analysis, precisely cluster analysis applied to a very well known dataset, the Wisconsin Breast Cancer dataset. After the introduction of the topics of the paper the cluster analysis concept is shortly explained and different methods of cluster analysis are compared. Further, the Kohonen model of self-organizing maps is briefly described together with an example and with explanations of how the cluster analysis can be performed using the maps. After describing the data set and the methodology used for the analysis we present the findings using textual as well as visual descriptions and conclude that the approach is a useful complement for assessing multidimensional data and that this dataset has been overused for automated decision benchmarking purposes, without a thorough analysis of the data it contains. PMID:15460731

  16. Ion Torrent sequencing for conducting genome-wide scans for mutation mapping analysis.

    PubMed

    Damerla, Rama Rao; Chatterjee, Bishwanath; Li, You; Francis, Richard J B; Fatakia, Sarosh N; Lo, Cecilia W

    2014-04-01

    Mutation mapping in mice can be readily accomplished by genome wide segregation analysis of polymorphic DNA markers. In this study, we showed the efficacy of Ion Torrent next generation sequencing for conducting genome-wide scans to map and identify a mutation causing congenital heart disease in a mouse mutant, Bishu, recovered from a mouse mutagenesis screen. The Bishu mutant line generated in a C57BL/6J (B6) background was intercrossed with another inbred strain, C57BL/10J (B10), and the resulting B6/B10 hybrid offspring were intercrossed to generate mutants used for the mapping analysis. For each mutant sample, a panel of 123 B6/B10 polymorphic SNPs distributed throughout the mouse genome was PCR amplified, bar coded, and then pooled to generate a single library used for Ion Torrent sequencing. Sequencing carried out using the 314 chip yielded >600,000 usable reads. These were aligned and mapped using a custom bioinformatics pipeline. Each SNP was sequenced to a depth >500×, allowing accurate automated calling of the B6/B10 genotypes. This analysis mapped the mutation in Bishu to an interval on the proximal region of mouse chromosome 4. This was confirmed by parallel capillary sequencing of the 123 polymorphic SNPs. Further analysis of genes in the map interval identified a splicing mutation in Dnaic1(c.204+1G>A), an intermediate chain dynein, as the disease causing mutation in Bishu. Overall, our experience shows Ion Torrent amplicon sequencing is high throughput and cost effective for conducting genome-wide mapping analysis and is easily scalable for other high volume genotyping analyses. PMID:24306492

  17. Biomass Thermogravimetric Analysis: Uncertainty Determination Methodology and Sampling Maps Generation

    PubMed Central

    Pazó, Jose A.; Granada, Enrique; Saavedra, Ángeles; Eguía, Pablo; Collazo, Joaquín

    2010-01-01

    The objective of this study was to develop a methodology for the determination of the maximum sampling error and confidence intervals of thermal properties obtained from thermogravimetric analysis (TG), including moisture, volatile matter, fixed carbon and ash content. The sampling procedure of the TG analysis was of particular interest and was conducted with care. The results of the present study were compared to those of a prompt analysis, and a correlation between the mean values and maximum sampling errors of the methods were not observed. In general, low and acceptable levels of uncertainty and error were obtained, demonstrating that the properties evaluated by TG analysis were representative of the overall fuel composition. The accurate determination of the thermal properties of biomass with precise confidence intervals is of particular interest in energetic biomass applications. PMID:20717532

  18. Structure-Activity Analysis of Gram-positive Bacterium-producing Lasso Peptides with Anti-mycobacterial Activity

    PubMed Central

    Inokoshi, Junji; Koyama, Nobuhiro; Miyake, Midori; Shimizu, Yuji; Tomoda, Hiroshi

    2016-01-01

    Lariatin A, an 18-residue lasso peptide encoded by the five-gene cluster larABCDE, displays potent and selective anti-mycobacterial activity. The structural feature is an N-terminal macrolactam ring, through which the C-terminal passed to form the rigid lariat-protoknot structure. In the present study, we established a convergent expression system by the strategy in which larA mutant gene-carrying plasmids were transformed into larA-deficient Rhodococcus jostii, and generated 36 lariatin variants of the precursor protein LarA to investigate the biosynthesis and the structure-activity relationships. The mutational analysis revealed that four amino acid residues (Gly1, Arg7, Glu8, and Trp9) in lariatin A are essential for the maturation and production in the biosynthetic machinery. Furthermore, the study on structure-activity relationships demonstrated that Tyr6, Gly11, and Asn14 are responsible for the anti-mycobacterial activity, and the residues at positions 15, 16 and 18 in lariatin A are critical for enhancing the activity. This study will not only provide a useful platform for genetically engineering Gram-positive bacterium-producing lasso peptides, but also an important foundation to rationally design more promising drug candidates for combatting tuberculosis. PMID:27457620

  19. Structure-Activity Analysis of Gram-positive Bacterium-producing Lasso Peptides with Anti-mycobacterial Activity

    NASA Astrophysics Data System (ADS)

    Inokoshi, Junji; Koyama, Nobuhiro; Miyake, Midori; Shimizu, Yuji; Tomoda, Hiroshi

    2016-07-01

    Lariatin A, an 18-residue lasso peptide encoded by the five-gene cluster larABCDE, displays potent and selective anti-mycobacterial activity. The structural feature is an N-terminal macrolactam ring, through which the C-terminal passed to form the rigid lariat-protoknot structure. In the present study, we established a convergent expression system by the strategy in which larA mutant gene-carrying plasmids were transformed into larA-deficient Rhodococcus jostii, and generated 36 lariatin variants of the precursor protein LarA to investigate the biosynthesis and the structure-activity relationships. The mutational analysis revealed that four amino acid residues (Gly1, Arg7, Glu8, and Trp9) in lariatin A are essential for the maturation and production in the biosynthetic machinery. Furthermore, the study on structure-activity relationships demonstrated that Tyr6, Gly11, and Asn14 are responsible for the anti-mycobacterial activity, and the residues at positions 15, 16 and 18 in lariatin A are critical for enhancing the activity. This study will not only provide a useful platform for genetically engineering Gram-positive bacterium-producing lasso peptides, but also an important foundation to rationally design more promising drug candidates for combatting tuberculosis.

  20. Biosom: gene synonym analysis by self-organizing map.

    PubMed

    Otemaier, K R; Steffens, M B R; Raittz, R T; Brawerman, A; Marchaukoski, J N

    2015-01-01

    There are several guidelines for gene nomenclature, but they are not always applied to the names of newly identified genes. The lack of standardization in naming genes generates inconsistent databases with errors such as genes with the same function and different names, genes with different functions and the same name, and use of an abbreviated name. This paper presents a methodology for predicting synonyms in a given gene nomenclature, thereby detecting and minimizing naming redundancy and inconsistency and facilitating the annotation of new genes and data mining in public databases. To identify gene synonyms, i.e., gene ambiguity, the methodology proposed begins by grouping genes according to their names using a Kohonen self-organizing map artificial neural network. Afterwards, it identifies the groups generated employing the Matrix-U technique. The employment of such techniques allows one to infer the synonyms of genes, to predict probable hypothetical gene names and to point out possible errors in a database record. Many mistakes related to gene nomenclature were detected in this research, demonstrating the importance of predicting synonyms. The methodology developed is applicable for describing hypothetical, putative and other types of genes without a known function. Moreover, it can also indicate a possible function for genes after grouping them. PMID:25730085

  1. A Conserved Epitope Mapped with a Monoclonal Antibody against the VP3 Protein of Goose Parvovirus by Using Peptide Screening and Phage Display Approaches

    PubMed Central

    Li, Chenxi; Liu, Hongyu; Li, Jinzhe; Liu, Dafei; Meng, Runze; Zhang, Qingshan; Shaozhou, Wulin; Bai, Xiaofei; Zhang, Tingting; Liu, Ming; Zhang, Yun

    2016-01-01

    Background Waterfowl parvovirus (WPV) infection causes high mortality and morbidity in both geese (Anser anser) and Muscovy ducks (Cairina moschata), resulting in significant losses to the waterfowl industries. The VP3 protein of WPV is a major structural protein that induces neutralizing antibodies in the waterfowl. However, B-cell epitopes on the VP3 protein of WPV have not been characterized. Methods and Results To understand the antigenic determinants of the VP3 protein, we used the monoclonal antibody (mAb) 4A6 to screen a set of eight partially expressed overlapping peptides spanning VP3. Using western blotting and an enzyme-linked immunosorbent assay (ELISA), we localized the VP3 epitope between amino acids (aa) 57 and 112. To identify the essential epitope residues, a phage library displaying 12-mer random peptides was screened with mAb 4A6. Phage clone peptides displayed a consensus sequence of YxRFHxH that mimicked the sequence 82Y/FNRFHCH88, which corresponded to amino acid residues 82 to 88 of VP3 protein of WPVs. mAb 4A6 binding to biotinylated fragments corresponding to amino acid residues 82 to 88 of the VP3 protein verified that the 82FxRFHxH88 was the VP3 epitope and that amino acids 82F is necessary to retain maximal binding to mAb 4A6. Parvovirus-positive goose and duck sera reacted with the epitope peptide by dot blotting assay, revealing the importance of these amino acids of the epitope in antibody-epitope binding reactivity. Conclusions and Significance We identified the motif FxRFHxH as a VP3-specific B-cell epitope that is recognized by the neutralizing mAb 4A6. This finding might be valuable in understanding of the antigenic topology of VP3 of WPV. PMID:27191594

  2. Statistical analysis on the evolution of OpenStreetMap road networks in Beijing

    NASA Astrophysics Data System (ADS)

    Zhao, Pengxiang; Jia, Tao; Qin, Kun; Shan, Jie; Jiao, Chenjing

    2015-02-01

    In recent years, extensive efforts have been paid on the investigation of OpenStreetMap (OSM) in developed countries, but little attention has been given to the cities in developing countries. This paper presents the results regarding the evolution of OSM road networks in Beijing, China, from four aspects. First, findings from general analysis indicate that (1) the overall growth pattern could be mainly explained by the increasing number of volunteers and their mapping contributions. Second, findings from geometric analysis suggest: (2) mapping intensity exhibits heavy-tailed pattern both for a certain time period and across time; (3) mapping direction moves from outskirts to downtown distinguished from other regions; and (4) mapping behaviors are mainly constrained by the underlying structure of road networks. Third, results of topological analysis indicate that (5) OSM road networks resemble the growth of real road networks and are undergoing an evolution process depicted by exploration and densification. Last, from the perspective of centrality analysis, (6) two kinds of nodes are identified with the ones accounting for the exploration and the other ones for the densification, which further hints the evolution process of continuous strong exploration accompanied by weak densification.

  3. Toward standardized mapping for left atrial analysis and cardiac ablation guidance

    NASA Astrophysics Data System (ADS)

    Rettmann, M. E.; Holmes, D. R.; Linte, C. A.; Packer, D. L.; Robb, R. A.

    2014-03-01

    In catheter-based cardiac ablation, the pulmonary vein ostia are important landmarks for guiding the ablation procedure, and for this reason, have been the focus of many studies quantifying their size, structure, and variability. Analysis of pulmonary vein structure, however, has been limited by the lack of a standardized reference space for population based studies. Standardized maps are important tools for characterizing anatomic variability across subjects with the goal of separating normal inter-subject variability from abnormal variability associated with disease. In this work, we describe a novel technique for computing flat maps of left atrial anatomy in a standardized space. A flat map of left atrial anatomy is created by casting a single ray through the volume and systematically rotating the camera viewpoint to obtain the entire field of view. The technique is validated by assessing preservation of relative surface areas and distances between the original 3D geometry and the flat map geometry. The proposed methodology is demonstrated on 10 subjects which are subsequently combined to form a probabilistic map of anatomic location for each of the pulmonary vein ostia and the boundary of the left atrial appendage. The probabilistic map demonstrates that the location of the inferior ostia have higher variability than the superior ostia and the variability of the left atrial appendage is similar to the superior pulmonary veins. This technique could also have potential application in mapping electrophysiology data, radio-frequency ablation burns, or treatment planning in cardiac ablation therapy.

  4. Study of immobilized metal affinity chromatography sorbents for the analysis of peptides by on-line solid-phase extraction capillary electrophoresis-mass spectrometry.

    PubMed

    Ortiz-Martin, Lorena; Benavente, Fernando; Medina-Casanellas, Silvia; Giménez, Estela; Sanz-Nebot, Victoria

    2015-03-01

    Several commercial immobilized metal affinity chromatography sorbents were evaluated in this study for the analysis of two small peptide fragments of the amyloid β-protein (Aβ) (Aβ(1-15) and Aβ(10-20) peptides) by on-line immobilized metal affinity SPE-CE (IMA-SPE-CE). The performance of a nickel metal ion (Ni(II)) sorbent based on nitrilotriacetic acid as a chelating agent was significantly better than two copper metal ion (Cu(II)) sorbents based on iminodiacetic acid. A BGE of 25 mM phosphate (pH 7.4) and an eluent of 50 mM imidazole (in BGE) yielded a 25-fold and 5-fold decrease in the LODs by IMA-SPE-CE-UV for Aβ(1-15) and Aβ(10-20) peptides (0.1 and 0.5 μg/mL, respectively) with regard to CE-UV (2.5 μg/mL for both peptides). The phosphate BGE was also used in IMA-SPE-CE-MS, but the eluent needed to be substituted by a 0.5% HAc v/v solution. Under optimum preconcentration and detection conditions, reproducibility of peak areas and migration times was acceptable (23.2 and 12.0%RSD, respectively). The method was more sensitive for Aβ(10-20) peptide, which could be detected until 0.25 μg/mL. Linearity for Aβ(10-20) peptide was good in a narrow concentration range (0.25-2.5 μg/mL, R(2) = 0.93). Lastly, the potential of the optimized Ni(II)-IMA-SPE-CE-MS method for the analysis of amyloid peptides in biological fluids was evaluated by analyzing spiked plasma and serum samples. PMID:25640944

  5. Easy and Rapid Binding Assay for Functional Analysis of Disulfide-Containing Peptides by a Pull-Down Method Using a Puromycin-Linker and a Cell-Free Translation System

    PubMed Central

    Tanemura, Yutaro; Mochizuki, Yuki; Kumachi, Shigefumi; Nemoto, Naoto

    2015-01-01

    Constrained peptides are an attractive class as affinity reagents or drug leads owing to their excellent binding properties. Many kinds of these peptides, such as cyclic peptides containing disulfide bridges, are found in nature or designed artificially by directed evolution. However, confirming the binding properties of the disulfide-rich peptides can be generally difficult, because of oxidative folding problems in the preparation steps. Therefore, a method for evaluating the binding properties of such peptides rapidly and easily is required. Here, we report an easy and rapid method for preparing biotin-attached peptides containing disulfide bridges or a chemical cross-linker using a cell-free translation system and a puromycin-linker, which is applicable to pull-down assays for protein (or peptide) molecular interaction analysis. PMID:25738808

  6. Analysis of Protein-RNA and Protein-Peptide Interactions in Equine Infectious Anemia

    SciTech Connect

    Lee, Jae-Hyung

    2007-01-01

    Macromolecular interactions are essential for virtually all cellular functions including signal transduction processes, metabolic processes, regulation of gene expression and immune responses. This dissertation focuses on the characterization of two important macromolecular interactions involved in the relationship between Equine Infectious Anemia Virus (EIAV) and its host cell in horse: (1) the interaction between the EIAV Rev protein and its binding site, the Rev-responsive element (RRE) and (2) interactions between equine MHC class I molecules and epitope peptides derived from EIAV proteins. EIAV, one of the most divergent members of the lentivirus family, has a single-stranded RNA genome and carries several regulatory and structural proteins within its viral particle. Rev is an essential EIAV regulatory encoded protein that interacts with the viral RRE, a specific binding site in the viral mRNA. Using a combination of experimental and computational methods, the interactions between EIAV Rev and RRE were characterized in detail. EIAV Rev was shown to have a bipartite RNA binding domain contain two arginine rich motifs (ARMs). The RRE secondary structure was determined and specific structural motifs that act as cis-regulatory elements for EIAV Rev-RRE interaction were identified. Interestingly, a structural motif located in the high affinity Rev binding site is well conserved in several diverse lentiviral genoes, including HIV-1. Macromolecular interactions involved in the immune response of the horse to EIAV infection were investigated by analyzing complexes between MHC class I proteins and epitope peptides derived from EIAV Rev, Env and Gag proteins. Computational modeling results provided a mechanistic explanation for the experimental finding that a single amino acid change in the peptide binding domain of the quine MHC class I molecule differentially affectes the recognitino of specific epitopes by EIAV-specific CTL. Together, the findings in this

  7. The Performance Analysis of a Uav Based Mobile Mapping System

    NASA Astrophysics Data System (ADS)

    Tsai, M. L.; Chiang, K. W.; Tseng, Y. H.; Rau, J. Y.; Huang, Y. W.; Lo, C. F.

    2012-07-01

    In order to facilitate applications such as environment detection or disaster monitoring, developing a quickly and low cost system to collect near real time spatial information is very important. Such a rapid spatial information collection capability has become an emerging trend in the technology of remote sensing and mapping application. In this study, a fixed-wing UAV based spatial information acquisition platform is developed and evaluated. The proposed UAV based platform has a direct georeferencing module including an low cost INS/GPS integrated system, low cost digital camera as well as other general UAV modules including immediately video monitoring communication system. This direct georeferencing module is able to provide differential GPS processing with single frequency carrier phase measurements to obtain sufficient positioning accuracy. All those necessary calibration procedures including interior orientation parameters, the lever arm and boresight angle are implemented. In addition, a flight test is performed to verify the positioning accuracy in direct georeferencing mode without using any ground control point that is required for most of current UAV based photogrammetric platforms. In other word, this is one of the pilot studies concerning direct georeferenced based UAV photogrammetric platform. The preliminary results in term of positioning accuracy in direct georeferenced mode without using any GCP illustrate horizontal positioning accuracies in x and y axes are both less than 20 meters, respectively. On the contrary, the positioning accuracy of z axis is less than 50 meters with 600 meters flight height above ground. Such accuracy is good for near real time disaster relief. Therefore, it is a relatively safe and cheap platform to collect critical spatial information for urgent response such as disaster relief and assessment applications where ground control points are not available.

  8. Using Curriculum Mapping to Engage Faculty Members in the Analysis of a Pharmacy Program

    PubMed Central

    Vercaigne, Lavern; Davies, Neal M.; Davis, Christine; Renaud, Robert; Kristjanson, Cheryl

    2014-01-01

    Objective. To develop a curriculum mapping process that supports continuous analysis and evidence-based decisions in a pharmacy program. Design. A curriculum map based on the national educational outcomes for pharmacy programs was created using conceptual frameworks grounded in cognitive learning and skill acquisition. Assessment. The curriculum map was used to align the intended curriculum with the national educational outcomes and licensing examination blueprint. The leveling and sequencing of content showed longitudinal progression of student learning and performance. There was good concordance between the intended and learned curricula as validated by survey responses from employers and graduating students. Conclusion. The curriculum mapping process was efficient and effective in providing an evidence-based approach to the continuous quality improvement of a pharmacy program. PMID:25258444

  9. A spherical electron-channelling pattern map for use in quartz petrofabric analysis

    USGS Publications Warehouse

    Lloyd, G.E.; Ferguson, C.C.

    1986-01-01

    Electron channelling patterns (ECP's) are formed in the scanning electron microscope (SEM) by the interaction between the incident electrons and the lattice of crystalline specimens. The patterns are unique for a particular crystallographic orientation and are therefore of considerable potential in petrofabric studies provided they can be accurately indexed. Indexing requires an ECP-map of the crystallographic stereogram or unit triangle covering all possible orientations and hence ECP patterns. Due to the presence of long-range distortions in planar ECP-maps, it is more convenient to construct the maps over a spherical surface. This also facilitates the indexing of individual ECP's. A spherical ECP-map for quartz is presented together with an example of its use in petrofabric analysis. ?? 1986.

  10. Combined sequence-based and genetic mapping analysis of complex traits in outbred rats

    PubMed Central

    Baud, Amelie; Hermsen, Roel; Guryev, Victor; Stridh, Pernilla; Graham, Delyth; McBride, Martin W.; Foroud, Tatiana; Calderari, Sophie; Diez, Margarita; Ockinger, Johan; Beyeen, Amennai D.; Gillett, Alan; Abdelmagid, Nada; Guerreiro-Cacais, Andre Ortlieb; Jagodic, Maja; Tuncel, Jonatan; Norin, Ulrika; Beattie, Elisabeth; Huynh, Ngan; Miller, William H.; Koller, Daniel L.; Alam, Imranul; Falak, Samreen; Osborne-Pellegrin, Mary; Martinez-Membrives, Esther; Canete, Toni; Blazquez, Gloria; Vicens-Costa, Elia; Mont-Cardona, Carme; Diaz-Moran, Sira; Tobena, Adolf; Hummel, Oliver; Zelenika, Diana; Saar, Kathrin; Patone, Giannino; Bauerfeind, Anja; Bihoreau, Marie-Therese; Heinig, Matthias; Lee, Young-Ae; Rintisch, Carola; Schulz, Herbert; Wheeler, David A.; Worley, Kim C.; Muzny, Donna M.; Gibbs, Richard A.; Lathrop, Mark; Lansu, Nico; Toonen, Pim; Ruzius, Frans Paul; de Bruijn, Ewart; Hauser, Heidi; Adams, David J.; Keane, Thomas; Atanur, Santosh S.; Aitman, Tim J.; Flicek, Paul; Malinauskas, Tomas; Jones, E. Yvonne; Ekman, Diana; Lopez-Aumatell, Regina; Dominiczak, Anna F; Johannesson, Martina; Holmdahl, Rikard; Olsson, Tomas; Gauguier, Dominique; Hubner, Norbert; Fernandez-Teruel, Alberto; Cuppen, Edwin; Mott, Richard; Flint, Jonathan

    2013-01-01

    Genetic mapping on fully sequenced individuals is transforming our understanding of the relationship between molecular variation and variation in complex traits. Here we report a combined sequence and genetic mapping analysis in outbred rats that maps 355 quantitative trait loci for 122 phenotypes. We identify 35 causal genes involved in 31 phenotypes, implicating novel genes in models of anxiety, heart disease and multiple sclerosis. The relation between sequence and genetic variation is unexpectedly complex: at approximately 40% of quantitative trait loci a single sequence variant cannot account for the phenotypic effect. Using comparable sequence and mapping data from mice, we show the extent and spatial pattern of variation in inbred rats differ significantly from those of inbred mice, and that the genetic variants in orthologous genes rarely contribute to the same phenotype in both species. PMID:23708188

  11. Combined sequence-based and genetic mapping analysis of complex traits in outbred rats.

    PubMed

    Baud, Amelie; Hermsen, Roel; Guryev, Victor; Stridh, Pernilla; Graham, Delyth; McBride, Martin W; Foroud, Tatiana; Calderari, Sophie; Diez, Margarita; Ockinger, Johan; Beyeen, Amennai D; Gillett, Alan; Abdelmagid, Nada; Guerreiro-Cacais, Andre Ortlieb; Jagodic, Maja; Tuncel, Jonatan; Norin, Ulrika; Beattie, Elisabeth; Huynh, Ngan; Miller, William H; Koller, Daniel L; Alam, Imranul; Falak, Samreen; Osborne-Pellegrin, Mary; Martinez-Membrives, Esther; Canete, Toni; Blazquez, Gloria; Vicens-Costa, Elia; Mont-Cardona, Carme; Diaz-Moran, Sira; Tobena, Adolf; Hummel, Oliver; Zelenika, Diana; Saar, Kathrin; Patone, Giannino; Bauerfeind, Anja; Bihoreau, Marie-Therese; Heinig, Matthias; Lee, Young-Ae; Rintisch, Carola; Schulz, Herbert; Wheeler, David A; Worley, Kim C; Muzny, Donna M; Gibbs, Richard A; Lathrop, Mark; Lansu, Nico; Toonen, Pim; Ruzius, Frans Paul; de Bruijn, Ewart; Hauser, Heidi; Adams, David J; Keane, Thomas; Atanur, Santosh S; Aitman, Tim J; Flicek, Paul; Malinauskas, Tomas; Jones, E Yvonne; Ekman, Diana; Lopez-Aumatell, Regina; Dominiczak, Anna F; Johannesson, Martina; Holmdahl, Rikard; Olsson, Tomas; Gauguier, Dominique; Hubner, Norbert; Fernandez-Teruel, Alberto; Cuppen, Edwin; Mott, Richard; Flint, Jonathan

    2013-07-01

    Genetic mapping on fully sequenced individuals is transforming understanding of the relationship between molecular variation and variation in complex traits. Here we report a combined sequence and genetic mapping analysis in outbred rats that maps 355 quantitative trait loci for 122 phenotypes. We identify 35 causal genes involved in 31 phenotypes, implicating new genes in models of anxiety, heart disease and multiple sclerosis. The relationship between sequence and genetic variation is unexpectedly complex: at approximately 40% of quantitative trait loci, a single sequence variant cannot account for the phenotypic effect. Using comparable sequence and mapping data from mice, we show that the extent and spatial pattern of variation in inbred rats differ substantially from those of inbred mice and that the genetic variants in orthologous genes rarely contribute to the same phenotype in both species. PMID:23708188

  12. Admixture Aberration Analysis: Application to Mapping in Admixed Population Using Pooled DNA

    NASA Astrophysics Data System (ADS)

    Bercovici, Sivan; Geiger, Dan

    Admixture mapping is a gene mapping approach used for the identification of genomic regions harboring disease susceptibility genes in the case of recently admixed populations such as African Americans. We present a novel method for admixture mapping, called admixture aberration analysis (AAA), that uses a DNA pool of affected admixed individuals. We demonstrate through simulations that AAA is a powerful and economical mapping method under a range of scenarios, capturing complex human diseases such as hypertension and end stage kidney disease. The method has a low false-positive rate and is robust to deviation from model assumptions. Finally, we apply AAA on 600 prostate cancer-affected African Americans, replicating a known risk locus. Simulation results indicate that the method can yield over 96% reduction in genotyping. Our method is implemented as a Java program called AAAmap and is freely available.

  13. Precision Analysis of Point-And Photogrammetric Measurements for Corridor Mapping: Preliminary Results

    NASA Astrophysics Data System (ADS)

    Molina, P.; Blázquez, M.; Sastre, J.; Colomina, I.

    2016-03-01

    This paper addresses the key aspects of the sensor orientation and calibration approach within the mapKITE concept for corridor mapping, focusing on the contribution analysis of point-and-scale measurements of kinematic ground control points. MapKITE is a new mobile, simultaneous terrestrial and aerial, geodata acquisition and post-processing method. On one hand, the acquisition system is a tandem composed of a terrestrial mobile mapping system and an unmanned aerial system, the latter equipped with a remote sensing payload, and linked through a 'virtual tether', that is, a real-time waypoint supply from the terrestrial vehicle to the unmanned aircraft. On the other hand, mapKITE entails a method for geodata post-processing (specifically, sensor orientation and calibration) based on the described acquisition paradigm, focusing on few key aspects: the particular geometric relationship of a mapKITE network - the aerial vehicle always observes the terrestrial one as they both move -, precise air and ground trajectory determination - the terrestrial vehicle is regarded as a kinematic ground control point - and new photogrammetric measurements - pointing on and measuring the scale of an optical target on the roof of the terrestrial vehicle - are exploited. In this paper, we analyze the performance of aerial image orientation and calibration in mapKITE for corridor mapping, which is the natural application niche of mapKITE, based on the principles and procedures of integrated sensor orientation with the addition of point-and-scale photogrammetric measurements of the kinematic ground control points. To do so, traditional (static ground control points, photogrammetric tie points, aerial control) and new (pointing-and-scaling of kinematic ground control points) measurements have been simulated for mapKITE corridor mapping missions, consisting on takeoff and calibration pattern, single-pass corridor operation potentially performing calibration patterns, and landing and

  14. Comparative analysis reveals loss of the appetite-regulating peptide hormone ghrelin in falcons.

    PubMed

    Seim, Inge; Jeffery, Penny L; Herington, Adrian C; Chopin, Lisa K

    2015-05-15

    Ghrelin and leptin are key peripherally secreted appetite-regulating hormones in vertebrates. Here we consider the ghrelin gene (GHRL) of birds (class Aves), where it has been reported that ghrelin inhibits rather than augments feeding. Thirty-one bird species were compared, revealing that most species harbour a functional copy of GHRL and the coding region for its derived peptides ghrelin and obestatin. We provide evidence for loss of GHRL in saker and peregrine falcons, and this is likely to result from the insertion of an ERVK retrotransposon in intron 0. We hypothesise that the loss of anorexigenic ghrelin is a predatory adaptation that results in increased food-seeking behaviour and feeding in falcons. PMID:25500363

  15. Impage Analysis for Mapping Immeasurable Phenotypes in Maize

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A majority of phenotypic variance in maize has qualitative aspects that are immeasurable by rulers or scalars. Image analysis may improve the phenotypic quantification by increasing the objectivity and granularity of quantification, which in turn may result in an increase in the rate at which the ge...

  16. Mapping Learning and Game Mechanics for Serious Games Analysis

    ERIC Educational Resources Information Center

    Arnab, Sylvester; Lim, Theodore; Carvalho, Maira B.; Bellotti, Francesco; de Freitas, Sara; Louchart, Sandy; Suttie, Neil; Berta, Riccardo; De Gloria, Alessandro

    2015-01-01

    Although there is a consensus on the instructional potential of Serious Games (SGs), there is still a lack of methodologies and tools not only for design but also to support analysis and assessment. Filling this gap is one of the main aims of the Games and Learning Alliance (http://www.galanoe.eu) European Network of Excellence on Serious Games,…

  17. Cascades/Aleutian Play Fairway Analysis: Data and Map Files

    SciTech Connect

    Lisa Shevenell

    2015-11-15

    Contains Excel data files used to quantifiably rank the geothermal potential of each of the young volcanic centers of the Cascade and Aleutian Arcs using world power production volcanic centers as benchmarks. Also contains shapefiles used in play fairway analysis with power plant, volcano, geochemistry and structural data.

  18. Centromere-Linkage Analysis and Consolidation of the Zebrafish Genetic Map

    PubMed Central

    Johnson, S. L.; Gates, M. A.; Johnson, M.; Talbot, W. S.; Horne, S.; Baik, K.; Rude, S.; Wong, J. R.; Postlethwait, J. H.

    1996-01-01

    The ease of isolating mutations in zebrafish will contribute to an understanding of a variety of processes common to all vertebrates. To facilitate genetic analysis of such mutations, we have identified DNA polymorphisms closely linked to each of the 25 centromeres of zebrafish, placed centromeres on the linkage map, increased the number of mapped PCR-based markers to 652, and consolidated the number of linkage groups to the number of chromosomes. This work makes possible centromere-linkage analysis, a novel, rapid method to assign mutations to a specific linkage group using half-tetrads. PMID:8846904

  19. Multipoint-likelihood maximization mapping on 4 segregating populations to achieve an integrated framework map for QTL analysis in pot azalea (Rhododendron simsii hybrids)

    PubMed Central

    2010-01-01

    Background Azalea (Rhododendron simsii hybrids) is the most important flowering pot plant produced in Belgium, being exported world-wide. In the breeding program, flower color is the main feature for selection, only in later stages cultivation related plant quality traits are evaluated. As a result, plants with attractive flowering are kept too long in the breeding cycle. The inheritance of flower color has been well studied; information on the heritability of cultivation related quality traits is lacking. For this purpose, QTL mapping in diverse genetic backgrounds appeared to be a must and therefore 4 mapping populations were made and analyzed. Results An integrated framework map on four individual linkage maps in Rhododendron simsii hybrids was constructed. For genotyping, mainly dominant scored AFLP (on average 364 per population) and MYB-based markers (15) were combined with co-dominant SSR (23) and EST markers (12). Linkage groups were estimated in JoinMap. A consensus grouping for the 4 mapping populations was made and applied in each individual mapping population. Finally, 16 stable linkage groups were set for the 4 populations; the azalea chromosome number being 13. A combination of regression mapping (JoinMap) and multipoint-likelihood maximization (Carthagène) enabled the construction of 4 maps and their alignment. A large portion of loci (43%) was common to at least two populations and could therefore serve as bridging markers. The different steps taken for map optimization and integration into a reference framework map for QTL mapping are discussed. Conclusions This is the first map of azalea up to our knowledge. AFLP and SSR markers are used as a reference backbone and functional markers (EST and MYB) were added as candidate genes for QTL analysis. The alignment of the 4 maps on the basis of framework markers will facilitate in turn the alignment of QTL regions detected in each of the populations. The approach we took is thoroughly different than the

  20. Mapping agroecological zones and time lag in vegetation growth by means of Fourier analysis of time series of NDVI images

    NASA Technical Reports Server (NTRS)

    Menenti, M.; Azzali, S.; Verhoef, W.; Van Swol, R.

    1993-01-01

    Examples are presented of applications of a fast Fourier transform algorithm to analyze time series of images of Normalized Difference Vegetation Index values. The results obtained for a case study on Zambia indicated that differences in vegetation development among map units of an existing agroclimatic map were not significant, while reliable differences were observed among the map units obtained using the Fourier analysis.

  1. Comparative Performance Analysis of a Hyper-Temporal Ndvi Analysis Approach and a Landscape-Ecological Mapping Approach

    NASA Astrophysics Data System (ADS)

    Ali, A.; de Bie, C. A. J. M.; Scarrott, R. G.; Ha, N. T. T.; Skidmore, A. K.

    2012-07-01

    Both agricultural area expansion and intensification are necessary to cope with the growing demand for food, and the growing threat of food insecurity which is rapidly engulfing poor and under-privileged sections of the global population. Therefore, it is of paramount importance to have the ability to accurately estimate crop area and spatial distribution. Remote sensing has become a valuable tool for estimating and mapping cropland areas, useful in food security monitoring. This work contributes to addressing this broad issue, focusing on the comparative performance analysis of two mapping approaches (i) a hyper-temporal Normalized Difference Vegetation Index (NDVI) analysis approach and (ii) a Landscape-ecological approach. The hyper-temporal NDVI analysis approach utilized SPOT 10-day NDVI imagery from April 1998-December 2008, whilst the Landscape-ecological approach used multitemporal Landsat-7 ETM+ imagery acquired intermittently between 1992 and 2002. Pixels in the time-series NDVI dataset were clustered using an ISODATA clustering algorithm adapted to determine the optimal number of pixel clusters to successfully generalize hyper-temporal datasets. Clusters were then characterized with crop cycle information, and flooding information to produce an NDVI unit map of rice classes with flood regime and NDVI profile information. A Landscape-ecological map was generated using a combination of digitized homogenous map units in the Landsat-7 ETM+ imagery, a Land use map 2005 of the Mekong delta, and supplementary datasets on the regions terrain, geo-morphology and flooding depths. The output maps were validated using reported crop statistics, and regression analyses were used to ascertain the relationship between land use area estimated from maps, and those reported in district crop statistics. The regression analysis showed that the hyper-temporal NDVI analysis approach explained 74% and 76% of the variability in reported crop statistics in two rice crop and three

  2. Alteration mapping at Goldfield, Nevada, by cluster and discriminant analysis of Landsat digital data. [mapping of hydrothermally altered volcanic rocks

    NASA Technical Reports Server (NTRS)

    Ballew, G.

    1977-01-01

    The ability of Landsat multispectral digital data to differentiate among 62 combinations of rock and alteration types at the Goldfield mining district of Western Nevada was investigated by using statistical techniques of cluster and discriminant analysis. Multivariate discriminant analysis was not effective in classifying each of the 62 groups, with classification results essentially the same whether data of four channels alone or combined with six ratios of channels were used. Bivariate plots of group means revealed a cluster of three groups including mill tailings, basalt and all other rock and alteration types. Automatic hierarchical clustering based on the fourth dimensional Mahalanobis distance between group means of 30 groups having five or more samples was performed using Johnson's HICLUS program. The results of the cluster analysis revealed hierarchies of mill tailings vs. natural materials, basalt vs. non-basalt, highly reflectant rocks vs. other rocks and exclusively unaltered rocks vs. predominantly altered rocks. The hierarchies were used to determine the order in which sets of multiple discriminant analyses were to be performed and the resulting discriminant functions were used to produce a map of geology and alteration which has an overall accuracy of 70 percent for discriminating exclusively altered rocks from predominantly altered rocks.

  3. Systematic Analysis of Intracellular-targeting Antimicrobial Peptides, Bactenecin 7, Hybrid of Pleurocidin and Dermaseptin, Proline-Arginine-rich Peptide, and Lactoferricin B, by Using Escherichia coli Proteome Microarrays.

    PubMed

    Ho, Yu-Hsuan; Shah, Pramod; Chen, Yi-Wen; Chen, Chien-Sheng

    2016-06-01

    Antimicrobial peptides (AMPs) act either through membrane lysis or by attacking intracellular targets. Intracellular targeting AMPs are a resource for antimicrobial agent development. Several AMPs have been identified as intracellular targeting peptides; however, the intracellular targets of many of these peptides remain unknown. In the present study, we used an Escherichia coli proteome microarray to systematically identify the protein targets of three intracellular targeting AMPs: bactenecin 7 (Bac7), a hybrid of pleurocidin and dermaseptin (P-Der), and proline-arginine-rich peptide (PR-39). In addition, we also included the data of lactoferricin B (LfcinB) from our previous study for a more comprehensive analysis. We analyzed the unique protein hits of each AMP in the Kyoto Encyclopedia of Genes and Genomes. The results indicated that Bac7 targets purine metabolism and histidine kinase, LfcinB attacks the transcription-related activities and several cellular carbohydrate biosynthetic processes, P-Der affects several catabolic processes of small molecules, and PR-39 preferentially recognizes proteins involved in RNA- and folate-metabolism-related cellular processes. Moreover, both Bac7 and LfcinB target purine metabolism, whereas LfcinB and PR-39 target lipopolysaccharide biosynthesis. This suggested that LfcinB and Bac7 as well as LfcinB and PR-39 have a synergistic effect on antimicrobial activity, which was validated through antimicrobial assays. Furthermore, common hits of all four AMPs indicated that all of them target arginine decarboxylase, which is a crucial enzyme for Escherichia coli survival in extremely acidic environments. Thus, these AMPs may display greater inhibition to bacterial growth in extremely acidic environments. We have also confirmed this finding in bacterial growth inhibition assays. In conclusion, this comprehensive identification and systematic analysis of intracellular targeting AMPs reveals crucial insights into the intracellular

  4. Structure-Function Analysis of Peptide Signaling in the Clostridium perfringens Agr-Like Quorum Sensing System

    PubMed Central

    Ma, Menglin; Li, Jihong

    2015-01-01

    ABSTRACT The accessory growth regulator (Agr)-like quorum sensing (QS) system of Clostridium perfringens controls the production of many toxins, including beta toxin (CPB). We previously showed (J. E. Vidal, M. Ma, J. Saputo, J. Garcia, F. A. Uzal, and B. A. McClane, Mol Microbiol 83:179–194, 2012, http://dx.doi.org/10.1111/j.1365-2958.2011.07925.x) that an 8-amino-acid, AgrD-derived peptide named 8-R upregulates CPB production by this QS system. The current study synthesized a series of small signaling peptides corresponding to sequences within the C. perfringens AgrD polypeptide to investigate the C. perfringens autoinducing peptide (AIP) structure-function relationship. When both linear and cyclic ring forms of these peptides were added to agrB null mutants of type B strain CN1795 or type C strain CN3685, the 5-amino-acid peptides, whether in a linear or ring (thiolactone or lactone) form, induced better signaling (more CPB production) than peptide 8-R for both C. perfringens strains. The 5-mer thiolactone ring peptide induced faster signaling than the 5-mer linear peptide. Strain-related variations in sensing these peptides were detected, with CN3685 sensing the synthetic peptides more strongly than CN1795. Consistent with those synthetic peptide results, Transwell coculture experiments showed that CN3685 exquisitely senses native AIP signals from other isolates (types A, B, C, and D), while CN1795 barely senses even its own AIP. Finally, a C. perfringens AgrD sequence-based peptide with a 6-amino-acid thiolactone ring interfered with CPB production by several C. perfringens strains, suggesting potential therapeutic applications. These results indicate that AIP signaling sensitivity and responsiveness vary among C. perfringens strains and suggest C. perfringens prefers a 5-mer AIP to initiate Agr signaling. IMPORTANCE Clostridium perfringens possesses an Agr-like quorum sensing (QS) system that regulates virulence, sporulation, and toxin production. The

  5. Value flow mapping: Using networks to inform stakeholder analysis

    NASA Astrophysics Data System (ADS)

    Cameron, Bruce G.; Crawley, Edward F.; Loureiro, Geilson; Rebentisch, Eric S.

    2008-02-01

    Stakeholder theory has garnered significant interest from the corporate community, but has proved difficult to apply to large government programs. A detailed value flow exercise was conducted to identify the value delivery mechanisms among stakeholders for the current Vision for Space Exploration. We propose a method for capturing stakeholder needs that explicitly recognizes the outcomes required of the value creating organization. The captured stakeholder needs are then translated into input-output models for each stakeholder, which are then aggregated into a network model. Analysis of this network suggests that benefits are infrequently linked to the root provider of value. Furthermore, it is noted that requirements should not only be written to influence the organization's outputs, but also to influence the propagation of benefit further along the value chain. A number of future applications of this model to systems architecture and requirement analysis are discussed.

  6. A Comparison of Spatial Analysis Methods for the Construction of Topographic Maps of Retinal Cell Density

    PubMed Central

    Garza-Gisholt, Eduardo; Hemmi, Jan M.; Hart, Nathan S.; Collin, Shaun P.

    2014-01-01

    Topographic maps that illustrate variations in the density of different neuronal sub-types across the retina are valuable tools for understanding the adaptive significance of retinal specialisations in different species of vertebrates. To date, such maps have been created from raw count data that have been subjected to only limited analysis (linear interpolation) and, in many cases, have been presented as iso-density contour maps with contour lines that have been smoothed ‘by eye’. With the use of stereological approach to count neuronal distribution, a more rigorous approach to analysing the count data is warranted and potentially provides a more accurate representation of the neuron distribution pattern. Moreover, a formal spatial analysis of retinal topography permits a more robust comparison of topographic maps within and between species. In this paper, we present a new R-script for analysing the topography of retinal neurons and compare methods of interpolating and smoothing count data for the construction of topographic maps. We compare four methods for spatial analysis of cell count data: Akima interpolation, thin plate spline interpolation, thin plate spline smoothing and Gaussian kernel smoothing. The use of interpolation ‘respects’ the observed data and simply calculates the intermediate values required to create iso-density contour maps. Interpolation preserves more of the data but, consequently includes outliers, sampling errors and/or other experimental artefacts. In contrast, smoothing the data reduces the ‘noise’ caused by artefacts and permits a clearer representation of the dominant, ‘real’ distribution. This is particularly useful where cell density gradients are shallow and small variations in local density may dramatically influence the perceived spatial pattern of neuronal topography. The thin plate spline and the Gaussian kernel methods both produce similar retinal topography maps but the smoothing parameters used may affect

  7. Peptide identification

    DOEpatents

    Jarman, Kristin H [Richland, WA; Cannon, William R [Richland, WA; Jarman, Kenneth D [Richland, WA; Heredia-Langner, Alejandro [Richland, WA

    2011-07-12

    Peptides are identified from a list of candidates using collision-induced dissociation tandem mass spectrometry data. A probabilistic model for the occurrence of spectral peaks corresponding to frequently observed partial peptide fragment ions is applied. As part of the identification procedure, a probability score is produced that indicates the likelihood of any given candidate being the correct match. The statistical significance of the score is known without necessarily having reference to the actual identity of the peptide. In one form of the invention, a genetic algorithm is applied to candidate peptides using an objective function that takes into account the number of shifted peaks appearing in the candidate spectrum relative to the test spectrum.

  8. U.S. Virgin Islands Energy Road Map: Analysis

    SciTech Connect

    Lantz, E.; Olis, D.; Warren, A.

    2011-09-01

    This report lays out the strategy envisioned by the stakeholders in the U.S. Virgin Islands, U.S. Department of Energy, and U.S. Department of Interior to achieve the ambitious goal of achieving a 60% reduction in business-as-usual fossil fuel demand by 2025 (60x25) within the electricity sector. This work and supporting analysis provides a framework within which decisions can begin to be made, a concrete vision of what the future might hold, and a guide to determine what questions should follow.

  9. Preliminary Evaluation of MapReduce for High-Performance Climate Data Analysis

    NASA Technical Reports Server (NTRS)

    Duffy, Daniel Q.; Schnase, John L.; Thompson, John H.; Freeman, Shawn M.; Clune, Thomas L.

    2012-01-01

    MapReduce is an approach to high-performance analytics that may be useful to data intensive problems in climate research. It offers an analysis paradigm that uses clusters of computers and combines distributed storage of large data sets with parallel computation. We are particularly interested in the potential of MapReduce to speed up basic operations common to a wide range of analyses. In order to evaluate this potential, we are prototyping a series of canonical MapReduce operations over a test suite of observational and climate simulation datasets. Our initial focus has been on averaging operations over arbitrary spatial and temporal extents within Modern Era Retrospective- Analysis for Research and Applications (MERRA) data. Preliminary results suggest this approach can improve efficiencies within data intensive analytic workflows.

  10. Mapping soils, crops, and rangelands by machine analysis of multitemporal ERTS-1 data. [Kansas and Texas

    NASA Technical Reports Server (NTRS)

    Baumgardner, M. F.; Henderson, J. A., Jr.

    1974-01-01

    ERTS-1 data, obtained during the period 25 August 1972 to 5 September 1973 over a range of test sites in the Central United States, have been used for identifying and mapping differences in soil patterns, species and conditions of cultivated crops, and conditions of rangelands. Multispectral scanner data from multiple ERTS passes over certain test sites have provided the opportunity to study temporal changes in the scene. Multispectral classifications delineating soils boundaries in different test sites compared well with existing soil association maps prepared by conventional means. Spectral analysis of ERTS data was used to identify, maps, and make areal measurements of wheat in western Kansas. Multispectral analysis of ERTS-1 data provided patterns in rangelands which can be related to soils differences, range management practices, and the extent of infestation of grasslands by mesquite (prosopis fuliflora) and juniper (juniperus spp.).

  11. Construction of Genetic Linkage Maps and Comparative Genome Analysis of Catfish Using Gene-Associated Markers

    PubMed Central

    Kucuktas, Huseyin; Wang, Shaolin; Li, Ping; He, Chongbo; Xu, Peng; Sha, Zhenxia; Liu, Hong; Jiang, Yanliang; Baoprasertkul, Puttharat; Somridhivej, Benjaporn; Wang, Yaping; Abernathy, Jason; Guo, Ximing; Liu, Lei; Muir, William; Liu, Zhanjiang

    2009-01-01

    A genetic linkage map of the channel catfish genome (N = 29) was constructed using EST-based microsatellite and single nucleotide polymorphism (SNP) markers in an interspecific reference family. A total of 413 microsatellites and 125 SNP markers were polymorphic in the reference family. Linkage analysis using JoinMap 4.0 allowed mapping of 331 markers (259 microsatellites and 72 SNPs) to 29 linkage groups. Each linkage group contained 3–18 markers. The largest linkage group contained 18 markers and spanned 131.2 cM, while the smallest linkage group contained 14 markers and spanned only 7.9 cM. The linkage map covered a genetic distance of 1811 cM with an average marker interval of 6.0 cM. Sex-specific maps were also constructed; the recombination rate for females was 1.6 times higher than that for males. Putative conserved syntenies between catfish and zebrafish, medaka, and Tetraodon were established, but the overall levels of genome rearrangements were high among the teleost genomes. This study represents a first-generation linkage map constructed by using EST-derived microsatellites and SNPs, laying a framework for large-scale comparative genome analysis in catfish. The conserved syntenies identified here between the catfish and the three model fish species should facilitate structural genome analysis and evolutionary studies, but more importantly should facilitate functional inference of catfish genes. Given that determination of gene functions is difficult in nonmodel species such as catfish, functional genome analysis will have to rely heavily on the establishment of orthologies from model species. PMID:19171943

  12. Calibration and systematic error analysis for the COBE(1) DMR 4year sky maps

    SciTech Connect

    Kogut, A.; Banday, A.J.; Bennett, C.L.; Gorski, K.M.; Hinshaw,G.; Jackson, P.D.; Keegstra, P.; Lineweaver, C.; Smoot, G.F.; Tenorio,L.; Wright, E.L.

    1996-01-04

    The Differential Microwave Radiometers (DMR) instrument aboard the Cosmic Background Explorer (COBE) has mapped the full microwave sky to mean sensitivity 26 mu K per 7 degrees held of view. The absolute calibration is determined to 0.7 percent with drifts smaller than 0.2 percent per year. We have analyzed both the raw differential data and the pixelized sky maps for evidence of contaminating sources such as solar system foregrounds, instrumental susceptibilities, and artifacts from data recovery and processing. Most systematic effects couple only weakly to the sky maps. The largest uncertainties in the maps result from the instrument susceptibility to Earth's magnetic field, microwave emission from Earth, and upper limits to potential effects at the spacecraft spin period. Systematic effects in the maps are small compared to either the noise or the celestial signal: the 95 percent confidence upper limit for the pixel-pixel rms from all identified systematics is less than 6 mu K in the worst channel. A power spectrum analysis of the (A-B)/2 difference maps shows no evidence for additional undetected systematic effects.

  13. Mapping Sleeping Bees within Their Nest: Spatial and Temporal Analysis of Worker Honey Bee Sleep

    PubMed Central

    Klein, Barrett Anthony; Stiegler, Martin; Klein, Arno; Tautz, Jürgen

    2014-01-01

    Patterns of behavior within societies have long been visualized and interpreted using maps. Mapping the occurrence of sleep across individuals within a society could offer clues as to functional aspects of sleep. In spite of this, a detailed spatial analysis of sleep has never been conducted on an invertebrate society. We introduce the concept of mapping sleep across an insect society, and provide an empirical example, mapping sleep patterns within colonies of European honey bees (Apis mellifera L.). Honey bees face variables such as temperature and position of resources within their colony's nest that may impact their sleep. We mapped sleep behavior and temperature of worker bees and produced maps of their nest's comb contents as the colony grew and contents changed. By following marked bees, we discovered that individuals slept in many locations, but bees of different worker castes slept in different areas of the nest relative to position of the brood and surrounding temperature. Older worker bees generally slept outside cells, closer to the perimeter of the nest, in colder regions, and away from uncapped brood. Younger worker bees generally slept inside cells and closer to the center of the nest, and spent more time asleep than awake when surrounded by uncapped brood. The average surface temperature of sleeping foragers was lower than the surface temperature of their surroundings, offering a possible indicator of sleep for this caste. We propose mechanisms that could generate caste-dependent sleep patterns and discuss functional significance of these patterns. PMID:25029445

  14. Mapping sleeping bees within their nest: spatial and temporal analysis of worker honey bee sleep.

    PubMed

    Klein, Barrett Anthony; Stiegler, Martin; Klein, Arno; Tautz, Jürgen

    2014-01-01

    Patterns of behavior within societies have long been visualized and interpreted using maps. Mapping the occurrence of sleep across individuals within a society could offer clues as to functional aspects of sleep. In spite of this, a detailed spatial analysis of sleep has never been conducted on an invertebrate society. We introduce the concept of mapping sleep across an insect society, and provide an empirical example, mapping sleep patterns within colonies of European honey bees (Apis mellifera L.). Honey bees face variables such as temperature and position of resources within their colony's nest that may impact their sleep. We mapped sleep behavior and temperature of worker bees and produced maps of their nest's comb contents as the colony grew and contents changed. By following marked bees, we discovered that individuals slept in many locations, but bees of different worker castes slept in different areas of the nest relative to position of the brood and surrounding temperature. Older worker bees generally slept outside cells, closer to the perimeter of the nest, in colder regions, and away from uncapped brood. Younger worker bees generally slept inside cells and closer to the center of the nest, and spent more time asleep than awake when surrounded by uncapped brood. The average surface temperature of sleeping foragers was lower than the surface temperature of their surroundings, offering a possible indicator of sleep for this caste. We propose mechanisms that could generate caste-dependent sleep patterns and discuss functional significance of these patterns. PMID:25029445

  15. Structure analysis of peptide deformylases from Streptococcus pneumoniae, Staphylococcus aureus, Thermotoga maritima and Pseudomonas aeruginosa: snapshots of the oxygen sensitivity of peptide deformylase.

    PubMed

    Kreusch, Andreas; Spraggon, Glen; Lee, Chris C; Klock, Heath; McMullan, Daniel; Ng, Ken; Shin, Tanya; Vincent, Juli; Warner, Ian; Ericson, Christer; Lesley, Scott A

    2003-07-01

    Peptide deformylase (PDF) has received considerable attention during the last few years as a potential target for a new type of antibiotics. It is an essential enzyme in eubacteria for the removal of the formyl group from the N terminus of the nascent polypeptide chain. We have solved the X-ray structures of four members of this enzyme family, two from the Gram-positive pathogens Streptococcus pneumoniae and Staphylococcus aureus, and two from the Gram-negative bacteria Thermotoga maritima and Pseudomonas aeruginosa. Combined with the known structures from the Escherichia coli enzyme and the recently solved structure of the eukaryotic deformylase from Plasmodium falciparum, a complete picture of the peptide deformylase structure and function relationship is emerging. This understanding could help guide a more rational design of inhibitors. A structure-based comparison between PDFs reveals some conserved differences between type I and type II enzymes. Moreover, our structures provide insights into the known instability of PDF caused by oxidation of the metal-ligating cysteine residue. PMID:12823970

  16. Develop advanced nonlinear signal analysis topographical mapping system

    NASA Technical Reports Server (NTRS)

    Jong, Jen-Yi

    1993-01-01

    As reported in the monthly technical progress report for July 1993, a new signal analysis technique called instantaneous frequency correlation (IFC) for time delay estimation was developed which will be incorporated into the ATMS system. In this report, a different technique for time delay estimation called phase difference time derivative estimator (FDTDE) will be discussed. The FDTDE technique does not replace the IFC method since their application conditions are different. The IFC technique can estimate the time delay between two spectral components of two measurement signals when the center frequency of the components is constant, while the FDTDE method can provide accurate time delay estimation when the frequency of the subject component changes linearly such as during engine startup or shut-down.

  17. Mapping anhedonia onto reinforcement learning: a behavioural meta-analysis

    PubMed Central

    2013-01-01

    Background Depression is characterised partly by blunted reactions to reward. However, tasks probing this deficiency have not distinguished insensitivity to reward from insensitivity to the prediction errors for reward that determine learning and are putatively reported by the phasic activity of dopamine neurons. We attempted to disentangle these factors with respect to anhedonia in the context of stress, Major Depressive Disorder (MDD), Bipolar Disorder (BPD) and a dopaminergic challenge. Methods Six behavioural datasets involving 392 experimental sessions were subjected to a model-based, Bayesian meta-analysis. Participants across all six studies performed a probabilistic reward task that used an asymmetric reinforcement schedule to assess reward learning. Healthy controls were tested under baseline conditions, stress or after receiving the dopamine D2 agonist pramipexole. In addition, participants with current or past MDD or BPD were evaluated. Reinforcement learning models isolated the contributions of variation in reward sensitivity and learning rate. Results MDD and anhedonia reduced reward sensitivity more than they affected the learning rate, while a low dose of the dopamine D2 agonist pramipexole showed the opposite pattern. Stress led to a pattern consistent with a mixed effect on reward sensitivity and learning rate. Conclusion Reward-related learning reflected at least two partially separable contributions. The first related to phasic prediction error signalling, and was preferentially modulated by a low dose of the dopamine agonist pramipexole. The second related directly to reward sensitivity, and was preferentially reduced in MDD and anhedonia. Stress altered both components. Collectively, these findings highlight the contribution of model-based reinforcement learning meta-analysis for dissecting anhedonic behavior. PMID:23782813

  18. Mapping temporal changes in connectivity using high-resolution aerial data and object based image analysis

    NASA Astrophysics Data System (ADS)

    Masselink, Rens; Anders, Niels; Keesstra, Saskia; Seeger, Manuel

    2014-05-01

    Within the field of geomorphology mapping has always been an important tool to interpret spatial and temporal distributions of phenomena and processes at the surface. In the field of connectivity however, although throughout the past decade many articles have been published, there are only very few that go into the mapping of connectivity. This study aimed at developing a new, automated method for mapping connectivity within agricultural catchments. The method, which is a combination of Object-Based Image Analysis (OBIA) and traditional geomorphological field mapping, was applied to two agricultural catchments in Navarre, Spain, both with an area of approximately 2 sq.km. An unmanned aerial vehicle (UAV) was used to take aerial photographs with a resolution of 6 cm, of which a DEM with a 12 cm resolution was created using structure-from-motion photogrammetry. Connectivity was mapped within the study areas using OBIA using a top down method, meaning that connectivity was mapped at different scale levels, starting at the largest scale. Firstly sub-catchments were automatically delineated, after which several characteristics and features that affect connectivity within the sub-catchments were classified, e.g. landuse, landslides, rills, gullies, riparian vegetation, changes in slope, ploughing direction etc. In two consecutive years (2013-2014) photographs were taken and connectivity of both catchments of both years will be compared. Future work will include a quantification of the mapped connectivity (highly connected years vs. low connected years), causes and consequences of these differences in connectivity, comparison to existing connectivity indices and comparison of mapped connectivity in sub-catchments and measured discharge.

  19. Error modeling based on geostatistics for uncertainty analysis in crop mapping using Gaofen-1 multispectral imagery

    NASA Astrophysics Data System (ADS)

    You, Jiong; Pei, Zhiyuan

    2015-01-01

    With the development of remote sensing technology, its applications in agriculture monitoring systems, crop mapping accuracy, and spatial distribution are more and more being explored by administrators and users. Uncertainty in crop mapping is profoundly affected by the spatial pattern of spectral reflectance values obtained from the applied remote sensing data. Errors in remotely sensed crop cover information and the propagation in derivative products need to be quantified and handled correctly. Therefore, this study discusses the methods of error modeling for uncertainty characterization in crop mapping using GF-1 multispectral imagery. An error modeling framework based on geostatistics is proposed, which introduced the sequential Gaussian simulation algorithm to explore the relationship between classification errors and the spectral signature from remote sensing data source. On this basis, a misclassification probability model to produce a spatially explicit classification error probability surface for the map of a crop is developed, which realizes the uncertainty characterization for crop mapping. In this process, trend surface analysis was carried out to generate a spatially varying mean response and the corresponding residual response with spatial variation for the spectral bands of GF-1 multispectral imagery. Variogram models were employed to measure the spatial dependence in the spectral bands and the derived misclassification probability surfaces. Simulated spectral data and classification results were quantitatively analyzed. Through experiments using data sets from a region in the low rolling country located at the Yangtze River valley, it was found that GF-1 multispectral imagery can be used for crop mapping with a good overall performance, the proposal error modeling framework can be used to quantify the uncertainty in crop mapping, and the misclassification probability model can summarize the spatial variation in map accuracy and is helpful for

  20. The diagnostic accuracy of the natriuretic peptides in heart failure: systematic review and diagnostic meta-analysis in the acute care setting

    PubMed Central

    Roberts, Emmert; Dworzynski, Katharina; Al-Mohammad, Abdallah; Cowie, Martin R; McMurray, John J V; Mant, Jonathan

    2015-01-01

    Objectives To determine and compare the diagnostic accuracy of serum natriuretic peptide levels (B type natriuretic peptide, N terminal probrain natriuretic peptide (NTproBNP), and mid-regional proatrial natriuretic peptide (MRproANP)) in people presenting with acute heart failure to acute care settings using thresholds recommended in the 2012 European Society of Cardiology guidelines for heart failure. Design Systematic review and diagnostic meta-analysis. Data sources Medline, Embase, Cochrane central register of controlled trials, Cochrane database of systematic reviews, database of abstracts of reviews of effects, NHS economic evaluation database, and Health Technology Assessment up to 28 January 2014, using combinations of subject headings and terms relating to heart failure and natriuretic peptides. Eligibility criteria for selecting studies Eligible studies evaluated one or more natriuretic peptides (B type natriuretic peptide, NTproBNP, or MRproANP) in the diagnosis of acute heart failure against an acceptable reference standard in consecutive or randomly selected adults in an acute care setting. Studies were excluded if they did not present sufficient data to extract or calculate true positives, false positives, false negatives, and true negatives, or report age independent natriuretic peptide thresholds. Studies not available in English were also excluded. Results 37 unique study cohorts described in 42 study reports were included, with a total of 48 test evaluations reporting 15 263 test results. At the lower recommended thresholds of 100 ng/L for B type natriuretic peptide and 300 ng/L for NTproBNP, the natriuretic peptides have sensitivities of 0.95 (95% confidence interval 0.93 to 0.96) and 0.99 (0.97 to 1.00) and negative predictive values of 0.94 (0.90 to 0.96) and 0.98 (0.89 to 1.0), respectively, for a diagnosis of acute heart failure. At the lower recommended threshold of 120 pmol/L, MRproANP has a sensitivity ranging from 0.95 (range 0

  1. Peptidomics of Circular Cysteine-Rich Plant Peptides: Analysis of the Diversity of Cyclotides from Viola tricolor by Transcriptome and Proteome Mining

    PubMed Central

    2015-01-01

    Cyclotides are plant-derived mini proteins. They are genetically encoded as precursor proteins that become post-translationally modified to yield circular cystine-knotted molecules. Because of this structural topology cyclotides resist enzymatic degradation in biological fluids, and hence they are considered as promising lead molecules for pharmaceutical applications. Despite ongoing efforts to discover novel cyclotides and analyze their biodiversity, it is not clear how many individual peptides a single plant specimen can express. Therefore, we investigated the transcriptome and cyclotide peptidome of Viola tricolor. Transcriptome mining enabled the characterization of cyclotide precursor architecture and processing sites important for biosynthesis of mature peptides. The cyclotide peptidome was explored by mass spectrometry and bottom-up proteomics using the extracted peptide sequences as queries for database searching. In total 164 cyclotides were discovered by nucleic acid and peptide analysis in V. tricolor. Therefore, violaceous plants at a global scale may be the source to as many as 150 000 individual cyclotides. Encompassing the diversity of V. tricolor as a combinatorial library of bioactive peptides, this commercially available medicinal herb may be a suitable starting point for future bioactivity-guided screening studies. PMID:26399495

  2. Structural and computational analysis of peptide recognition mechanism of class-C type penicillin binding protein, alkaline D-peptidase from Bacillus cereus DF4-B.

    PubMed

    Nakano, Shogo; Okazaki, Seiji; Ishitsubo, Erika; Kawahara, Nobuhiro; Komeda, Hidenobu; Tokiwa, Hiroaki; Asano, Yasuhisa

    2015-01-01

    Alkaline D-peptidase from Bacillus cereus DF4-B, called ADP, is a D-stereospecific endopeptidase reacting with oligopeptides containing D-phenylalanine (D-Phe) at N-terminal penultimate residue. ADP has attracted increasing attention because it is useful as a catalyst for synthesis of D-Phe oligopeptides or, with the help of substrate mimetics, L-amino acid peptides and proteins. Structure and functional analysis of ADP is expected to elucidate molecular mechanism of ADP. In this study, the crystal structure of ADP (apo) form was determined at 2.1 Å resolution. The fold of ADP is similar to that of the class C penicillin-binding proteins of type-AmpH. Docking simulations and fragment molecular orbital analyses of two peptides, (D-Phe)4 and (D-Phe)2-(L-Phe)2, with the putative substrate binding sites of ADP indicated that the P1 residue of the peptide interacts with hydrophobic residues at the S1 site of ADP. Furthermore, molecular dynamics simulation of ADP for 50 nsec suggested that the ADP forms large cavity at the active site. Formation of the cavity suggested that the ADP has open state in the solution. For the ADP, having the open state is convenient to bind the peptides having bulky side chain, such as (D-Phe)4. Taken together, we predicted peptide recognition mechanism of ADP. PMID:26370172

  3. Mapping an Annual Weed with Color-infrared Photography and Image Analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Silverleaf sunflower (Helianthus argophyllus Torr. and Gray) is an annual weed found on rangelands in south and southeast Texas. Color-infrared aerial photography and computer image analysis techniques were evaluated for detecting and mapping silverleaf sunflower infestations on a south Texas range...

  4. Sporting Bodies, Ageing, Narrative Mapping and Young Team Athletes: An Analysis of Possible Selves

    ERIC Educational Resources Information Center

    Phoenix, Cassandra; Sparkes, Andrew C.

    2007-01-01

    Drawing on life history data generated from interviews with young athletes at an English university, this paper explores the narrative maps provided to them by older team members and the ways in which these influence perceptions of self-ageing. Three possible selves associated with mid-life emerged from the analysis for detailed focus. These are…

  5. Genetic analysis of genome-wide transcriptional regulation through eQTL mapping in soybean

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Gene expression Quantitative Trait Loci (eQTL) mapping is a powerful tool for identifying the genetic basis of gene expression variation. Coincident genetic locations of eQTL and phenotypic QTL provide the basis for further investigation of the molecular mechanisms involved. Genetic analysis of expr...

  6. Mapping Broom Snakeweed Through Image Analysis of Color-infrared Photography and Digital Imagery

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A study was conducted on a south Texas rangeland area to evaluate aerial color-infrared (CIR) photography and CIR digital imagery combined with unsupervised image analysis techniques to map broom snakeweed [Gutierrezia sarothrae (Pursh.) Britt. and Rusby]. Accuracy assessments performed on compute...

  7. Genetic Analysis of Genome-Wide Transcriptional Regulation through eQTL Mapping in Soy

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Variation in gene transcript accumulation levels can be measured to map underlying expression Quantitative Trait Loci (eQTL). Coincident genetic locations of eQTL and phenotypic QTL provide the basis for further investigation of the molecular mechanisms involved. Genetic analysis of expression trait...

  8. Functional cluster analysis of CT perfusion maps: a new tool for diagnosis of acute stroke?

    PubMed

    Baumgartner, Christian; Gautsch, Kurt; Böhm, Christian; Felber, Stephan

    2005-09-01

    CT perfusion imaging constitutes an important contribution to the early diagnosis of acute stroke. Cerebral blood flow (CBF), cerebral blood volume (CBV) and time-to-peak (TTP) maps are used to estimate the severity of cerebral damage after acute ischemia. We introduce functional cluster analysis as a new tool to evaluate CT perfusion in order to identify normal brain, ischemic tissue and large vessels. CBF, CBV and TTP maps represent the basis for cluster analysis applying a partitioning (k-means) and density-based (density-based spatial clustering of applications with noise, DBSCAN) paradigm. In patients with transient ischemic attack and stroke, cluster analysis identified brain areas with distinct hemodynamic properties (gray and white matter) and segmented territorial ischemia. CBF, CBV and TTP values of each detected cluster were displayed. Our preliminary results indicate that functional cluster analysis of CT perfusion maps may become a helpful tool for the interpretation of perfusion maps and provide a rapid means for the segmentation of ischemic tissue. PMID:15827821

  9. Peptides derived from CXCL8 based on in silico analysis inhibit CXCL8 interactions with its receptor CXCR1

    NASA Astrophysics Data System (ADS)

    Jiang, Shinn-Jong; Liou, Je-Wen; Chang, Chun-Chun; Chung, Yi; Lin, Lee-Fong; Hsu, Hao-Jen

    2015-12-01

    Chemokine CXCL8 is crucial for regulation of inflammatory and immune responses via activating its cognate receptor CXCR1. In this study, molecular docking and binding free energy calculations were combined to predict the initial binding event of CXCL8 to CXCR1 for peptide drug design. The simulations reveal that in the initial binding, the N-loop of CXCL8 interacts with the N-terminus of CXCR1, which is dominated by electrostatic interactions. The derived peptides from the binding region of CXCL8 are synthesized for further confirmation. Surface plasmon resonance analyses indicate that the CXCL8 derived peptide with 14 residues is able to bind to the receptor CXCR1 derived peptide with equilibrium KD of 252 μM while the peptide encompassing a CXCL8 K15A mutation hardly binds to CXCR1 derived peptide (KD = 1553 μM). The cell experiments show that the designed peptide inhibits CXCL8-induced and LPS-activated monocytes adhesion and transmigration. However, when the peptides were mutated on two lysine residues (K15 and K20), the inhibition effects were greatly reduced indicating these two amino acids are key residues for the initial binding of CXCL8 to CXCR1. This study demonstrates that in silico prediction based functional peptide design can be effective for developing anti-inflammation drugs.

  10. Peptides derived from CXCL8 based on in silico analysis inhibit CXCL8 interactions with its receptor CXCR1.

    PubMed

    Jiang, Shinn-Jong; Liou, Je-Wen; Chang, Chun-Chun; Chung, Yi; Lin, Lee-Fong; Hsu, Hao-Jen

    2015-01-01

    Chemokine CXCL8 is crucial for regulation of inflammatory and immune responses via activating its cognate receptor CXCR1. In this study, molecular docking and binding free energy calculations were combined to predict the initial binding event of CXCL8 to CXCR1 for peptide drug design. The simulations reveal that in the initial binding, the N-loop of CXCL8 interacts with the N-terminus of CXCR1, which is dominated by electrostatic interactions. The derived peptides from the binding region of CXCL8 are synthesized for further confirmation. Surface plasmon resonance analyses indicate that the CXCL8 derived peptide with 14 residues is able to bind to the receptor CXCR1 derived peptide with equilibrium KD of 252 μM while the peptide encompassing a CXCL8 K15A mutation hardly binds to CXCR1 derived peptide (KD = 1553 μM). The cell experiments show that the designed peptide inhibits CXCL8-induced and LPS-activated monocytes adhesion and transmigration. However, when the peptides were mutated on two lysine residues (K15 and K20), the inhibition effects were greatly reduced indicating these two amino acids are key residues for the initial binding of CXCL8 to CXCR1. This study demonstrates that in silico prediction based functional peptide design can be effective for developing anti-inflammation drugs. PMID:26689258

  11. Peptides derived from CXCL8 based on in silico analysis inhibit CXCL8 interactions with its receptor CXCR1

    PubMed Central

    Jiang, Shinn-Jong; Liou, Je-Wen; Chang, Chun-Chun; Chung, Yi; Lin, Lee-Fong; Hsu, Hao-Jen

    2015-01-01

    Chemokine CXCL8 is crucial for regulation of inflammatory and immune responses via activating its cognate receptor CXCR1. In this study, molecular docking and binding free energy calculations were combined to predict the initial binding event of CXCL8 to CXCR1 for peptide drug design. The simulations reveal that in the initial binding, the N-loop of CXCL8 interacts with the N-terminus of CXCR1, which is dominated by electrostatic interactions. The derived peptides from the binding region of CXCL8 are synthesized for further confirmation. Surface plasmon resonance analyses indicate that the CXCL8 derived peptide with 14 residues is able to bind to the receptor CXCR1 derived peptide with equilibrium KD of 252 μM while the peptide encompassing a CXCL8 K15A mutation hardly binds to CXCR1 derived peptide (KD = 1553 μM). The cell experiments show that the designed peptide inhibits CXCL8-induced and LPS-activated monocytes adhesion and transmigration. However, when the peptides were mutated on two lysine residues (K15 and K20), the inhibition effects were greatly reduced indicating these two amino acids are key residues for the initial binding of CXCL8 to CXCR1. This study demonstrates that in silico prediction based functional peptide design can be effective for developing anti-inflammation drugs. PMID:26689258

  12. Genetic Analysis of the Atrial Natriuretic Peptide Gene Polymorphisms among Essential Hypertensive Patients in Malaysia

    PubMed Central

    Ghodsian, Nooshin; Ismail, Patimah; Ahmadloo, Salma; Eskandarian, Narges; Etemad, Ali

    2016-01-01

    Background. Atrial natriuretic peptide (ANP) considerably influences blood pressure regulation through water and sodium homoeostasis. Several of the studies have utilized anonymous genetic polymorphic markers and made inconsequent claims about the ANP relevant disorders. Thus, we screened Insertion/Deletion (ID) and G191A polymorphisms of ANP to discover sequence variations with potential functional significance and to specify the linkage disequilibrium pattern between polymorphisms. The relationships of detected polymorphisms with EH with or without Type 2 Diabetes Mellitus (T2DM) status were tested subsequently. Method. ANP gene polymorphisms (I/D and A191G) were specified utilizing mutagenically separated Polymerase Chain Reaction (PCR) in 320 subjects including 163 EH case subjects and 157 controls. Result. This case-control study discovered a significant association between I/D polymorphisms of ANP gene in EH patient without T2DM. However, the study determined no association between G191A polymorphisms of ANP in EH with or without T2DM. In addition, sociodemographic factors in the case and healthy subjects exhibited strong differences (P < 0.05). Conclusion. As a risk factor, ANP gene polymorphisms may affect hypertension. Despite the small sample size in this study, it is the first research assessing the ANP gene polymorphisms in both EH and T2DM patients among Malaysian population. PMID:27413750

  13. Proteome Analysis of Renoprotection Mediated by a Novel Cyclic Helix B Peptide in Acute Kidney Injury.

    PubMed

    Yang, Cheng; Liu, Junjun; Li, Long; Hu, Meiyu; Long, Yaqiu; Liu, Xiaohui; Zhu, Tongyu; Huang, Xiao; Zhao, Shouliang; Liu, Shangfeng; Rong, Ruiming

    2015-01-01

    We developed a novel, erythropoietin-derived, non-erythropoiesis, cyclic helix B peptide (CHBP) that displays potent renoprotection against acute kidney injury (AKI). To determine the mechanism of CHBP-mediated protection, we investigated the proteomic profile of mice treated with CHBP in a kidney ischemia-reperfusion (IR) injury model. The isobaric tags for relative and absolute quantitation (iTRAQ)-labeled samples were analyzed using a QSTAR XL LC/MS system. In total, 38 differentially expressed proteins (DEPs) were shared by all experimental groups, while 3 DEPs were detected specifically in the IR + CHBP group. Eight significant pathways were identified, and oxidative phosphorylation was shown to be the most important pathway in CHBP-mediated renoprotection. The significant DEPs in the oxidative phosphorylation pathway elicited by CHBP are NADH-ubiquinone oxidoreductase Fe-S protein 6 (NDUFS6), alpha-aminoadipic semialdehyde synthase (AASS) and ATP-binding cassette sub-family D member 3 (ABCD3). The DEPs mentioned above were verified by RT-qPCR and immunostaining in mouse kidneys. We tested 6 DEPs in human biopsy samples from kidney transplant recipients. The trend of differential expression was consistent with that in the murine model. In conclusion, this study helps to elucidate the pharmacological mechanisms of CHBP before clinical translation. PMID:26655840

  14. Quantitative analysis of co-oligomer formation by amyloid-beta peptide isoforms

    NASA Astrophysics Data System (ADS)

    Iljina, Marija; Garcia, Gonzalo A.; Dear, Alexander J.; Flint, Jennie; Narayan, Priyanka; Michaels, Thomas C. T.; Dobson, Christopher M.; Frenkel, Daan; Knowles, Tuomas P. J.; Klenerman, David

    2016-06-01

    Multiple isoforms of aggregation-prone proteins are present under physiological conditions and have the propensity to assemble into co-oligomers with different properties from self-oligomers, but this process has not been quantitatively studied to date. We have investigated the amyloid-β (Aβ) peptide, associated with Alzheimer’s disease, and the aggregation of its two major isoforms, Aβ40 and Aβ42, using a statistical mechanical modelling approach in combination with in vitro single-molecule fluorescence measurements. We find that at low concentrations of Aβ, corresponding to its physiological abundance, there is little free energy penalty in forming co-oligomers, suggesting that the formation of both self-oligomers and co-oligomers is possible under these conditions. Our model is used to predict the oligomer concentration and size at physiological concentrations of Aβ and suggests the mechanisms by which the ratio of Aβ42 to Aβ40 can affect cell toxicity. An increased ratio of Aβ42 to Aβ40 raises the fraction of oligomers containing Aβ42, which can increase the hydrophobicity of the oligomers and thus promote deleterious binding to the cell membrane and increase neuronal damage. Our results suggest that co-oligomers are a common form of aggregate when Aβ isoforms are present in solution and may potentially play a significant role in Alzheimer’s disease.

  15. Proteome Analysis of Renoprotection Mediated by a Novel Cyclic Helix B Peptide in Acute Kidney Injury

    PubMed Central

    Yang, Cheng; Liu, Junjun; Li, Long; Hu, Meiyu; Long, Yaqiu; Liu, Xiaohui; Zhu, Tongyu; Huang, Xiao; Zhao, Shouliang; Liu, Shangfeng; Rong, Ruiming

    2015-01-01

    We developed a novel, erythropoietin-derived, non-erythropoiesis, cyclic helix B peptide (CHBP) that displays potent renoprotection against acute kidney injury (AKI). To determine the mechanism of CHBP-mediated protection, we investigated the proteomic profile of mice treated with CHBP in a kidney ischemia-reperfusion (IR) injury model. The isobaric tags for relative and absolute quantitation (iTRAQ)-labeled samples were analyzed using a QSTAR XL LC/MS system. In total, 38 differentially expressed proteins (DEPs) were shared by all experimental groups, while 3 DEPs were detected specifically in the IR + CHBP group. Eight significant pathways were identified, and oxidative phosphorylation was shown to be