WorldWideScience

Sample records for arthrobacter chlorophenolicus proteome

  1. Impact of phenolic substrate and growth temperature on the arthrobacter chlorophenolicus proteome

    Energy Technology Data Exchange (ETDEWEB)

    Unell, Maria; Abraham, Paul E.; Shah, Manesh; Zhang, Bing; Ruckert, Christian; VerBerkmoes, Nathan C.; Jansson, Janet K.

    2009-02-15

    We compared the Arthrobacter chlorophenolicus proteome during growth on 4-chlorophenol, 4-nitrophenol or phenol at 5 C and 28 C; both for the wild type and a mutant strain with mass spectrometry based proteomics. A label free workflow employing spectral counting identified 3749 proteins across all growth conditions, representing over 70% of the predicted genome and 739 of these proteins form the core proteome. Statistically significant differences were found in the proteomes of cells grown under different conditions including differentiation of hundreds of unknown proteins. The 4-chlorophenol-degradation pathway was confirmed, but not that for phenol.

  2. Impact of Phenolic Substrate and Growth Temperature on the Arthrobacter chlorophenolicus Proteome

    Energy Technology Data Exchange (ETDEWEB)

    Unell, Maria [Swedish University of Agricultural Sciences, Upsalla, Sweden; Abraham, Paul E [ORNL; Shah, Manesh B [ORNL; Zhang, B [Vanderbilt University; Ruckert, Christian [Bielefeld University, Center for Biotechnology, Bielefeld, Germany; Verberkmoes, Nathan C [ORNL; Jansson, J [Swedish University of Agricultural Sciences, Upsalla, Sweden

    2009-01-01

    We compared the Arthrobacter chlorophenolicus proteome during growth on 4-chlorophenol, 4-nitrophenol, or phenol at 5 and 28 C, both for the wild-type and a mutant strain with mass spectrometry based proteomics. A label-free workflow employing spectral counting identified 3749 proteins across all growth conditions, representing over 70% of the predicted genome and 739 of these proteins form the core proteome. Statistically significant differences were found in the proteomes of cells grown under different conditions including differentiation of hundreds of unknown proteins. The 4-chlorophenol- degradation pathway was confirmed, but not that for phenol.

  3. Draft Genome Sequence of Arthrobacter chlorophenolicus Strain Mor30.16, Isolated from the Bean Rhizosphere

    OpenAIRE

    Miranda-Ríos, José Antonio; Ramírez-Trujillo, José Augusto; Nova-Franco, Bárbara; Lozano-Aguirre Beltrán, Luis Fernando; Iturriaga, Gabriel; Suárez-Rodríguez, Ramón

    2015-01-01

    Bacteria of the genus Arthrobacter are commonly found in the soil and plant rhizosphere. In this study we report the draft genome of Arthrobacter chlorophenolicus strain Mor30.16 that was isolated from rhizosphere of beans grown in Cuernavaca Morelos, Mexico. This strain promotes growth and ameliorates drought stress in bean plants.

  4. Evaluation of 4-bromophenol biodegradation in mixed pollutants system by Arthrobacter chlorophenolicus A6 in an upflow packed bed reactor.

    Science.gov (United States)

    Sahoo, Naresh Kumar; Pakshirajan, Kannan; Ghosh, Pranab Kumar

    2014-09-01

    Bromophenol is listed as priority pollutant by U.S. EPA, however, there is no report so far on its removal in mixed pollutants system by any biological reactor operated in continuous mode. Furthermore, bromophenol along with chlorophenol and nitrophenol are usually the major constituents of paper pulp and pesticide industrial effluent. The present study investigated simultaneous biodegradation of these three pollutants with specially emphasis on substrate competition and crossed inhibition by Arthrobacter chlorophenolicus A6 in an upflow packed bed reactor (UPBR). A 2(3) full factorial design was employed with these pollutants at two different levels by varying their influent concentration in the range of 250-450 mg l(-1). Almost complete removal of all these pollutants and 97 % effluent toxicity removal were achieved in the UPBR at a pollutant loading rate of 1707 mg l(-1) day(-1) or lesser. However, at higher loading rates, the reactor performance deteriorated due to transient accumulation of toxic intermediates. Statistical analysis of the results revealed a strong negative interaction of 4-CP on 4-NP biodegradation. On the other hand, interaction effect between 4-CP and 4-BP was found to be insignificant. Among these three pollutants 4-NP preferentially degraded, however, 4-CP exerted more inhibitory effect on 4-NP biodegradation. This study demonstrated the potential of A. chlorophenolicus A6 for biodegradation of 4-BP in mixed pollutants system by a flow through UPBR system. PMID:24934870

  5. A method for the production of D-tagatose using a recombinant Pichia pastoris strain secreting β-D-galactosidase from Arthrobacter chlorophenolicus and a recombinant L-arabinose isomerase from Arthrobacter sp. 22c

    Directory of Open Access Journals (Sweden)

    Wanarska Marta

    2012-08-01

    Full Text Available Abstract Background D-Tagatose is a natural monosaccharide which can be used as a low-calorie sugar substitute in food, beverages and pharmaceutical products. It is also currently being tested as an anti-diabetic and obesity control drug. D-Tagatose is a rare sugar, but it can be manufactured by the chemical or enzymatic isomerization of D-galactose obtained by a β-D-galactosidase-catalyzed hydrolysis of milk sugar lactose and the separation of D-glucose and D-galactose. L-Arabinose isomerases catalyze in vitro the conversion of D-galactose to D-tagatose and are the most promising enzymes for the large-scale production of D-tagatose. Results In this study, the araA gene from psychrotolerant Antarctic bacterium Arthrobacter sp. 22c was isolated, cloned and expressed in Escherichia coli. The active form of recombinant Arthrobacter sp. 22c L-arabinose isomerase consists of six subunits with a combined molecular weight of approximately 335 kDa. The maximum activity of this enzyme towards D-galactose was determined as occurring at 52°C; however, it exhibited over 60% of maximum activity at 30°C. The recombinant Arthrobacter sp. 22c L-arabinose isomerase was optimally active at a broad pH range of 5 to 9. This enzyme is not dependent on divalent metal ions, since it was only marginally activated by Mg2+, Mn2+ or Ca2+ and slightly inhibited by Co2+ or Ni2+. The bioconversion yield of D-galactose to D-tagatose by the purified L-arabinose isomerase reached 30% after 36 h at 50°C. In this study, a recombinant Pichia pastoris yeast strain secreting β-D-galactosidase Arthrobacter chlorophenolicus was also constructed. During cultivation of this strain in a whey permeate, lactose was hydrolyzed and D-glucose was metabolized, whereas D-galactose was accumulated in the medium. Moreover, cultivation of the P. pastoris strain secreting β-D-galactosidase in a whey permeate supplemented with Arthrobacter sp. 22c L-arabinose isomerase resulted in a 90% yield

  6. Transcriptional profiling of Gram-positive Arthrobacter in the phyllosphere: induction of pollutant degradation genes by natural plant phenolic compounds

    NARCIS (Netherlands)

    Scheublin, T.R.; Deusch, S.; Moreno-Forero, S.K.; Müller, J.A.; van der Meer, J.R.; Leveau, J.H.J.

    2014-01-01

    Arthrobacter chlorophenolicus A6 is a Gram-positive, 4-chlorophenol degrading soil bacterium that was recently shown to be an effective colonizer of plant leaf surfaces. The genetic basis for this phyllosphere competency is unknown. In this paper, we describe the genome-wide expression profile of A.

  7. Bioavailability of Ag(I) with Arthrobacter oxidas and Arthrobacter globiformis

    CERN Document Server

    Gelagutashvili, E; Ginturi, E; Bagdavadze, N; Kuchava, N; Tsakadze, K; Janjalia, M

    2012-01-01

    The biosorption of Ag(I)_ Arthrobacter species (Arthrobacter globiformis 151B and Arthrobacter oxidas 61B) was studied at simultaneous application of dialysis and atomic absorption analysis. The biosorption constants and nature of interaction for Ag(I) -Arthrobacter oxidas and Ag(I) -Arthrobacter globiformis were determined. The biosorption constants for Ag(I)- -Arthrobacter globiformis and for Ag(I) -Arthrobacter oxidas equal to 65.0 x10-4 and 35.0 x10-4 respectively.

  8. s-triazine degrading bacterial isolate Arthrobacter sp. AK-YN10, a candidate for bioaugmentation of atrazine contaminated soil.

    Science.gov (United States)

    Sagarkar, Sneha; Bhardwaj, Pooja; Storck, Veronika; Devers-Lamrani, Marion; Martin-Laurent, Fabrice; Kapley, Atya

    2016-01-01

    The Arthrobacter sp. strain AK-YN10 is an s-triazine pesticide degrading bacterium isolated from a sugarcane field in Central India with history of repeated atrazine use. AK-YN10 was shown to degrade 99 % of atrazine in 30 h from media supplemented with 1000 mg L(-1) of the herbicide. Draft genome sequencing revealed similarity to pAO1, TC1, and TC2 catabolic plasmids of the Arthrobacter taxon. Plasmid profiling analyses revealed the presence of four catabolic plasmids. The trzN, atzB, and atzC atrazine-degrading genes were located on a plasmid of approximately 113 kb.The flagellar operon found in the AK-YN10 draft genome suggests motility, an interesting trait for a bioremediation agent, and was homologous to that of Arthrobacter chlorophenolicus. The multiple s-triazines degradation property of this isolate makes it a good candidate for bioremediation of soils contaminated by s-triazine pesticides. PMID:26403923

  9. Proteomics

    DEFF Research Database (Denmark)

    Tølbøll, Trine Højgaard; Danscher, Anne Mette; Andersen, Pia Haubro;

    2012-01-01

    grouped manually to one or more of five major functional groups related to metabolism, cell structure, immunity, apoptosis and angiogenesis. These were chosen to represent basic cell functions and biological processes potentially involved in the pathogenesis of CHD. The LC–MS/MS-based proteomic analysis...... presented here is the largest published survey, so far, of the bovine claw tissue proteome....

  10. Proteomics

    DEFF Research Database (Denmark)

    Dam, Svend; Stougaard, Jens

    2014-01-01

    Proteomics is an efficient tool to identify proteins present in specific tissues, cell types, or organelles. The resulting proteome reference maps and/or comparative analyses provide overviews of regulated proteins between wild type and mutants or between different conditions together with a...... comprehensive list of proteins. Post translation modifications (PTMs), such as glycosylation and phosphorylation, are pivotal for protein stability and function. Several strategies for enrichment of PTMs have been developed where targeted proteomic approaches are used to identify these PTMs. The sequenced and...... annotated Lotus japonicus (Lotus) genome has been essential for obtaining high-quality protein identifications from proteomics studies. Furthermore, additional genomics and transcriptomics studies from several Lotus species/ecotypes support putative gene structures and these can be further supported using...

  11. Transcriptional profiling of Gram-positive Arthrobacter in the phyllosphere: induction of pollutant degradation genes by natural plant phenolic compounds.

    Science.gov (United States)

    Scheublin, Tanja R; Deusch, Simon; Moreno-Forero, Silvia K; Müller, Jochen A; van der Meer, Jan Roelof; Leveau, Johan H J

    2014-07-01

    Arthrobacter chlorophenolicus A6 is a Gram-positive, 4-chlorophenol-degrading soil bacterium that was recently shown to be an effective colonizer of plant leaf surfaces. The genetic basis for this phyllosphere competency is unknown. In this paper, we describe the genome-wide expression profile of A.chlorophenolicus on leaves of common bean (Phaseolus vulgaris) compared with growth on agar surfaces. In phyllosphere-grown cells, we found elevated expression of several genes known to contribute to epiphytic fitness, for example those involved in nutrient acquisition, attachment, stress response and horizontal gene transfer. A surprising result was the leaf-induced expression of a subset of the so-called cph genes for the degradation of 4-chlorophenol. This subset encodes the conversion of the phenolic compound hydroquinone to 3-oxoadipate, and was shown to be induced not only by 4-chlorophenol but also hydroquinone, its glycosylated derivative arbutin, and phenol. Small amounts of hydroquinone, but not arbutin or phenol, were detected in leaf surface washes of P.vulgaris by gas chromatography-mass spectrometry. Our findings illustrate the utility of genomics approaches for exploration and improved understanding of a microbial habitat. Also, they highlight the potential for phyllosphere-based priming of bacteria to stimulate pollutant degradation, which holds promise for the application of phylloremediation. PMID:24373130

  12. Uptake of Glyphosate by an Arthrobacter sp

    OpenAIRE

    Pipke, Rüdiger; Schulz, Arno; Amrhein, Nikolaus

    1987-01-01

    The uptake of glyphosate (N-[phosphonomethyl]glycine) by an Arthrobacter sp. which can utilize this herbicide as its sole source of phosphorus was investigated. Orthophosphate suppressed the expression of the uptake system for glyphosate and also competed with glyphosate for uptake. The Km for glyphosate uptake was 125 μM, and the Ki for orthophosphate was 24 μM. Organophosphonates as well as organophosphates inhibited glyphosate uptake, but only organophosphates and orthophosphate suppressed...

  13. Biodegradation of α-, β-, and γ-hexachlorocyclohexane by Arthrobacter fluorescens and Arthrobacter giacomelloi.

    Science.gov (United States)

    De Paolis, M R; Lippi, D; Guerriero, E; Polcaro, C M; Donati, E

    2013-06-01

    The organochlorine pesticide γ-hexachlorocyclohexane (γ-HCH, lindane) and its non-insecticidal isomers α-, β-, and δ- continue to pose serious environmental and health concerns, although their use has been restricted or completely banned for decades. The present study reports the first results on the ability of two Arthrobacter strains, not directly isolated from a HCH-polluted site, to grow in a mineral salt medium containing α-, β-, or γ-HCH (100 mgl(-1)) as sole source of carbon. Growth of cultures and HCHs degradation by Arthrobacter fluorescens and Arthrobacter giacomelloi were investigated after 1, 2, 3, 4, and 7 days of incubation by enumerating colony forming units and GC with ECD detection, respectively. Both bacteria are able to metabolize the HCHs: A. giacomelloi is the most effective one, as after 72 h of incubation it produces 88 % degradation of α-, 60 % of β-, and 56 % of γ-HCH. The formation of possible persistent compounds was studied by GC/MS and by HPLC analysis. Pentachlorocyclohexenes and tetrachlorocyclohexenes have been detected as metabolites, which are almost completely eliminated after 72 h of incubation, while no phenolic compounds were found. PMID:23553101

  14. Biosorption of Cr(VI)_ and Cr(III)_Arthrobacter species

    OpenAIRE

    Gelagutashvili, E.; Pataraia, E. Ginturi D.; Gurielidze, M.

    2011-01-01

    The biosorption of Cr(VI)_ and Cr(III)_ Arthrobacter species (Arthrobacter globiformis and Arthrobacter oxidas) was studied simultaneous application dialysis and atomic absorption analysis. Also biosorption of Cr(VI) in the presence of Zn(II) during growth of Arthrobacter species and Cr(III) in the presence of Mn(II) were discussed. Comparative Cr(VI)_ and Cr(III)_ Arthrobacter species shown, that Cr(III) was more effectively adsorbed by both bacterium than Cr(VI). The adsorption capacity is ...

  15. Cloning and sequencing of the trpE gene from Arthrobacter globiformis ATCC 8010 and several related subsurface Arthrobacter isolates

    Energy Technology Data Exchange (ETDEWEB)

    Chernova, T.; Viswanathan, V.K.; Austria, N.; Nichols, B.P.

    1998-09-01

    Tryptophan dependent mutants of Arthrobacter globiformis ATCC 8010 were isolated and trp genes were cloned by complementation and marker rescue of the auxotrophic strains. Rescue studies and preliminary sequence analysis reveal that at least the genes trpE, trpC, and trpB are clustered together in this organism. In addition, sequence analysis of the entire trpE gene, which encodes component I of anthranilate synthase, is described. Segments of the trpE gene from 17 subsurface isolates of Arthrobacter sp. were amplified by PCR and sequenced. The partial trpE sequences from the various strains were aligned and subjected to phylogenetic analysis. The data suggest that in addition to single base changes, recombination and genetic exchange play a major role in the evolution of the Arthrobacter genome.

  16. Beta-galactosidase from psychrotrophic microorganism (strain arthrobacter)

    Czech Academy of Sciences Publication Activity Database

    Hašek, Jindřich; Skálová, Tereza; Petroková, Hana; Vondráčková-Buchtelová, Eva; Dohnálek, Jan; Spiwok, V.; Lipovová, P.; Strnad, H.; Králová, B.

    2004-01-01

    Roč. 11, č. 1 (2004), s. 18-19. ISSN 1211-5894 R&D Projects: GA ČR GA204/02/0843 Institutional research plan: CEZ:AV0Z4050913 Keywords : .beta.-galactoside * cold active enzymes * Arthrobacter Subject RIV: EB - Genetics ; Molecular Biology

  17. Degradation of Swainsonine by the NADP-Dependent Alcohol Dehydrogenase A1R6C3 in Arthrobacter sp. HW08

    Directory of Open Access Journals (Sweden)

    Yan Wang

    2016-05-01

    Full Text Available Swainsonine is an indolizidine alkaloid that has been found in locoweeds and some fungi. Our previous study demonstrated that Arthrobacter sp. HW08 or its crude enzyme extract could degrade swainsonie efficiently. However, the mechanism of swainsonine degradation in bacteria remains unclear. In this study, we used label-free quantitative proteomics method based on liquid chromatography-electrospray ionization-tandem mass spectrometry to dissect the mechanism of swainsonine biodegradation by Arthrobacter sp. HW08. The results showed that 129 differentially expressed proteins were relevant to swainsonine degradation. These differentially expressed proteins were mostly related to the biological process of metabolism and the molecular function of catalytic activity. Among the 129 differentially expressed proteins, putative sugar phosphate isomerase/epimerase A1R5X7, Acetyl-CoA acetyltransferase A0JZ95, and nicotinamide adenine dinucleotide phosphate (NADP-dependent alcohol dehydrogenase A1R6C3 were found to contribute to the swainsonine degradation. Notably, NADP-dependent alcohol dehyrodgenase A1R6C3 appeared to play a major role in degrading swainsonine, but not as much as Arthrobacter sp. HW08 did. Collectively, our findings here provide insights to understand the mechanism of swainsonine degradation in bacteria.

  18. Degradation of Swainsonine by the NADP-Dependent Alcohol Dehydrogenase A1R6C3 in Arthrobacter sp. HW08

    Science.gov (United States)

    Wang, Yan; Zhai, A’guan; Zhang, Yanqi; Qiu, Kai; Wang, Jianhua; Li, Qinfan

    2016-01-01

    Swainsonine is an indolizidine alkaloid that has been found in locoweeds and some fungi. Our previous study demonstrated that Arthrobacter sp. HW08 or its crude enzyme extract could degrade swainsonie efficiently. However, the mechanism of swainsonine degradation in bacteria remains unclear. In this study, we used label-free quantitative proteomics method based on liquid chromatography-electrospray ionization-tandem mass spectrometry to dissect the mechanism of swainsonine biodegradation by Arthrobacter sp. HW08. The results showed that 129 differentially expressed proteins were relevant to swainsonine degradation. These differentially expressed proteins were mostly related to the biological process of metabolism and the molecular function of catalytic activity. Among the 129 differentially expressed proteins, putative sugar phosphate isomerase/epimerase A1R5X7, Acetyl-CoA acetyltransferase A0JZ95, and nicotinamide adenine dinucleotide phosphate (NADP)-dependent alcohol dehydrogenase A1R6C3 were found to contribute to the swainsonine degradation. Notably, NADP-dependent alcohol dehyrodgenase A1R6C3 appeared to play a major role in degrading swainsonine, but not as much as Arthrobacter sp. HW08 did. Collectively, our findings here provide insights to understand the mechanism of swainsonine degradation in bacteria. PMID:27196926

  19. Proteomics Core

    Data.gov (United States)

    Federal Laboratory Consortium — Proteomics Core is the central resource for mass spectrometry based proteomics within the NHLBI. The Core staff help collaborators design proteomics experiments in...

  20. Isolation of Arthrobacter species from the phyllosphere and demonstration of their epiphytic fitness

    OpenAIRE

    Scheublin, T.R.; Leveau, J.H.J.

    2013-01-01

    Bacteria of the genus Arthrobacter are common inhabitants of the soil environment, but can also be recovered from leaf surfaces (the phyllosphere). Using enrichment cultures on 4-chlorophenol, we succeeded in specifically isolating Arthrobacter bacteria from ground cover vegetation in an apple orchard. Based on 16S rRNA gene sequencing, the isolates were found to belong to at least three different species of Arthrobacter. Compared to the model bacterial epiphyte Pantoea agglomerans, the Arthr...

  1. Arthrobacter deserti sp. nov., isolated from a desert soil sample.

    Science.gov (United States)

    Hu, Qing-Wen; Chu, Xiao; Xiao, Min; Li, Chang-Tian; Yan, Zheng-Fei; Hozzein, Wael N; Kim, Chang-Jin; Zhi, Xiao-Yang; Li, Wen-Jun

    2016-05-01

    A Gram-stain-positive, non-motile, rod-shaped, catalase-positive and oxidase-negative bacterium, designated YIM CS25T, was isolated from a soil sample collected from Turpan desert in Xinjiang Uyghur Autonomous Region, north-western China. The isolate grew at 15-40 °C, at pH 6.0-8.0 and with 0-6 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences revealed that strain YIM CS25T belonged to the genus Arthrobacter and was closely related to Arthrobacter halodurans JSM 078085T (95.89 % similarity). The peptidoglycan type contained lysine, alanine and glutamic acid. The major whole-cell sugars were galactose, glucose and ribose. The isolate contained diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol as the major polar lipids and MK-9 (H2) as the predominant menaquinone. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and anteiso-C17 : 1ω9c. The genomic DNA G+C content was 68.3 mol%. On the basis of phylogenetic, phenotypic and chemotaxonomic analysis, strain YIM CS25T is considered to represent a novel species of the genus Arthrobacter, for which the name Arthrobacter deserti sp. nov. is proposed. The type strain is YIM CS25T ( = KCTC 39544T = CGMCC 1.15091T). PMID:26908080

  2. Wide Distribution of Closely Related, Antibiotic-Producing Arthrobacter Strains throughout the Arctic Ocean

    DEFF Research Database (Denmark)

    Wietz, Matthias; Månsson, Maria; Bowman, Jeff S.;

    2012-01-01

    We isolated 16 antibiotic-producing bacterial strains throughout the central Arctic Ocean, including seven Arthrobacter spp. with almost identical 16S rRNA gene sequences. These strains were numerically rare, as revealed using 454 pyrosequencing libraries. Arthrobacter spp. produced arthrobacilin...

  3. Intracellular inclusions of a n-alkane-grown Arthrobacter

    International Nuclear Information System (INIS)

    The ultrastructural changes associated with the growth of a marine Arthrobacter sp. on n-hexadecane were demonstrated by transmission electron microscopy. Multiple electron translucent areas (ETI), similar to inclusions described by other investigators, were found in hydrocarbon-grown cells but not in peptone-grown cells. Stereological planimetry demonstrated that the ETI occupy as much as 40% of the hydrocarbon-grown cell's volume. Electron dense structures (EDI) were observed in hexadecane and in peptone-grown cells. Gas chromatographic analysis indicated traces of n-hexadecane associated with the hydrocarbon-grown cells: however, the hydrocarbon levels were not high enough to suggest the presence of hydrocarbon inclusions in the cells. Solvent partition studies with disrupted 14C-n-hexadecane-grown cells suggested that the intracellular radioactivity was associated with polar compounds. Acrylate-inhibited, hydrocarbon-grown Arthrobacter sp. did not form ETI, suggesting that the formation of ETI involves the participation of Coenzyme A. Thin-layer and gas chromatography indicated that the major intracellular components were glycerides, with one or more R groups composed of palmitic acid and free palmitic acid. 27 references, 5 figures, 2 tables

  4. Ability of Cyanobacteria and Arthrobacter Species to Remove Gold Ions from Solution

    CERN Document Server

    Gelagutashvili, E; Rcheulichvili, A; Tsakadze, K; Bagdavadze, N; Kuchava, N; Djandjalia, M

    2012-01-01

    The biosorption of Au(III) - Spirulina platensis and Au(III) - Arthrobacter species (Arthrobacter globiformis and Arthrobacter oxidas) were studied at simultaneous application of dialysis and atomic absorption analysis. Also biosorption of Au(III) - Spirulina platensis at various pH were discussed. Biosorption constants for Au-cyanobacteris Spirulina platensis at different pH, and for Arthrobacter oxidas and Arthrobacter globiformis at pH=7.1 are : 1. K=3.91 x 10-4 (Au- Arthrobacter oxidas 61B, pH=7.1) 2. K=14.17 x 10-4 . (Au- Arthrobacter globiformis 151B, pH=7.1). 3. K=2.07x10-4 (Au- Spirulina platensis, pH=7.1) 4. K= 4.87x10-4 (Au- Spirulina platensis, pH=6.2) 5. K=8.7x10-4 (Au- Spirulina platensis, pH=8.4)

  5. Biosorption of Cr(VI)_ and Cr(III)_Arthrobacter species

    CERN Document Server

    Gelagutashvili, E; Gurielidze, M

    2011-01-01

    The biosorption of Cr(VI)_ and Cr(III)_ Arthrobacter species (Arthrobacter globiformis and Arthrobacter oxidas) was studied simultaneous application dialysis and atomic absorption analysis. Also biosorption of Cr(VI) in the presence of Zn(II) during growth of Arthrobacter species and Cr(III) in the presence of Mn(II) were discussed. Comparative Cr(VI)_ and Cr(III)_ Arthrobacter species shown, that Cr(III) was more effectively adsorbed by both bacterium than Cr(VI). The adsorption capacity is the same for both the Chromium-Arthrobacter systems. The biosorption constants for Cr(III) is higher than for Cr(VI) 5.7-5.9- fold for both species. Comparative Freundlich biosorption characteristics Cr(VI) Arthrobacter species of living and dry cells shown, that capacity(n) is in both cases the same(1.25,1.35). Dry cells have larger biosorption constant for both species, than living cells. Biosorption characteristics (K) and (n) for A. oxidas are without Mn(II) and in the presence of Mn(II) 2.6 x 10-4 (K), 1.37 (n) and 2...

  6. Adhesion of an Amylolytic Arthrobacter sp. to Starch-Containing Plastic Films

    OpenAIRE

    Imam, Syed H.; Gould, J. Michael

    1990-01-01

    Cells of the amylolytic bacterium KB-1 (thought to be an Arthrobacter sp.) adhered (∼70%) to the surface of plastic films composed of starch-poly (methylacrylate) graft copolymer (starch-PMA), but did not adhere (

  7. Degradation of the Phosphonate Herbicide Glyphosate by Arthrobacter atrocyaneus ATCC 13752

    OpenAIRE

    Pipke, Rüdiger; Amrhein, Nikolaus

    1988-01-01

    Of nine authentic Arthrobacter strains tested, only A. atrocyaneus ATCC 13752 was capable of using the herbicide glyphosate [N-(phosphonomethyl)glycine] as its sole source of phosphorus. Contrary to the previously isolated Arthrobacter sp. strain GLP-1, which degrades glyphosate via sarcosine, A. atrocyaneus metabolized glyphosate to aminomethylphosphonic acid. The carbon of aminomethylphosphonic acid was entirely converted to CO2. This is the first report on glyphosate degradation by a bacte...

  8. Plant compounds that induce polychlorinated biphenyl biodegradation by Arthrobacter sp. strain B1B.

    OpenAIRE

    Gilbert, E S; Crowley, D. E.

    1997-01-01

    Plant compounds that induced Arthrobacter sp. strain B1B to cometabolize polychlorinated biphenyls (PCBs) were identified by a screening assay based on the formation of a 4,4'-dichlorobiphenyl ring fission product. A chemical component of spearmint (Mentha spicata), l-carvone, induced Arthrobacter sp. strain B1B to cometabolize Aroclor 1242, resulting in significant degradation of 26 peaks in the mixture, including selected tetra- and pentachlorobiphenyls. Evidence for PCB biodegradation incl...

  9. Erythema caused by a localised skin infection with Arthrobacter mysorens

    Directory of Open Access Journals (Sweden)

    Chakraborty Trinad

    2010-12-01

    Full Text Available Abstract Background Skin erythemas of unknown origin are a frequent reason for consulting the general practitioner or dermatologist. Case presentation Here we report a case of an erythema resembling the erythema migrans manifestation of Lyme disease, but with atypical symptoms like persistent pruritus. The patient had no history of a recent tick-bite but displayed a positive serology for an advanced stage of Lyme borreliosis, which stood in contrast to the clinical manifestation of erythema migrans as a symptom of early Lyme disease. Three skin swabs and soil samples, collected in the area where the patient possibly acquired the infection, were examined by bacterial and fungal culture methods. Microorganisms were identified by using 16 S rRNA gene sequencing and bioinformatics. The patient and soil isolates were compared by employing RAPD analysis. The serum samples of the patient were examined by immunoblotting. Arthrobacter mysorens, a soil bacterium, was isolated from the collected skin and soil samples. The identity of both isolates was determined by molecular fingerprinting methods. A. mysorens was proven to be causative for the erythema by direct isolation from the affected skin and a positive serology, thus explaining the atypical appearance of the erythema compared to erythema migrans caused by Borrelia infection. Conclusions Infections with A.mysorens might be underreported and microbiological diagnostic techniques should be applied in cases of patients with unclear erythemas, resembling erythema migrans, without a history of tick bites.

  10. Review of the taxonomy of the genus Arthrobacter, emendation of the genus Arthrobacter sensu lato, proposal to reclassify selected species of the genus Arthrobacter in the novel genera Glutamicibacter gen. nov., Paeniglutamicibacter gen. nov., Pseudoglutamicibacter gen. nov., Paenarthrobacter gen. nov. and Pseudarthrobacter gen. nov., and emended description of Arthrobacter roseus.

    Science.gov (United States)

    Busse, Hans-Jürgen

    2016-01-01

    In this paper, the taxonomy of the genus Arthrobacter is discussed, from its first description in 1947 to the present state. Emphasis is given to intrageneric phylogeny and chemotaxonomic characteristics, concentrating on quinone systems, peptidoglycan compositions and polar lipid profiles. Internal groups within the genus Arthrobacter indicated from homogeneous chemotaxonomic traits and corresponding to phylogenetic grouping and/or high 16S rRNA gene sequence similarities are highlighted. Furthermore, polar lipid profiles and quinone systems of selected species are shown, filling some gaps concerning these chemotaxonomic traits. Based on phylogenetic groupings, 16S rRNA gene sequence similarities and homogeneity in peptidoglycan types, quinone systems and polar lipid profiles, a description of the genus Arthrobacter sensu lato and an emended description of Arthrobacter roseus are provided. Furthermore, reclassifications of selected species of the genus Arthrobacter into novel genera are proposed, namely Glutamicibacter gen. nov. (nine species), Paeniglutamicibacter gen. nov. (six species), Pseudoglutamicibacter gen. nov. (two species), Paenarthrobacter gen. nov. (six species) and Pseudarthrobacter gen. nov. (ten species). PMID:26486726

  11. Application of NAA method to study chromium uptake by Arthrobacter oxydans

    International Nuclear Information System (INIS)

    To study chromium uptake by Arthrobacter oxydans (Cr(VI)-reducer bacteria isolated from Columbia basalt rocks, USA) instrumental neutron activation analysis method was applied. It was established that chromate accumulation is dose-dependent and it is more intensive in the interval of concentrations of Cr(VI) (10-50 mg/l). At low concentrations of Cr(VI) (up to 50 mg/l) the most intensive formation of Cr(V) was also found (using ESR method). Besides, it was estimated that reduction from Cr(VI) to Cr(V) is faster process than the uptake of Cr(VI). According to ENAA measurements Cr(III), in constant to Cr(VI), is not accumulated in Arthrobacter oxydans cells up to concentration of 200 mg/l. Using epithermal neutron activation analysis the background levels of 17 major, minor and trace elements were determined in Arthrobacter oxydans

  12. Transplantation proteomics

    OpenAIRE

    Traum, Avram Z.; Schachter, Asher D.

    2005-01-01

    The field of proteomics is developing at a rapid pace in the post-genome era. Translational proteomics investigations aim to apply a combination of established methods and new technologies to learn about protein expression profiles predictive of clinical events, therapeutic response, and underlying mechanisms. However, in contrast to genetic studies and in parallel with gene expression studies, the dynamic nature of the proteome in conjunction with the challenges of accounting for post-transl...

  13. Arthrobacter nitroguajacolicus sp. nov., a novel 4-nitroguaiacol-degrading actinobacterium

    Czech Academy of Sciences Publication Activity Database

    Koutoučková, L.; Schumann, P.; Durnová, E.; Spröer, C.; Sedláček, I.; Neča, J.; Zdráhal, Zbyněk; Němec, M.

    2004-01-01

    Roč. 54, č. 3 (2004), s. 773-777. ISSN 1466-5026 R&D Projects: GA ČR GA204/00/P095 Institutional research plan: CEZ:AV0Z4031919 Keywords : Nitroguaiacol * actinobacterium * Arthrobacter Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 3.015, year: 2004

  14. Purification and Characterization of Two Extracellular Alkaline Phosphatases from a Psychrophilic Arthrobacter Isolate

    OpenAIRE

    Prada, P; Brenchley, J E

    1997-01-01

    Two extracellular, heat-labile alkaline phosphatases were purified from a psychrophilic Arthrobacter isolate, D10. The enzymes were active over different pH ranges, used distinct substrates, and had different kinetic properties. Each enzyme reacted specifically to its own antibody during immunoblot analysis. One had both monophosphatase and diesterase activities.

  15. [Heterotrophic Nitrification and Aerobic Denitrification of the Hypothermia Aerobic Denitrification Bacterium: Arthrobacter arilaitensis].

    Science.gov (United States)

    He, Teng-xia; Ni, Jiu-pai; Li, Zhen-lun; Sun, Quan; Ye Qing; Xu, Yi

    2016-03-15

    High concentrations of ammonium, nitrate and nitrite nitrogen were employed to clarify the abilities of heterotrophic nitrification and aerobic denitrification of Arthrobacter arilaitensis strain Y-10. Meanwhile, by means of inoculating the strain suspension into the mixed ammonium and nitrate, ammonium and nitrite nitrogen simulated wastewater, we studied the simultaneous nitrification and denitrification ability of Arthrobacter arilaitensis strain Y-10. In addition, cell optical density was assayed in each nitrogen removal process to analyze the relationship of cell growth and nitrogen removal efficiency. The results showed that the hypothermia denitrification strain Arthrobacter arilaitensis Y-10 exhibited high nitrogen removal efficiency during heterotrophic nitrification and aerobic denitrification. The ammonium, nitrate and nitrite removal rates were 65.0%, 100% and 61.2% respectively when strain Y-10 was cultivated for 4 d at 15°C with initial ammonium, nitrate and nitrite nitrogen concentrations of 208.43 mg · L⁻¹, 201.16 mg · L⁻¹ and 194.33 mg · L⁻¹ and initial pH of 7.2. Nitrite nitrogen could only be accumulated in the medium containing nitrate nitrogen during heterotrophic nitrification and aerobic denitrification process. Additionally, the ammonium nitrogen was mainly removed in the inorganic nitrogen mixed synthetic wastewater. In short, Arthrobacter arilaitensis Y-10 could conduct nitrification and denitrification effectively under aerobic condition and the ammonium nitrogen removal rate was more than 80.0% in the inorganic nitrogen mixed synthetic wastewater. PMID:27337904

  16. What Is Cancer Proteomics?

    Science.gov (United States)

    ... What is Proteomics? Video Tutorial What is Cancer Proteomics? Print This Page The term "proteome" refers to ... that a cell or organism undergoes. The term "proteomics" is a large-scale comprehensive study of a ...

  17. Improved biosorption for Cr(VI) reduction and removal by Arthrobacter viscosus using zeolite

    OpenAIRE

    Silva, Bruna Andreia Nogueira Airosa; Figueiredo, Hugo; Quintelas, C.; Neves, Isabel C.; Tavares, M.T.

    2012-01-01

    The aim of the present work was to optimize the reduction and removal of chromium from aqueous solutions by a biosorption system consisting of a bacteria supported on a zeolite. The system proposed combines the biosorption properties of Arthrobacter viscosus, with the ion exchange capacity of NaY zeolite. Experiments were also performed without the zeolite for comparison purposes. Experimental parameters such as solution pH, biomass concentration and initial Cr(VI) concentration were investig...

  18. Biodegradation by an Arthrobacter Species of Hydrocarbons Partitioned into an Organic Solvent

    OpenAIRE

    Efroymson, Rebecca A.; Alexander, Martin

    1991-01-01

    An Arthrobacter strain mineralized naphthalene and n-hexadecane dissolved in 2,2,4,4,6,8,8-heptamethylnonane. The extent of mineralization increased with greater volumes of solvent. Measurements under aseptic conditions of the partitioning of naphthalene into the aqueous phase from the solid phase or from heptamethylnonane showed that the rates were rapid and did not limit mineralization. The rate of mineralization of hexadecane was rapid, although partitioning of the compound into aqueous so...

  19. Improving the Survival of Arthrobacter sp., CW9 during Spray Drying Monitored by Scan Electric Microscope

    OpenAIRE

    Zhenqiang Xia; Ming Zhu; Yanqiu Zhang

    2014-01-01

    The culture of an aquaculture probiotic, i.e., Arthrobacter sp., CW9, was spray dried with different carriers/protectants, in which Scan Electric Microscope (SEM) was used to analyze the surface of micro-paticles produced by spray-drying. Matrix of protectants, inlet temperature and feed rate were optimized according to the survival rate after spray drying. Scanning electron micrographs showed that cracks formed on the particle surface were a key factor in enhancing bacteria survival during s...

  20. Isolation and Preliminary Characterization of Twenty Bacteriophages Infecting Either Brevibacterium or Arthrobacter Strains

    OpenAIRE

    Trautwetter, Annie; Blanco, Carlos

    1988-01-01

    Thirty-seven bacteriophages plaquing on Corynebacterium, Brevibacterium, or Arthrobacter strains were isolated from soil or vegetation samples. Restriction analysis of phage DNA indicated that 20 phages were unique; one of them produced entirely turbid plaques on Brevibacterium ketoglutamicum and was characterized as temperate. All these phages were assigned to group B of the classification of Bradley (Bacteriol. Rev. 31:230-314, 1967) and had relatively narrow host ranges.

  1. New metabolic pathway for degradation of 2-nitrobenzoate by Arthrobacter sp. SPG

    Directory of Open Access Journals (Sweden)

    Pankaj Kumar Arora

    2015-06-01

    Full Text Available Arthrobacter sp. SPG utilized 2-nitrobenzoate as its sole source of carbon and energy and degraded it with accumulation of stoichiometric amounts of nitrite ions. Salicylate and catechol were detected as metabolites of the 2-nitrobenzoate degradation using high performance liquid chromatography and gas chromatography-mass spectrometry. Enzyme activities for 2-nitrobenzoate-2-monooxygenase, salicylate hydroxylase, and catechol-1,2-dioxygenase were detected in the crude extracts of the 2-nitrobenzoate-induced cells of strain SPG. The 2-nitrobenzoate-monooxygenase activity resulted in formation of salicylate and nitrite from 2-nitrobenzoate whereas salicylate hydroxylase catalyzed the conversion of salicylate to catechol. The ring-cleaving enzyme, catechol-1,2-dioxygenase cleaved catechol to cis, cis-muconic acid. Cells of strain SPG were able to degrade 2-nitrobenzoate in sterile as well as non-sterile soil microcosms. The results of microcosm studies showed that strain SPG degraded more than 90% of 2-nitrobenzoate within 10-12 days. This study clearly shows that Arthrobacter sp. SPG degraded 2-nitrobenzoate via a new pathway with formation of salicylate and catechol as metabolites. Arthrobacter sp. SPG may be used for bioremediation of 2-nitrobenzoate-contaminated sites due to its ability to degrade 2-nitrobenzoate in soil.

  2. Complete genome sequence and metabolic potential of the quinaldine-degrading bacterium Arthrobacter sp. Rue61a

    Directory of Open Access Journals (Sweden)

    Niewerth Heiko

    2012-10-01

    Full Text Available Abstract Background Bacteria of the genus Arthrobacter are ubiquitous in soil environments and can be considered as true survivalists. Arthrobacter sp. strain Rue61a is an isolate from sewage sludge able to utilize quinaldine (2-methylquinoline as sole carbon and energy source. The genome provides insight into the molecular basis of the versatility and robustness of this environmental Arthrobacter strain. Results The genome of Arthrobacter sp. Rue61a consists of a single circular chromosome of 4,736,495 bp with an average G + C content of 62.32%, the circular 231,551-bp plasmid pARUE232, and the linear 112,992-bp plasmid pARUE113 that was already published. Plasmid pARUE232 is proposed to contribute to the resistance of Arthrobacter sp. Rue61a to arsenate and Pb2+, whereas the linear plasmid confers the ability to convert quinaldine to anthranilate. Remarkably, degradation of anthranilate exclusively proceeds via a CoA-thioester pathway. Apart from quinaldine utilization, strain Rue61a has a limited set of aromatic degradation pathways, enabling the utilization of 4-hydroxy-substituted aromatic carboxylic acids, which are characteristic products of lignin depolymerization, via ortho cleavage of protocatechuate. However, 4-hydroxyphenylacetate degradation likely proceeds via meta cleavage of homoprotocatechuate. The genome of strain Rue61a contains numerous genes associated with osmoprotection, and a high number of genes coding for transporters. It encodes a broad spectrum of enzymes for the uptake and utilization of various sugars and organic nitrogen compounds. A. aurescens TC-1 is the closest sequenced relative of strain Rue61a. Conclusions The genome of Arthrobacter sp. Rue61a reflects the saprophytic lifestyle and nutritional versatility of the organism and a strong adaptive potential to environmental stress. The circular plasmid pARUE232 and the linear plasmid pARUE113 contribute to heavy metal resistance and to the ability to degrade

  3. 2,3-Dihydroxybiphenyl dioxygenase gene was first discovered in Arthrobacter sp. strain P J3

    Institute of Scientific and Technical Information of China (English)

    YANG MeiYing; MA PengDa; LI WenMing; LIU JinYing; LI Liang; ZHU XiaoJuan; WANG XingZhi

    2007-01-01

    Bacterium strain PJ3, isolated from wastewater and identified as Arthrobacter sp. bacterium based on its 16S rDNA gene, could use carbazole as the sole carbon, nitrogen and energy source. The genomic libraryof strain PJ3 was constructed and a positive clone JM109 (pUCW402) was screened out for the expression of dioxygenase by the ability to form yellow ring-fission product. A 2,3-dihydroxybiphenyl dioxygenase (23DHBD) gene of 933 bp was found in the 3360 bp exogenous fragment of pUCW402 by GenSCAN software and BLAST analysis. The phylogenetic analysis showed that 23DHBD from strain PJ3 formed a deep branch separate from a cluster containing most known 23DHBD in GenBank.Southern hybridization confirmed for the first time that the 23DHBD gene was from the genomic DNA of Arthrobacter sp. PJ3. In order to test the gene function, recombinant bacterium BL21 (pETW-8) was constructed to express 23DHBD. The expression level in BL21 (pETW-8) was highest compared with the recombinant bacteria JM109 (pUCW402) and strain PJ3. We observed that 23DHBD was not absolute specific. The enzyme activity was higher with 2,3-dihydroxybiphenyl as a substrate than with catechol.The substrate specificity assay suggested that 23DHBD was essential for cleavage of bi-cyclic aromatic compounds during the course of aromatic compound biodegradation in Arthrobacter sp. strain PJ3.

  4. Proteome Sci.

    OpenAIRE

    Mann Matthias; Poustka Albert J; Mann Karlheinz

    2010-01-01

    Abstract Background Sea urchin is a major model organism for developmental biology and biomineralization research. However, identification of proteins involved in larval skeleton formation and mineralization processes in the embryo and adult, and the molecular characterization of such proteins, has just gained momentum with the sequencing of the Strongylocentrotus purpuratus genome and the introduction of high-throughput proteomics into the field. Results The present report contains the deter...

  5. Accumulation of rare earth elements by siderophore-forming Arthrobacter luteolus isolated from rare earth environment of Chavara, India

    Indian Academy of Sciences (India)

    E S Challaraj Emmanuel; T Ananthi; B Anandkumar; S Maruthamuthu

    2012-03-01

    In this study, Arthrobacter luteolus, isolated from rare earth environment of Chavara (Quilon district, Kerala, India), were found to produce catechol-type siderophores. The bacterial strain accumulated rare earth elements such as samarium and scandium. The siderophores may play a role in the accumulation of rare earth elements. Catecholate siderophore and low-molecular-weight organic acids were found to be present in experiments with Arthrobacter luteolus. The influence of siderophore on the accumulation of rare earth elements by bacteria has been extensively discussed.

  6. Metabolic pathway for degradation of 2-chloro-4-aminophenol by Arthrobacter sp. SPG

    OpenAIRE

    Arora, Pankaj Kumar; Mohanta, Tapan Kumar; Srivastava, Alok; Bae, Hanhong; Singh, Vijay Pal

    2014-01-01

    A degradation pathway of 2-chloro-4-aminophenol (2C4AP) was studied in an Arthrobacter sp. SPG that utilized 2C4AP as its sole source of carbon and energy. The 2C4AP degradation was initiated by a 2C4AP-deaminase that catalyzed the conversion of 2C4AP into chlorohydroquinone (CHQ) with removal of ammonium ion. In the next step, a CHQ-dehalogenase dehalogenated CHQ to hydroquinone (HQ) that cleaved into γ-hydroxymuconic semialdehyde by a HQ-dioxygenase. The 2C4AP degradation was also investiga...

  7. Draft Genome Sequence of Arthrobacter enclensis NCIM 5488T for Secondary Metabolism

    Science.gov (United States)

    Neurgaonkar, Priya S.; Dharne, Mahesh S.

    2016-01-01

    Here, we report the draft genome sequence of Arthrobacter enclensis NCIM 5488T, an actinobacterium isolated from a marine sediment sample from Chorao Island, Goa, India. This draft genome sequence consists of 4,226,231 bp with a G+C content of 67.08%, 3,888 protein-coding genes, 50 tRNAs, and 10 rRNAs. Analysis of the genome using bioinformatics tools such as antiSMASH and NaPDoS showed the presence of many unique natural product biosynthetic gene clusters. PMID:27257206

  8. Heavy metal resistance in Arthrobacter ramosus strain G2 isolated from mercuric salt-contaminated soil

    International Nuclear Information System (INIS)

    Present study describes isolation of a multiple metal-resistant Arthrobacter ramosus strain from mercuric salt-contaminated soil. The isolate was found to resist and bioaccumulate several metals, such as cadmium, cobalt, zinc, chromium and mercury. Maximum tolerated concentrations for above metals were found to be 37, 525, 348, 1530 and 369 μM, respectively. The isolate could also reduce and detoxify redox-active metals like chromium and mercury, indicating that it has great potential in bioremediation of heavy metal-contaminated sites. Chromate reductase and mercuric reductase (MerA) activities in protein extract of the culture were found to be 2.3 and 0.17 units mg-1 protein, respectively. MerA enzyme was isolated from the culture by (NH4)2SO4 precipitation followed by dye affinity chromatography and its identity was confirmed by nano-LC-MS/MS. Its monomeric molecular weight, and optimum pH and temperature were 57 kDa, 7.4 and 55 deg. C, respectively. Thus, the enzyme was mildly thermophilic as compared to other MerA enzymes. Km and Vmax of the enzyme were 16.9 μM HgCl2 and 6.2 μmol min-1 mg-1 enzyme, respectively. The enzyme was found to be NADPH-specific. To our knowledge this is the first report on characterization of MerA enzyme from an Arthrobacter sp.

  9. Genetic differentiation of Arthrobacter population from heavy metal-contaminated environment

    Institute of Scientific and Technical Information of China (English)

    ZHANG Hanbo; REN Weimin; SHAO Qiyong; DUAN Changqun

    2007-01-01

    Six samples containing extremely high concentration of Pb,Zn,and Cd were obtained from the layers of 5-10 cm and 25-30 cm three tailing piles,with ages of about 10,20 and more than 80 years,respectively.Then,48 bacterial strains were obtained from these samples,and subsequently their phylogenetic positions were determined by analysis on the partial sequence of 16S rRNA gene (fragment length ranging from 474 to 708 bp).These isolates were members of the Arthrobacter genus,phylogenetically close to A.keyseri and A.ureafaciens,with sequence ranging from 99.1%to 100%.Furthermore,genetic variation between subpopulations from different samples was revealed by analysis on their randomly amplified polymorphic DNA profile.Nei genetic distance showed that the greatest differentiation occurred between subpopulation A and C.Notably,either genetic distance between subpopulations from the layers of 5-10 cm and 25-30 cm of each tailing pile or between same layers of different tailing pile increased with the history of tailings.Moreover,correlation analysis showed that soluble Pb has a significantly negative relationship with Nei'gene diversity of subpopulation.It was assumed that soluble Pb may be responsible for the reduced genetic diversity of the Arthrobacter population.Our data provided evidence that genetic differentiation of microbial populations was consistent with the changes of environmental factors,particularly heavy metals.

  10. Isolation of Indole Utilizing Bacteria Arthrobacter sp. and Alcaligenes sp. From Livestock Waste.

    Science.gov (United States)

    Kim, Minsu; Lee, Jin-Hyung; Kim, Eonmi; Choi, Hyukjae; Kim, Younghoon; Lee, Jintae

    2016-06-01

    Indole is an interspecies and interkingdom signaling molecule widespread in different environmental compartment. Although multifaceted roles of indole in different biological systems have been established, little information is available on the microbial utilization of indole in the context of combating odor emissions from different types of waste. The present study was aimed at identifying novel bacteria capable of utilizing indole as the sole carbon and energy source. From the selective enrichment of swine waste and cattle feces, we identified Gram-positive and Gram-negative bacteria belonging to the genera Arthrobacter and Alcaligenes. Bacteria belonging to the genus Alcaligenes showed higher rates of indole utilization than Arthrobacter. Indole at 1.0 mM for growth was completely utilized by Alcaligenes sp. in 16 h. Both strains produced two intermediates, anthranilic acid and isatin, during aerobic indole metabolism. These isolates were also able to grow on several indole derivatives. Interestingly, an adaptive response in terms of a decrease in cell size was observed in both strains in the presence of indole. The present study will help to explain the degradation of indole by different bacteria and also the pathways through which it is catabolized. Furthermore, these novel bacterial isolates could be potentially useful for the in situ attenuation of odorant indole and its derivatives emitted from different types of livestock waste. PMID:27570307

  11. One-pot conversion of levan prepared from Serratia levanicum NN to difructose anhydride IV by Arthrobacter nicotinovorans levan fructotransferase.

    Science.gov (United States)

    Kikuchi, Hiroto; Sakurai, Hiroaki; Nagura, Taizo; Aritsuka, Tsutomu; Tomita, Fusao; Yokota, Atsushi

    2010-03-01

    The newly established difructose anhydride IV (DFA IV) production system is comprised of the effective production of levan from sucrose by Serratia levanicum NN, the conversion of the levan into DFA IV by levan fructotransferase from Arthrobacter nicotinovorans GS-9, which is highly expressed in an Escherichiacoli transformant, and a practical purification step. The chemical properties of DFA IV were also investigated. PMID:20159571

  12. Draft Genome Sequence of a Papaverine-Degrading, Gram-positive Arthrobacter sp., Isolated from Soil Near Hohenheim, Germany

    OpenAIRE

    Reznicek, Ondrej; Facey, Sandra J; Hauer, Bernhard

    2015-01-01

    We present the 4.8-Mb draft genome of a soil bacterium identified as Arthrobacter sp. This Gram-positive soil bacterium is able to use the aromatic compound papaverine as sole carbon source and will be examined for novel oxygenases.

  13. Optimization of cultural conditions for growth associated chromate reduction by Arthrobacter sp. SUK 1201 isolated from chromite mine overburden

    International Nuclear Information System (INIS)

    Highlights: ► Isolation of a potent Cr(VI) resistant and reducing Arthrobacter SUK 1201 from chromite mine overburdens of Orissa, India. ► Phylogenetically (16S rDNA analysis), Arthrobacter SUK 1201 showed 99% nucleotide base pair similarity with Arthrobacter GZK-1. ► Production of insoluble chromium precipitates during chromate reduction under batch culture by the isolate SUK 1201. ► Confirmation of formation of insoluble chromium precipitate during reduction studies by EDX analysis. ► Optimization of cultural conditions for Cr(VI) reduction under batch culture leading to complete reduction of 2 mM of Cr(VI). - Abstract: Arthrobacter sp. SUK 1201, a chromium resistant and reducing bacterium having 99% sequence homology of 16S rDNA with Arthrobacter sp. GZK-1 was isolated from chromite mine overburden dumps of Orissa, India. The objective of the present study was to optimize the cultural conditions for chromate reduction by Arthrobacter sp. SUK 1201. The strain showed 67% reduction of 2 mM chromate in 7 days and was associated with the formation of green insoluble precipitate, which showed characteristic peak of chromium in to energy dispersive X-ray analysis. However, Fourier transform infrared spectra have failed to detect any complexation of end products of Cr(VI) reduction with the cell mass. Reduction of chromate increased with increased cell density and was maximum at 1010 cells/ml, but the reduction potential decreased with increase in Cr(VI) concentration. Chromate reducing efficiency was promoted when glycerol and glucose was used as electron donors. Optimum pH and temperature of Cr(VI) reduction was 7.0 and 35 °C respectively. The reduction process was inhibited by several metal ions and metabolic inhibitors but not by Cu(II) and DNP. These findings suggest that Arthrobacter sp. SUK 1201 has great promise for use in Cr(VI) detoxification under a wide range of environmental conditions.

  14. Arthrobacter pokkalii sp nov, a Novel Plant Associated Actinobacterium with Plant Beneficial Properties, Isolated from Saline Tolerant Pokkali Rice, Kerala, India

    Science.gov (United States)

    Krishnan, Ramya; Menon, Rahul Ravikumar; Tanaka, Naoto; Busse, Hans-Jürgen; Krishnamurthi, Srinivasan; Rameshkumar, Natarajan

    2016-01-01

    A novel yellow colony-forming bacterium, strain P3B162T was isolated from the pokkali rice rhizosphere from Kerala, India, as part of a project study aimed at isolating plant growth beneficial rhizobacteria from saline tolerant pokkali rice and functionally evaluate their abilities to promote plant growth under saline conditions. The novel strain P3B162T possesses plant growth beneficial traits such as positive growth on 1-aminocyclopropane-1-carboxylic acid (ACC), production of indole acetic acid (IAA) and siderophore. In addition, it also showed important phenotypic characters such as ability to form biofilm and utilization of various components of plant root exudates (sugars, amino acids and organic acids), clearly indicating its lifestyle as a plant rhizosphere associated bacterium. Taxonomically, the novel strain P3B162T was affiliated to the genus Arthrobacter based on the collective results of phenotypic, genotypic and chemotaxonomic analyses. Moreover, molecular analysis using 16S rRNA gene showed Arthrobacter globiformis NBRC 12137T, Arthrobacter pascens DSM 20545T and Arthrobacter liuii DSXY973T as the closely related phylogenetic neighbours, showing more than 98% 16S rRNA similarity values, whereas the recA gene analysis displayed Arthrobacter liuii JCM 19864T as the nearest neighbour with 94.7% sequence similarity and only 91.7% to Arthrobacter globiformis LMG 3813T and 88.7% to Arthrobacter pascens LMG 16255T. However, the DNA-DNA hybridization values between strain P3B162T, Arthrobacter globiformis LMG 3813T, Arthrobacter pascens LMG 16255T and Arthrobacter liuii JCM 19864T was below 50%. In addition, the novel strain P3B162T can be distinguished from its closely related type strains by several phenotypic characters such as colony pigment, tolerance to NaCl, motility, reduction of nitrate, hydrolysis of DNA, acid from sucrose, cell wall sugars and cell wall peptidoglycan structure. In conclusion, the combined results of this study support the

  15. Arthrobacter pokkalii sp nov, a Novel Plant Associated Actinobacterium with Plant Beneficial Properties, Isolated from Saline Tolerant Pokkali Rice, Kerala, India.

    Science.gov (United States)

    Krishnan, Ramya; Menon, Rahul Ravikumar; Tanaka, Naoto; Busse, Hans-Jürgen; Krishnamurthi, Srinivasan; Rameshkumar, Natarajan

    2016-01-01

    A novel yellow colony-forming bacterium, strain P3B162T was isolated from the pokkali rice rhizosphere from Kerala, India, as part of a project study aimed at isolating plant growth beneficial rhizobacteria from saline tolerant pokkali rice and functionally evaluate their abilities to promote plant growth under saline conditions. The novel strain P3B162T possesses plant growth beneficial traits such as positive growth on 1-aminocyclopropane-1-carboxylic acid (ACC), production of indole acetic acid (IAA) and siderophore. In addition, it also showed important phenotypic characters such as ability to form biofilm and utilization of various components of plant root exudates (sugars, amino acids and organic acids), clearly indicating its lifestyle as a plant rhizosphere associated bacterium. Taxonomically, the novel strain P3B162T was affiliated to the genus Arthrobacter based on the collective results of phenotypic, genotypic and chemotaxonomic analyses. Moreover, molecular analysis using 16S rRNA gene showed Arthrobacter globiformis NBRC 12137T, Arthrobacter pascens DSM 20545T and Arthrobacter liuii DSXY973T as the closely related phylogenetic neighbours, showing more than 98% 16S rRNA similarity values, whereas the recA gene analysis displayed Arthrobacter liuii JCM 19864T as the nearest neighbour with 94.7% sequence similarity and only 91.7% to Arthrobacter globiformis LMG 3813T and 88.7% to Arthrobacter pascens LMG 16255T. However, the DNA-DNA hybridization values between strain P3B162T, Arthrobacter globiformis LMG 3813T, Arthrobacter pascens LMG 16255T and Arthrobacter liuii JCM 19864T was below 50%. In addition, the novel strain P3B162T can be distinguished from its closely related type strains by several phenotypic characters such as colony pigment, tolerance to NaCl, motility, reduction of nitrate, hydrolysis of DNA, acid from sucrose, cell wall sugars and cell wall peptidoglycan structure. In conclusion, the combined results of this study support the

  16. Urine in clinical proteomics.

    OpenAIRE

    Decramer, Stéphane; Gonzalez de Peredo, Anne; Breuil, Benjamin; Mischak, Harald; Monsarrat, Bernard; Bascands, Jean-Loup; Schanstra, Joost P

    2008-01-01

    Urine has become one of the most attractive biofluids in clinical proteomics as it can be obtained non-invasively in large quantities and is stable compared with other biofluids. The urinary proteome has been studied by almost any proteomics technology, but mass spectrometry-based urinary protein and peptide profiling has emerged as most suitable for clinical application. After a period of descriptive urinary proteomics the field is moving out of the discovery phase into an era of validation ...

  17. Mining the granule proteome

    DEFF Research Database (Denmark)

    Albrethsen, Jakob; Goetze, Jens P; Johnsen, Anders H

    2015-01-01

    Proteomics of secretory granules is an emerging strategy for identifying secreted proteins, including potentially novel candidate biomarkers and peptide hormones. In addition, proteomics can provide information about the abundance, localization and structure (post-translational modification) of...... granule proteins and peptides. Analytical strategies within this research line include so-called 'subtractive proteomics', 'peptidomics' and granule purification by the use of multiple gradient centrifugations. Here we review the literature, and describe the challenges and opportunities in proteomics of...

  18. Application of zeolite-Arthrobacter viscosus system for the removal of heavy metal and dye : chromium and azure B

    OpenAIRE

    Rosales, E.; Pazos, M.; Sanromán, M. A.; Tavares, M. T.

    2012-01-01

    A hybrid system combining the ion-exchange properties of a NaY zeolite and the characteristics of the bacterium Arthrobacter viscosus was investigated to treat polluted effluents with dye and toxic metals. In this study, the dye and the metal ion employed were a thiazine dye, Azure B, and chromium (VI), respectively. Initially, the removal of dye by the zeolite was tested. The analysis of dye equilibrium isotherms data was done using Langmuir, Freundlich, Sips and Redlich–Peterson models. Red...

  19. Characterization of the in vitro assembly of FtsZ in Arthrobacter strain A3 using light scattering.

    Science.gov (United States)

    Yang, Fan; Zhang, Shanshan; Ding, Shenglong; Hou, Yannan; Yu, Linghui; Chen, Ximing; Xiao, Jianxi

    2016-10-01

    The self-assembly of FtsZ, the bacterial homolog of tubulin, plays an essential role in cell division. Light scattering technique is applied to real-time monitor the in vitro assembly of FtsZ in Arthrobacter strain A3, a newly isolated psychrotrophic bacterium. The critical concentration needed for the assembly is estimated as 6.7μM. The polymerization of FtsZ in Arthrobacter strain A3 requires both GTP and divalent metal ions, while salt is an unfavorable condition for the assembly. The FtsZ polymerizes under a wide range of pHs, with the fastest rate around pH 6.0. The FtsZ from Arthrobacter strain A3 resembles Mycobacterium tuberculosis FtsZ in terms of the dependence on divalent metal ions and the slow polymerization rate, while it is different from M. tuberculosis FtsZ considering the sensitivity to salt and pH. The comparison of FtsZ from different organisms will greatly advance our understanding of the biological role of the key cell division protein. PMID:27164494

  20. Metabolic pathway for degradation of 2-chloro-4-aminophenol by Arthrobacter sp. SPG.

    Science.gov (United States)

    Arora, Pankaj Kumar; Mohanta, Tapan Kumar; Srivastava, Alok; Bae, Hanhong; Singh, Vijay Pal

    2014-01-01

    A degradation pathway of 2-chloro-4-aminophenol (2C4AP) was studied in an Arthrobacter sp. SPG that utilized 2C4AP as its sole source of carbon and energy. The 2C4AP degradation was initiated by a 2C4AP-deaminase that catalyzed the conversion of 2C4AP into chlorohydroquinone (CHQ) with removal of ammonium ion. In the next step, a CHQ-dehalogenase dehalogenated CHQ to hydroquinone (HQ) that cleaved into γ-hydroxymuconic semialdehyde by a HQ-dioxygenase. The 2C4AP degradation was also investigated in sterile and non-sterile soil microcosms using strain SPG. The results show that the SPG cells degraded 2C4AP more rapidly in sterile soil than non-sterile soil. Our studies showed that strain SPG may be used for bioremediation of 2C4AP-contaminated sites. This is the first report of the 2C4AP degradation by any bacteria. PMID:25427856

  1. Genetic analysis of phenylacetic acid catabolism in Arthrobacter oxydans CECT386.

    Science.gov (United States)

    Navarro-Llorens, Juana María; Drzyzga, Oliver; Perera, Julián

    2008-07-01

    Arthrobacter oxydans CECT386 is a Gram-positive bacterium able to use either phenylacetic acid or phenylacetaldehyde as the sole carbon and energy source for aerobic growth. Genes responsible for the catabolism of these compounds have been located at two chromosomal regions and were organized in one isolated paaN gene and two putative paa operons, one consisting of the paaD, paaF, tetR and prot genes, and one consisting of the paaG, paaH, paaI, paaJ, paaK and paaB genes. The identity of the paaF and paaN genes was supported by functional complementation experiments. A comparison with the paa catabolic genes and/or gene clusters of other bacteria that degrade these aromatic compounds is presented. The results of this study broaden the knowledge regarding the range of metabolic potential of this strain and eventually make it attractive for environmental applications. PMID:18437357

  2. IN-VITRO BIOREDUCTION OF HEXAVALENT CHROMIUM BY VIABLE WHOLE CELLS OF Arthrobacter sp. SUK 1201

    Directory of Open Access Journals (Sweden)

    Satarupa Dey

    2014-08-01

    Full Text Available A chromium resistant and reducing bacterium Arthrobacter sp. SUK 1201 was isolated from chromite mine overburden dumps of Orissa, India. Viable whole cells of this isolate was capable of completely reducing 100 µM Cr(VI in chemically defined MS medium within 28 h of incubation under batch cultivation. Reduction of chromate increased with increased cell density and was maximum at a density of 1010 cells/ml, but the reduction potential of the suspended cells decreased with increase in Cr(VI concentration in the medium. Chromate reducing efficiency was promoted when glycerol and glucose was used as electron donors, while the optimum pH and temperature of Cr(VI reduction was found to be 7.0 and 35°C respectively. The reduction process was inhibited by divalent cations Ni, Co and Cd, but not by Cu and Fe. Similarly, carbonyl cyanide m-chlorophenylhydrazone (CCCP, N,N,-Di cyclohexyl carboiimide (DCC, sodium azide and sodium fluoride were inhibitory to chromate reduction, while in presence of 2,4 dinitrophenol (2,4 DNP chromate reduction by SUK 1201 cells remained unaffected.

  3. The rhizobacterium Arthrobacter agilis produces dimethylhexadecylamine, a compound that inhibits growth of phytopathogenic fungi in vitro.

    Science.gov (United States)

    Velázquez-Becerra, Crisanto; Macías-Rodríguez, Lourdes I; López-Bucio, José; Flores-Cortez, Idolina; Santoyo, Gustavo; Hernández-Soberano, Christian; Valencia-Cantero, Eduardo

    2013-12-01

    Plant diseases caused by fungal pathogens such as Botrytis cinerea and the oomycete Phytophthora cinnamomi affect agricultural production worldwide. Control of these pests can be done by the use of fungicides such as captan, which may have deleterious effects on human health. This study demonstrates that the rhizobacterium Arthrobacter agilis UMCV2 produces volatile organic compounds that inhibit the growth of B. cinerea in vitro. A single compound from the volatile blends, namely dimethylhexadecylamine (DMHDA), could inhibit the growth of both B. cinerea and P. cinnamomi when supplied to the growth medium in low concentrations. DMHDA also inhibited the growth of beneficial fungi Trichoderma virens and Trichoderma atroviride but at much higher concentrations. DMHDA-related aminolipids containing 4, 8, 10, 12, and 14 carbons in the alkyl chain were tested for their inhibitory effect on the growth of the pathogens. The results show that the most active compound from those tested was dimethyldodecylamine. This effect correlates with a decrease in the number of membrane lipids present in the mycelium of the pathogen including eicosanoic acid, (Z)-9-hexadecenoic acid, methyl ester, and (Z)-9-octadecenoic acid, methyl ester. Strawberry leaflets treated with DMHDA were not injured by the compound. These data indicate that DMHDA and related compounds, which can be produced by microorganisms may effectively inhibit the proliferation of certain plant pathogens. PMID:23674267

  4. Chromate reduction by Arthrobacter CR47 in biofilm packed bed reactors

    International Nuclear Information System (INIS)

    Bacterial strain Cr47 was isolated from a landfarming process soil sample. It was identified, by 16s rDNA sequencing, as Arthrobacter sp. The time course of the Cr(VI) reduction was monitored in batch operated packed bed biofilm reactors (12mL void volume) and in recirculating packed bed biofilm reactors (100 mL void volume) inoculated with bacterial strain Cr47. The reduction was evaluated with, 30 mg L-1 Cr(VI) laboratory solutions prepared with K2Cr2O7 and enriched with glucose-minimal medium, and with 30 mg L-1 Cr(VI) industrial model solutions prepared with chrome plating waste waters enriched with sucrose-minimal medium. Under batch mode the reduction reaction by the biofilm seemed to fit well an exponential-decay model with a first order kinetic parameter of 0.071 mg(L h)-1 Cr(VI). In the recirculating reactor, monitored after 4 weeks from inoculation and fed with laboratory solutions the removal rate was 0.79 mg(L h)-1. In the reactor fed with the industrial model solutions the maximum Cr(VI) removal rate attained was 0.49 mg(L h)-1. Artrobacter sp. packed bed biofilm reactors achieved Cr(VI) reduction rates comparable to other aerobic and anaerobic fixed film bioreactors previously reported

  5. Use of Arthrobacter davidanieli as a live vaccine against Renibacterium salmoninarum and Piscirickettsia salmonis in salmonids.

    Science.gov (United States)

    Salonius, K; Siderakis, C; MacKinnon, A M; Griffiths, S G

    2005-01-01

    Arthrobacter davidanieli (proposed species nomenclature) is a non-pathogenic Gram-variable bacterium related to, but taxonomically distinct from, Renibacterium salmoninarum, the aetiological agent of bacterial kidney disease (BKD). We have demonstrated that vaccination with live A. davidanieli is effective against BKD in Atlantic salmon (Salmo salar) showing above 80 relative percent survival in experimental challenge trials. Good protection was also demonstrated in long-term field trials where Atlantic salmon were naturally exposed to R. salmoninarum challenge until 23 months after vaccination. The same vaccine, which is licensed in Canada against BKD has also proved effective in reducing mortality from experimental challenge of coho salmon (Oncorhynchus kisutch) with Piscirickettsia salmonis, the causative agent of piscirickettsiosis. Under field conditions in Chile, use of the vaccine led to a significant reduction in piscirickettsiosis mortality in coho salmon over 10 months following sea transfer. The vaccine strain is unique in that it is the first live organism to be licensed as a vaccine for use in aquaculture. Potential mechanisms of protection against the two taxonomically disparate pathogens are discussed. PMID:15962482

  6. PROTEOMICS in aquaculture

    DEFF Research Database (Denmark)

    Rodrigues, Pedro M.; Silva, Tomé S.; Dias, Jorge;

    2012-01-01

    proteomics in seafood biology research. Proteomics, as a powerful comparative tool, has therefore been increasingly used over the last decade to address different questions in aquaculture, regarding welfare, nutrition, health, quality, and safety. In this paper we will give an overview of these biological...... questions and the role of proteomics in their investigation, outlining the advantages, disadvantages and future challenges. A brief description of the proteomics technical approaches will be presented. Special focus will be on the latest trends related to the aquaculture production of fish with defined...... nutritional, health or quality properties for functional foods and the integration of proteomics techniques in addressing this challenging issue. This article is part of a Special Issue entitled: Farm animal proteomics....

  7. STEM CELLS AND PROTEOMICS

    Institute of Scientific and Technical Information of China (English)

    ZHOU Yong-ming; GUO Tian-nan; HUANG Shi-ang

    2006-01-01

    The distinctive features of proteomics are large-scale and high throughput. The key techniques of proteomics are two-dimensional gel electrophoresis, mass spectrometry and bioinformatics. Stem cell can differentiate into all kinds of cells, tissues and organs. There are many proteins and cytokines involved in the process of differentiation. Applying proteomics techniques to the research of the complex process of stem cell differentiation is of great importance to study the mechanism and applications of stem cell differentiation.

  8. Proteomics Technologies and Challenges

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Proteomics is the study of proteins and their interactions in a cell. With the completion of the Human Genome Project, the emphasis is shifting to the protein compliment of the human organism. Because proteome reflects more accurately on the dynamic state of a cell, tissue, or organism, much is expected from proteomics to yield better disease markers for diagnosis and therapy monitoring. The advent of proteomics technologies for global detection and quantitation of proteins creates new opportunities and challenges for those seeking to gain greater understanding of diseases. High-throughput proteomics technologies combining with advanced bioinformatics are extensively used to identify molecular signatures of diseases based on protein pathways and signaling cascades. Mass spectrometry plays a vital role in proteomics and has become an indispensable tool for molecular and cellular biology. While the potential is great, many challenges and issues remain to be solved, such as mining low abundant proteins and integration of proteomics with genomics and metabolomics data. Nevertheless, proteomics is the foundation for constructing and extracting useful knowledge to biomedical research. In this review, a snapshot of contemporary issues in proteomics technologies is discussed.

  9. Characterization and molecular cloning of a novel enzyme, inorganic polyphosphate/ATP-glucomannokinase, of Arthrobacter sp. strain KM.

    Science.gov (United States)

    Mukai, Takako; Kawai, Shigeyuki; Matsukawa, Hirokazu; Matuo, Yuhsi; Murata, Kousaku

    2003-07-01

    A bacterium exhibiting activities of several inorganic polyphosphate [poly(P)]- and ATP-dependent kinases, including glucokinase, NAD kinase, mannokinase, and fructokinase, was isolated, determined to belong to the genus Arthrobacter, and designated Arthrobacter sp. strain KM. Among the kinases, a novel enzyme responsible for the poly(P)- and ATP-dependent mannokinase activities was purified 2,200-fold to homogeneity from a cell extract of the bacterium. The purified enzyme was a monomer with a molecular mass of 30 kDa. This enzyme phosphorylated glucose and mannose with a high affinity for glucose, utilizing poly(P) as well as ATP, and was designated poly(P)/ATP-glucomannokinase. The K(m) values of the enzyme for glucose, mannose, ATP, and hexametaphosphate were determined to be 0.50, 15, 0.20, and 0.02 mM, respectively. The catalytic sites for poly(P)-dependent phosphorylation and ATP-dependent phosphorylation of the enzyme were found to be shared, and the poly(P)-utilizing mechanism of the enzyme was shown to be nonprocessive. The gene encoding the poly(P)/ATP-glucomannokinase was cloned from Arthrobacter sp. strain KM, and its nucleotide sequence was determined. This gene contained an open reading frame consisting of 804 bp coding for a putative polypeptide with a calculated molecular mass of 29,480 Da. The deduced amino acid sequence of the polypeptide exhibited homology to the amino acid sequences of the poly(P)/ATP-glucokinase of Mycobacterium tuberculosis H37Rv (level of homology, 45%), ATP-dependent glucokinases of Corynebacterium glutamicum (45%), Renibacterium salmoninarum (45%), and Bacillus subtilis (35%), and proteins of bacteria belonging to the order Actinomyces whose functions are not known. Alignment of these homologous proteins revealed seven conserved regions. The mannose and poly(P) binding sites of poly(P)/ATP-glucomannokinase are discussed. PMID:12839753

  10. Genome sequence of the fish pathogen Renibacterium salmoninarum suggests reductive evolution away from an environmental Arthrobacter ancestor.

    Science.gov (United States)

    Wiens, Gregory D; Rockey, Daniel D; Wu, Zaining; Chang, Jean; Levy, Ruth; Crane, Samuel; Chen, Donald S; Capri, Gina R; Burnett, Jeffrey R; Sudheesh, Ponnerassery S; Schipma, Matthew J; Burd, Henry; Bhattacharyya, Anamitra; Rhodes, Linda D; Kaul, Rajinder; Strom, Mark S

    2008-11-01

    Renibacterium salmoninarum is the causative agent of bacterial kidney disease and a significant threat to healthy and sustainable production of salmonid fish worldwide. This pathogen is difficult to culture in vitro, genetic manipulation is challenging, and current therapies and preventative strategies are only marginally effective in preventing disease. The complete genome of R. salmoninarum ATCC 33209 was sequenced and shown to be a 3,155,250-bp circular chromosome that is predicted to contain 3,507 open-reading frames (ORFs). A total of 80 copies of three different insertion sequence elements are interspersed throughout the genome. Approximately 21% of the predicted ORFs have been inactivated via frameshifts, point mutations, insertion sequences, and putative deletions. The R. salmoninarum genome has extended regions of synteny to the Arthrobacter sp. strain FB24 and Arthrobacter aurescens TC1 genomes, but it is approximately 1.9 Mb smaller than both Arthrobacter genomes and has a lower G+C content, suggesting that significant genome reduction has occurred since divergence from the last common ancestor. A limited set of putative virulence factors appear to have been acquired via horizontal transmission after divergence of the species; these factors include capsular polysaccharides, heme sequestration molecules, and the major secreted cell surface antigen p57 (also known as major soluble antigen). Examination of the genome revealed a number of ORFs homologous to antibiotic resistance genes, including genes encoding beta-lactamases, efflux proteins, macrolide glycosyltransferases, and rRNA methyltransferases. The genome sequence provides new insights into R. salmoninarum evolution and may facilitate identification of chemotherapeutic targets and vaccine candidates that can be used for prevention and treatment of infections in cultured salmonids. PMID:18723615

  11. Genome Sequence of the Fish Pathogen Renibacterium salmoninarum Suggests Reductive Evolution away from an Environmental Arthrobacter Ancestor▿ †

    Science.gov (United States)

    Wiens, Gregory D.; Rockey, Daniel D.; Wu, Zaining; Chang, Jean; Levy, Ruth; Crane, Samuel; Chen, Donald S.; Capri, Gina R.; Burnett, Jeffrey R.; Sudheesh, Ponnerassery S.; Schipma, Matthew J.; Burd, Henry; Bhattacharyya, Anamitra; Rhodes, Linda D.; Kaul, Rajinder; Strom, Mark S.

    2008-01-01

    Renibacterium salmoninarum is the causative agent of bacterial kidney disease and a significant threat to healthy and sustainable production of salmonid fish worldwide. This pathogen is difficult to culture in vitro, genetic manipulation is challenging, and current therapies and preventative strategies are only marginally effective in preventing disease. The complete genome of R. salmoninarum ATCC 33209 was sequenced and shown to be a 3,155,250-bp circular chromosome that is predicted to contain 3,507 open-reading frames (ORFs). A total of 80 copies of three different insertion sequence elements are interspersed throughout the genome. Approximately 21% of the predicted ORFs have been inactivated via frameshifts, point mutations, insertion sequences, and putative deletions. The R. salmoninarum genome has extended regions of synteny to the Arthrobacter sp. strain FB24 and Arthrobacter aurescens TC1 genomes, but it is approximately 1.9 Mb smaller than both Arthrobacter genomes and has a lower G+C content, suggesting that significant genome reduction has occurred since divergence from the last common ancestor. A limited set of putative virulence factors appear to have been acquired via horizontal transmission after divergence of the species; these factors include capsular polysaccharides, heme sequestration molecules, and the major secreted cell surface antigen p57 (also known as major soluble antigen). Examination of the genome revealed a number of ORFs homologous to antibiotic resistance genes, including genes encoding β-lactamases, efflux proteins, macrolide glycosyltransferases, and rRNA methyltransferases. The genome sequence provides new insights into R. salmoninarum evolution and may facilitate identification of chemotherapeutic targets and vaccine candidates that can be used for prevention and treatment of infections in cultured salmonids. PMID:18723615

  12. Characterizing the Catalytic Potential of Deinococcus, Arthrobacter and other Robust Bacteria in Contaminated Subsurface Environments of the Hanford Site

    Energy Technology Data Exchange (ETDEWEB)

    Daly, Michael J.

    2005-06-01

    Natural selection in highly radioactive waste sites may yield bacteria with favorable bioremediating characteristics. However, until recently the microbial ecology of such environments has remained unexplored because of the high costs and technical complexities associated with extracting and characterizing samples from such sites. We have examined the bacterial ecology within radioactive sediments from a high-level nuclear waste plume in the vadose zone on the DOE?s Hanford Site in south-central Washington state (Fredrickson et al, 2004). Manganese-dependent, radiation resistant bacteria have been isolated from this contaminated site including the highly Mn-dependent Deinococcus and Arthrobacter spp.

  13. SPS’ Digest: the Swiss Proteomics Society selection of proteomics articles

    OpenAIRE

    Hoogland, C.; Lion, N.; Palagi, P.M.; Sanchez, J. C.; Tissot, J. D.

    2005-01-01

    Despite the consolidation of the specialized proteomics literature around a few established journals, such as Proteomics, Molecular and Cellular Proteomics, and the Journal of Proteome Research, a lot of information is still spread in many different publications from different fields, such as analytical sciences, MS, bioinformatics, etc. The purpose of SPS’ Digest is to gather a selection of proteomics articles, to categorize them, and to make the list available on a periodic basis through a ...

  14. Optimization of Endoglucanase Production from a Novel Bacterial Isolate, Arthrobacter sp. HPG166 and Characterization of Its Properties

    Directory of Open Access Journals (Sweden)

    Shengwei Huang

    2015-10-01

    Full Text Available ABSTRACTIn this study, a potential novel cellulolytic bacteriumArthrobacter sp. HPG166 was isolated from the hindgut of root-feeding larvaeHolotrichia parallela. Optimization of fermentation factors for endoglucanase production byArthrobacter sp. HPG166 was carried out via response surface methodology. Sodium carboxymethylcellulose 1.19% (w/v and beef extract 0.35% (w/v were the ideal combination of carbon and nitrogen sources for enzyme production; the optimum temperature and pH for cellulase production were 34°C and pH 8.0 respectively. Under the optimized fermentation conditions, the maximum endoglucanase activity of 1.411 U mL-1 was obtained. The crude endoglucanase was thermotolerant as it retained 50.31% of its activity after incubation at 70°C for an hour. Metal profile of the enzyme indicated that Mg2+ and Na+ were strong stimulators while Mn2+ and Co+ drastically inhibited its activity. Due to its particular characteristics, this enzyme could have potential for industrial applications.

  15. Studies on Bioflocculant Production by Arthrobacter sp. Raats, a Freshwater Bacteria Isolated from Tyume River, South Africa

    Directory of Open Access Journals (Sweden)

    Uchechukwu Nwodo

    2012-01-01

    Full Text Available A bioflocculant-producing bacteria was isolated from Tyume River in the Eastern Cape Province, South Africa and identified by 16S rRNA gene nucleotide sequence to have 91% similarity to Arthrobacter sp. 5J12A, and the nucleotide sequence was deposited in GenBank as Arthrobacter sp. Raats (accession number HQ875723. The bacteria produced an extracellular bioflocculant when grown aerobically in a production medium containing glucose as sole carbon source and had an initial pH of 7.0. Influences of carbon, nitrogen and metal ions sources, as well as initial pH on flocculating activity were investigated. The bacteria optimally produced the bioflocullant when lactose and urea were used as sole sources of carbon and nitrogen respectively with flocculating activities of 75.4% and 83.4% respectively. Also, the bacteria produced the bioflocculant optimally when initial pH of the medium was 7.0 (flocculating activity 84%, and when Mg2+ was used as cation (flocculating activity 77%. Composition analyses indicated the bioflocculant to be principally a glycoprotein made up of about 56% protein and 25% total carbohydrate.

  16. Optimization of four types of antimicrobial agents to increase the inhibitory ability of marine Arthrobacter oxydans KQ11 dextranase mouthwash

    Science.gov (United States)

    Ren, Wei; Wang, Shujun; Lü, Mingsheng; Wang, Xiaobei; Fang, Yaowei; Jiao, Yuliang; Hu, Jianen

    2016-03-01

    We adopted the response surface methodology using single factor and orthogonal experiments to optimize four types of antimicrobial agents that could inhibit biofilm formation by Streptococcus mutans, which is commonly found in the human oral cavity and causes tooth decay. The objective was to improve the function of marine Arthrobacter oxydans KQ11 dextranase mouthwash (designed and developed by our laboratory). The experiment was conducted in a three-level, four-variable central composite design to determine the best combination of ZnSO4, lysozyme, citric acid and chitosan. The optimized antibacterial agents were 2.16 g/L ZnSO4, 14 g/L lysozyme, 4.5 g/L citric acid and 5 g/L chitosan. The biofilm formation inhibition reached 84.49%. In addition, microscopic observation of the biofilm was performed using scanning electron microscopy and confocal laser scanning microscopy. The optimized formula was tested in marine dextranase Arthrobacter oxydans KQ11 mouthwash and enhanced the inhibition of S. mutans. This work may be promoted for the design and development of future marine dextranase oral care products.

  17. [Proteomics in infectious diseases].

    Science.gov (United States)

    Quero, Sara; Párraga-Niño, Noemí; García-Núñez, Marian; Sabrià, Miquel

    2016-04-01

    Infectious diseases have a high incidence in the population, causing a major impact on global health. In vitro culture of microorganisms is the first technique applied for infection diagnosis which is laborious and time consuming. In recent decades, efforts have been focused on the applicability of «Omics» sciences, highlighting the progress provided by proteomic techniques in the field of infectious diseases. This review describes the management, processing and analysis of biological samples for proteomic research. PMID:25583331

  18. The Redox Proteome*

    OpenAIRE

    Go, Young-Mi; Jones, Dean P.

    2013-01-01

    The redox proteome consists of reversible and irreversible covalent modifications that link redox metabolism to biologic structure and function. These modifications, especially of Cys, function at the molecular level in protein folding and maturation, catalytic activity, signaling, and macromolecular interactions and at the macroscopic level in control of secretion and cell shape. Interaction of the redox proteome with redox-active chemicals is central to macromolecular structure, regulation,...

  19. Collaborations in Proteomics Research - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The National Cancer Institute (NCI), through the Office of Cancer Clinical Proteomics Research (OCCPR), has signed two Memorandums of Understanding (MOUs) in the sharing of proteomics reagents and protocols

  20. Proteomics analysis of human oligodendroglioma proteome.

    Science.gov (United States)

    Khaghani-Razi-Abad, Solmaz; Hashemi, Mehrdad; Pooladi, Mehdi; Entezari, Maliheh; Kazemi, Elham

    2015-09-10

    Proteomics analyses enable the identification and quantitation of proteins. From a purely clinical perspective, the application of proteomics based on innovations, may greatly affect the future management of malignant brain tumors. This optimism is based on four main reasons: diagnosis, prognosis, selection of targeted therapy based on molecular profile of the brain tumor and monitoring therapeutic response, or resistance. We extracted the proteins of tumor and normal brain tissues, and then evaluated the protein purity by Bradford test. In this study, we separated the proteins by two-dimensional (2DG) gel electrophoresis methods. Then spots were analyzed, compared using statistical data and specific software and were identified by pH isoelectric, molecular weights and data banks. The protein profiles were determined using 2D gel electrophoresis and MALDI TOF/TOF mass spectrometry approaches. Simple statistical tests were used to establish a putative hierarchy in which the change in protein level was ranked according to a cut-off point with pProteomics is a powerful way to identifying multiple proteins which are altered following a neuropharmacological intervention in a CNS disease. PMID:26002447

  1. Proteomics approaches to fibrotic disorders

    OpenAIRE

    Gucek Marjan

    2012-01-01

    Abstract This review provides an introduction to mass spectrometry based proteomics and discusses several proteomics approaches that are relevant in understanding the pathophysiology of fibrotic disorders and the approaches that are frequently used in biomarker discovery.

  2. Characterizing the Catalytic Potential of Deinococcus, Arthrobacter and other Robust Bacteria in Contaminated Subsurface Environments of the Hanford Site

    International Nuclear Information System (INIS)

    Ionizing Radiation (IR) Resistance in Bacteria. Until recently, there have been no clear physiologic predictors of a cell's ability to recover from ionizing radiation (IR) and other DOE-relevant oxidative stress conditions. In general, the most resistant bacteria have been Gram-positive (e.g., Deinococcus, Arthrobacter, Lactobacillus and Enterococcus spp.) and the most sensitive have been Gram-negative (e.g., Pseudomonas, Shewanella and Neisseria spp.). However, there are several reported exceptions to this paradigm, the Gram-negative cyanobacterium Chroococcidiopsis is extremely resistant to IR, whereas the Gram-positive Micrococcus luteus is sensitive. We have identified biomolecular signatures for radiation sensitivity and resistance which are independent of phylogeny, where very high and very low intracellular Mn/Fe concentration ratios correlated with very high and very low resistances, respectively; and restricting Mn(II) in the famously resistant Deinococcus radiodurans sensitized this eubacterium to IR

  3. Characterizing the Catalytic Potential of Deinococcus, Arthrobacter and other Robust Bacteria in Contaminated Subsurface Environments of the Hanford Site

    Energy Technology Data Exchange (ETDEWEB)

    Daly, Michael J.

    2006-05-01

    Ionizing Radiation (IR) Resistance in Bacteria. Until recently, there have been no clear physiologic predictors of a cell's ability to recover from ionizing radiation (IR) and other DOE-relevant oxidative stress conditions. In general, the most resistant bacteria have been Gram-positive (e.g., Deinococcus, Arthrobacter, Lactobacillus & Enterococcus spp.) and the most sensitive have been Gram-negative (e.g., Pseudomonas, Shewanella & Neisseria spp.). However, there are several reported exceptions to this paradigm, the Gram-negative cyanobacterium Chroococcidiopsis is extremely resistant to IR, whereas the Gram-positive Micrococcus luteus is sensitive. We have identified biomolecular signatures for radiation sensitivity and resistance which are independent of phylogeny, where very high and very low intracellular Mn/Fe concentration ratios correlated with very high and very low resistances, respectively; and restricting Mn(II) in the famously resistant Deinococcus radiodurans sensitized this eubacterium to IR.

  4. Characterizing the Catalytic Potential of Deinococcus, Arthrobacter and other Robust Bacteria in Contaminated Subsurface Environments of the Hanford Site

    Energy Technology Data Exchange (ETDEWEB)

    Fredrickson, Jim K.; Daly, Michael J.

    2006-06-01

    Until recently, there have been no clear physiologic predictors of a cell's ability to recover from ionizing radiation (IR), desiccation, and other DOE-relevant oxidative stress conditions. In general, the most resistant bacteria have been Gram-positive (e.g., Deinococcus, Arthrobacter, Lactobacillus & Enterococcus spp.) and the most sensitive have been Gram-negative (e.g., Pseudomonas, Shewanella & Neisseria spp.). However, there are several reported exceptions to this paradigm, the Gram-negative cyanobacterium Chroococcidiopsis is extremely resistant to IR, whereas the Gram-positive Micrococcus luteus is sensitive. We have identified biomolecular signatures for radiation sensitivity and resistance which are independent of phylogeny, where very high and very low intracellular Mn/Fe concentration ratios correlated with very high and very low resistances, respectively; and restricting Mn(II) in the famously resistant Deinococcus radiodurans sensitized this eubacterium to IR (http://cfyn.ifas.ufl.edu/radiation.pdf).

  5. Proteomics - new analytical approaches

    International Nuclear Information System (INIS)

    Full text: Recent developments in the sequencing of the human genome have indicated that the number of coding gene sequences may be as few as 30,000. It is clear, however, that the complexity of the human species is dependent on the much greater diversity of the corresponding protein complement. Estimates of the diversity (discrete protein species) of the human proteome range from 200,000 to 300,000 at the lower end to 2,000,000 to 3,000,000 at the high end. In addition, proteomics (the study of the protein complement to the genome) has been subdivided into two main approaches. Global proteomics refers to a high throughput examination of the full protein set present in a cell under a given environmental condition. Focused proteomics refers to a more detailed study of a restricted set of proteins that are related to a specified biochemical pathway or subcellular structure. While many of the advances in proteomics will be based on the sequencing of the human genome, de novo characterization of protein microheterogeneity (glycosylation, phosphorylation and sulfation as well as the incorporation of lipid components) will be required in disease studies. To characterize these modifications it is necessary to digest the protein mixture with an enzyme to produce the corresponding mixture of peptides. In a process analogous to sequencing of the genome, shot-gun sequencing of the proteome is based on the characterization of the key fragments produced by such a digest. Thus, a glycopeptide and hence a specific glycosylation motif will be identified by a unique mass and then a diagnostic MS/MS spectrum. Mass spectrometry will be the preferred detector in these applications because of the unparalleled information content provided by one or more dimensions of mass measurement. In addition, highly efficient separation processes are an absolute requirement for advanced proteomic studies. For example, a combination of the orthogonal approaches, HPLC and HPCE, can be very powerful

  6. Translational plant proteomics: A perspective

    NARCIS (Netherlands)

    Agrawal, G.K.; Pedreschi, R.; Barkla, B.J.; Bindschedler, L.V.; Cramer, R.; Sarkar, A.; Renaut, J.; Job, D.; Rakwal, R.

    2012-01-01

    Translational proteomics is an emerging sub-discipline of the proteomics field in the biological sciences. Translational plant proteomics aims to integrate knowledge from basic sciences to translate it into field applications to solve issues related but not limited to the recreational and economic v

  7. High-Throughput Proteomics

    Science.gov (United States)

    Zhang, Zhaorui; Wu, Si; Stenoien, David L.; Paša-Tolić, Ljiljana

    2014-06-01

    Mass spectrometry (MS)-based high-throughput proteomics is the core technique for large-scale protein characterization. Due to the extreme complexity of proteomes, sophisticated separation techniques and advanced MS instrumentation have been developed to extend coverage and enhance dynamic range and sensitivity. In this review, we discuss the separation and prefractionation techniques applied for large-scale analysis in both bottom-up (i.e., peptide-level) and top-down (i.e., protein-level) proteomics. Different approaches for quantifying peptides or intact proteins, including label-free and stable-isotope-labeling strategies, are also discussed. In addition, we present a brief overview of different types of mass analyzers and fragmentation techniques as well as selected emerging techniques.

  8. Proteomics in uveal melanoma.

    LENUS (Irish Health Repository)

    Ramasamy, Pathma

    2014-01-01

    Uveal melanoma is the most common primary intraocular malignancy in adults, with an incidence of 5-7 per million per year. It is associated with the development of metastasis in about 50% of cases, and 40% of patients with uveal melanoma die of metastatic disease despite successful treatment of the primary tumour. The survival rates at 5, 10 and 15 years are 65%, 50% and 45% respectively. Unlike progress made in many other areas of cancer, uveal melanoma is still poorly understood and survival rates have remained similar over the past 25 years. Recently, advances made in molecular genetics have improved our understanding of this disease and stratification of patients into low risk and high risk for developing metastasis. However, only a limited number of studies have been performed using proteomic methods. This review will give an overview of various proteomic technologies currently employed in life sciences research, and discuss proteomic studies of uveal melanoma.

  9. Establishing Substantial Equivalence: Proteomics

    Science.gov (United States)

    Lovegrove, Alison; Salt, Louise; Shewry, Peter R.

    Wheat is a major crop in world agriculture and is consumed after processing into a range of food products. It is therefore of great importance to determine the consequences (intended and unintended) of transgenesis in wheat and whether genetically modified lines are substantially equivalent to those produced by conventional plant breeding. Proteomic analysis is one of several approaches which can be used to address these questions. Two-dimensional PAGE (2D PAGE) remains the most widely available method for proteomic analysis, but is notoriously difficult to reproduce between laboratories. We therefore describe methods which have been developed as standard operating procedures in our laboratory to ensure the reproducibility of proteomic analyses of wheat using 2D PAGE analysis of grain proteins.

  10. Proteomics and insect immunity

    Directory of Open Access Journals (Sweden)

    L Shi

    2006-01-01

    Full Text Available Insect innate immunity is both a model for vertebrate immunity as well as a key system that impactsmedically important pathogens that are transmitted by insects. Recent developments in proteomics andprotein identification techniques combined with the completion of genome sequences for Anophelesgambiae and Drosophila melanogaster provided the tools for examining insect immunity at a new level ofmolecular detail. Application of proteomics to insect immunity resulted in predictions of new roles inimmunity for proteins already known in other contexts (e.g. ferritin, transferrin, Chi-lectins and helped totarget specific members of multi-gene families that respond to different pathogens (e.g. serine proteases,thioester proteins. In addition, proteomics studies verify that post-translational modifications play a keyrole in insect immunity since many of the identified proteins are modified in some way. These studiescomplement recent work on insect transcriptomes and provide new directions for further investigation ofinnate immunity.

  11. Computing the functional proteome

    DEFF Research Database (Denmark)

    O'Brien, Edward J.; Palsson, Bernhard

    2015-01-01

    -Models). Recent expansions in network content to encompass proteome synthesis have resulted in models of metabolism and protein expression (ME-Models). ME-Models advance the predictions possible with constraint-based models from network flux states to the spatially resolved molecular composition of a cell....... Specifically, ME-Models enable the prediction of transcriptome and proteome allocation and limitations, and basal expression states and regulatory needs. Continued expansion in reconstruction content and constraints will result in an increasingly refined representation of cellular composition and behavior....

  12. Complete Genome Sequencing of Protease-Producing Novel Arthrobacter sp. Strain IHBB 11108 Using PacBio Single-Molecule Real-Time Sequencing Technology

    OpenAIRE

    Kiran, Shashi; Swarnkar, Mohit K.; Pal, Mohinder; Thakur, Rishu; Tewari, Rupinder; Singh, Anil Kumar; Gulati, Arvind

    2015-01-01

    A previously uncharacterized species of the genus Arthrobacter, strain IHBB 11108 (MCC 2780), is a Gram-positive, strictly aerobic, nonmotile, cold-adapted, and protease-producing alkaliphilic actinobacterium, isolated from shallow undersurface water from Chandra Tal Lake, Lahaul-Spiti, India. The complete genome of the strain is 3.6 Mb in size with an average 58.97% G+C content.

  13. Cutting edge proteomics

    DEFF Research Database (Denmark)

    Bunkenborg, Jakob; Espadas, Guadalupe; Molina, Henrik

    2013-01-01

    Tryptic digestion is an important component of most proteomics experiments, and trypsin is available from many sources with a cost that varies by more than 1000-fold. This high-mass-accuracy LC-MS study benchmarks six commercially available trypsins with respect to autolytic species and sequence...

  14. Alleviating salt stress in tomato seedlings using Arthrobacter and Bacillus megaterium isolated from the rhizosphere of wild plants grown on saline-alkaline lands.

    Science.gov (United States)

    Fan, Pengfei; Chen, Daitao; He, Yanan; Zhou, Qingxia; Tian, Yongqiang; Gao, Lihong

    2016-11-01

    Salt-induced soil degradation is common in farmlands and limits the growth and development of numerous crop plants in the world. In this study, we isolated salt-tolerant bacteria from the rhizosphere of Tamarix chinensis, Suaeda salsa and Zoysia sinica, which are common wild plants grown on a saline-alkaline land, to test these bacteria's efficiency in alleviating salt stress in tomato plants. We screened out seven strains (TF1-7) that are efficient in reducing salt stress in tomato seedlings. The sequence data of 16S rRNA genes showed that these strains belong to Arthrobacter and Bacillus megaterium. All strains could hydrolyze casein and solubilize phosphate, and showed at least one plant growth promotion (PGP)-related gene, indicating their potential in promoting plant growth. The Arthrobacter strains TF1 and TF7 and the Bacillus megaterium strain TF2 and TF3 could produce indole acetic acid under salt stress, further demonstrating their PGP potential. Tomato seed germination, seedling length, vigor index, and plant fresh and dry weight were enhanced by inoculation of Arthrobacter and B. megaterium strains under salt stress. Our results demonstrated that salt-tolerant bacteria isolated from the rhizosphere of wild plants grown on saline-alkaline lands could be used for alleviating salt stress in crop plants. PMID:27196364

  15. Genomes to Proteomes

    Energy Technology Data Exchange (ETDEWEB)

    Panisko, Ellen A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Grigoriev, Igor [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Daly, Don S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Webb-Robertson, Bobbie-Jo [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Baker, Scott E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2009-03-01

    Biologists are awash with genomic sequence data. In large part, this is due to the rapid acceleration in the generation of DNA sequence that occurred as public and private research institutes raced to sequence the human genome. In parallel with the large human genome effort, mostly smaller genomes of other important model organisms were sequenced. Projects following on these initial efforts have made use of technological advances and the DNA sequencing infrastructure that was built for the human and other organism genome projects. As a result, the genome sequences of many organisms are available in high quality draft form. While in many ways this is good news, there are limitations to the biological insights that can be gleaned from DNA sequences alone; genome sequences offer only a bird's eye view of the biological processes endemic to an organism or community. Fortunately, the genome sequences now being produced at such a high rate can serve as the foundation for other global experimental platforms such as proteomics. Proteomic methods offer a snapshot of the proteins present at a point in time for a given biological sample. Current global proteomics methods combine enzymatic digestion, separations, mass spectrometry and database searching for peptide identification. One key aspect of proteomics is the prediction of peptide sequences from mass spectrometry data. Global proteomic analysis uses computational matching of experimental mass spectra with predicted spectra based on databases of gene models that are often generated computationally. Thus, the quality of gene models predicted from a genome sequence is crucial in the generation of high quality peptide identifications. Once peptides are identified they can be assigned to their parent protein. Proteins identified as expressed in a given experiment are most useful when compared to other expressed proteins in a larger biological context or biochemical pathway. In this chapter we will discuss the automatic

  16. Proteomics Discovery of Disease Biomarkers

    OpenAIRE

    Mamoun Ahram; Petricoin, Emanuel F.

    2008-01-01

    Recent technological developments in proteomics have shown promising initiatives in identifying novel biomarkers of various diseases. Such technologies are capable of investigating multiple samples and generating large amount of data end-points. Examples of two promising proteomics technologies are mass spectrometry, including an instrument based on surface enhanced laser desorption/ionization, and protein microarrays. Proteomics data must, however, undergo analytical processing using bioinfo...

  17. Production of Xylanase from Arthrobacter sp. MTCC 6915 Using Saw Dust As Substrate under Solid State Fermentation

    Directory of Open Access Journals (Sweden)

    Sevanan Murugan

    2011-01-01

    Full Text Available Saw dust was used as substrate for xylanase production from Arthrobacter sp. MTCC 6915. The study of period of incubation, temperature, pH, carbon, and nitrogen sources for xylanase production was optimized. Xylanase production was found to be optimum at an incubation period of 96 hrs (117.0 U/mL, temperature 30°C (105.0 U/mL, and pH 9.0 (102.9 U/mL. The results showed that the xylanase production was found to be higher in the presence of carboxymethylcellulose (176.4 U/mL and dextrose (126.0 U/mL. It was also observed that peptone (170.1 U/mL and beef extract (161.7 U/mL supported maximum xylanase production.The enzyme was characterized and found to be fairly active at pH 9 (764.4 U/mL and temperature 60°C (819 U/mL. Even in the present study, a major difference in the production temperature (30°C and optimal temperature (60°C of the enzyme activity was observed. However, the pH of the production media and the enzyme activity were found to be the same (pH 9.

  18. TIME DEPENDENT ACCUMULATION OF NICOTINE DERIVATIVES IN THE CULTURE MEDIUM OF ARTHROBACTER NICOTINOVORANS pAO1

    Directory of Open Access Journals (Sweden)

    Răzvan Ștefan Boiangiu

    2014-12-01

    Full Text Available Previous studies have shown that the metabolic intermediate 6-hidroxy-D-nicotine (6HNic found in the Arthrobacter nicotinovorans pAO1+ nicotine catabolic pathway has the ability to bind nicotinic acetylcholine receptors and to sustain spatial memory in rats. These properties make 6HNic a valuable compound with some potential for medical applications, thereby a suitable, simple and efficient method for producing 6-hidroxy-D-nicotine is necessary. Here, we focus on identifying the best moment for harvesting A. nicotinovorans cells in order to directly convert nicotine to 6HNic with the best yield.  The growth of  A. nicotinovorans pAO1+ was monitored and the correlation between the growth phases and nicotine metabolism was established. After about 5 hours of lag,the strain entered the log phase and was fully grown after 10 hours. The nicotine concentration began to drop dramatically as the pAO1+ culture reached saturation and was depleted in 5 hours. As the nicotine concentration dropped, 6HNic began to accumulate, reaching the maximum levels after about 11 hours of growth. Two other products could be detected by HPLC, one which was identified as the nicotine-blue (NB pigment and a second a still unknown end-product. 

  19. Synergistic effect using vermiculite as media with a bacterial biofilm of Arthrobacter sp. for biodegradation of di-(2-ethylhexyl) phthalate.

    Science.gov (United States)

    Wen, Zhi-Dan; Wu, Wei-Min; Ren, Nan-Qi; Gao, Da-Wen

    2016-03-01

    Vermiculite is one of matrix material used for constructed wetland (CW) for the treatment of municipal wastewater. Arthrobacter sp. strain C21 (CGMCC No. 7671), isolated from a constructed wetland receiving municipal wastewater, forms biofilm on the surface of vermiculite. Di-(2-ethylhexyl) phthalate (DEHP), a typical phthalate pollutant in environment, can be degraded by the biofilm of strain C21 formed on vermiculite. Results of laboratory studies indicated that DEHP was removed from aqueous phase via biodegradation, adsorption by vermiculite, and adsorption by biofilm biomass. Synergistic effect of these three reactions enhanced the overall DEHP removal efficiency. During a batch incubation test with vermiculite and the cell suspension, bacterial adhesion to the media surface occurred within 5h and the phthalate esters (PEs) removal was due to both biodegradation and vermiculite adsorption. As the biofilm developed on surface of vermiculite (5-36 h), biodegradation became the predominance for PEs removal. As mature biofilm was formed (36-54 h), the adsorption of PEs by biofilm biomass became a main driving force for the removal of PEs from aqueous phase. The content of extracellular polymers (EPS) of the biofilm and DEHP removal performance showed a significant positive correlation (rp>0.86). PMID:26547620

  20. The plant mitochondrial proteome

    DEFF Research Database (Denmark)

    Millar, A.H.; Heazlewood, J.L.; Kristensen, B.K.;

    2005-01-01

    The plant mitochondrial proteome might contain as many as 2000-3000 different gene products, each of which might undergo post-translational modification. Recent studies using analytical methods, such as one-, two- and three-dimensional gel electrophoresis and one- and two-dimensional liquid...... context to be defined for them. There are indications that some of these proteins add novel activities to mitochondrial protein complexes in plants....

  1. Proteomics of the Lysosome

    OpenAIRE

    Lübke, Torben; Lobel, Peter; Sleat, David

    2008-01-01

    Defects in lysosomal function have been associated with numerous monogenic human diseases typically classified as lysosomal storage diseases. However, there is increasing evidence that lysosomal proteins are also involved in more widespread human diseases including cancer and Alzheimer disease. Thus, there is a continuing interest in understanding the cellular functions of the lysosome and an emerging approach to this is the identification of its constituent proteins by proteomic analyses. To...

  2. Proteomics research in India: an update.

    Science.gov (United States)

    Reddy, Panga Jaipal; Atak, Apurva; Ghantasala, Saicharan; Kumar, Saurabh; Gupta, Shabarni; Prasad, T S Keshava; Zingde, Surekha M; Srivastava, Sanjeeva

    2015-09-01

    After a successful completion of the Human Genome Project, deciphering the mystery surrounding the human proteome posed a major challenge. Despite not being largely involved in the Human Genome Project, the Indian scientific community contributed towards proteomic research along with the global community. Currently, more than 76 research/academic institutes and nearly 145 research labs are involved in core proteomic research across India. The Indian researchers have been major contributors in drafting the "human proteome map" along with international efforts. In addition to this, virtual proteomics labs, proteomics courses and remote triggered proteomics labs have helped to overcome the limitations of proteomics education posed due to expensive lab infrastructure. The establishment of Proteomics Society, India (PSI) has created a platform for the Indian proteomic researchers to share ideas, research collaborations and conduct annual conferences and workshops. Indian proteomic research is really moving forward with the global proteomics community in a quest to solve the mysteries of proteomics. A draft map of the human proteome enhances the enthusiasm among intellectuals to promote proteomic research in India to the world.This article is part of a Special Issue entitled: Proteomics in India. PMID:25868663

  3. Isolation and characterization of atrazine-degrading Arthrobacter sp. AD26 and use of this strain in bioremediation of contaminated soil

    Institute of Scientific and Technical Information of China (English)

    LI Qingyan; LI Ying; ZHU Xikun; CAI Baoli

    2008-01-01

    A bacterial strain (AD26) capable of utilizing atrazine as a sole nitrogen source for growth was isolated from an industrial wastewatersample by enrichment culture. The 16S rRNA gene sequencing identified AD26 as anArthrobacter sp. PCR assays indicated that AD26contained atrazine-degrading genes trzN and atzBC. The trzN gene of AD26 only differs from the trzN ofArthrobacter aurescens TC1by one base (A→T at 907) and one amino acid (Met→Leu at 303). The specific activity of trzN of AD26 in crude cell extract was0.28 U/mg, which was 1.2 times that of TC 1. This strain has shown faster growth and atrazine-degradation rates in atrazine-containingminimal media than two well characterized atrazine-degrading bacteria, Pseudomonas sp. ADP and Arthrobacter aurescens TC 1. Afterincubating for 48 h at 30℃, the OD600 of AD26 reached 2.6 compared with 1.33 of ADP. AD26 was capable of degrading 500 mg/Lof atrazine in minimal medium at 95% in 72 h, while the degradative rates by TC1 and ADP were only 90% and 86%, respectively. Abioremediation trial of contaminated soil has indicated that AD26 can degrade as high as 98% of atrazine contained in soil (300 mg/kg)after incubating for 20 d at 26℃, nominating this strain as a good candidate for use in bioremediation programs.

  4. The minotaur proteome

    DEFF Research Database (Denmark)

    Bunkenborg, Jakob; García, Guadalupe Espadas; Paz, Marcia Ivonne Peña;

    2010-01-01

    Cell culture is a fundamental tool in proteomics where mammalian cells are cultured in vitro using a growth medium often supplemented with 5-15% FBS. Contamination by bovine proteins is difficult to avoid because of adherence to the plastic vessel and the cultured cells. We have generated peptides...... from bovine serum using four sample preparation methods and analyzed the peptides by high mass accuracy LC-MS/MS. Distinguishing between bovine and human peptides is difficult because of a considerable overlap of identical tryptic peptide sequences. Pitfalls in interpretation, different database search...

  5. capA, a cspA-like gene that encodes a cold acclimation protein in the psychrotrophic bacterium Arthrobacter globiformis SI55.

    OpenAIRE

    Berger, F.; Normand, P.; Potier, P

    1997-01-01

    By use of Arthrobacter globiformis SI55, a psychrotrophic bacterium capable of growth between -5 and +32 degrees C, we cloned and sequenced capA, a gene homologous to cspA encoding the major cold shock protein in Escherichia coli. The deduced protein sequence has a high level of identity with the sequences of other CspA-related proteins from various sources, and no particular residue or domain that could be specific to cold-adapted microorganisms emerged. We show that CapA was produced very r...

  6. Proizvodnja β-fruktofuranozidaze s pomoću bakterije Arthrobacter sp. i primjena tog enzima u pretvorbi steviozida i rebaudiozida A

    OpenAIRE

    Xu, Zhong-Wei; Li, Yu-Qiang; Wang, Yong-Hua; Yang, Bo; Ning, Zheng-Xiang

    2009-01-01

    U proizvodnji enzima β-fruktofuranozidaze upotrijebljen je soj bakterije Arthrobacter sp. 10137. Kao najbolji izvori ugljika i dušika za proizvodnju enzima u pokusu na tresilici upotrijebljeni su saharoza i kukuruzni ekstrakt u omjeru 10:1. Maksimalna aktivnost β-fruktofuranozidaze od 26,69 U/mL postignuta je šaržnim uzgojem nakon 22,5 h. Sirovi enzim β-fruktofuranozidaza, dobiven ultrafiltracijom i frakcioniranjem s (NH4)2SO4, pročišćen je 7 puta, što je potvrđeno usporedbom specifične aktiv...

  7. Isolation and Characterization of IS1409, an Insertion Element of 4-Chlorobenzoate-Degrading Arthrobacter sp. Strain TM1, and Development of a System for Transposon Mutagenesis

    OpenAIRE

    Gartemann, Karl-Heinz; Eichenlaub, Rudolf

    2001-01-01

    A new insertion element of 1,449 bp with 25-bp perfect terminal repeats, designated IS1409, was identified in the chromosome of 4-chlorobenzoate-degrading Arthrobacter sp. strain TM1 NCIB12013. Upon insertion, IS1409 causes a target duplication of 8 bp. IS1409 carries only a single open reading frame of 435 codons encoding the transposase TnpA. Both TnpA and the overall organization of IS1409 are highly similar to those of some related insertion elements of the ISL3 group (J. Mahillon and M. ...

  8. Enhanced U(VI) release from autunite mineral by aerobic Arthrobacter sp. in the presence of aqueous bicarbonate

    Energy Technology Data Exchange (ETDEWEB)

    Katsenovich, Yelena; Carvajal, Denny A.; Wellman, Dawn M.; Lagos, Leonel

    2012-04-20

    The bacterial effect on U(VI) leaching from the autunite mineral (Ca[(UO{sub 2})(PO{sub 4})]{sub 2} {center_dot} 3H{sub 2}O) was investigated to provide a more comprehensive understanding into important microbiological processes affecting autunite stability within subsurface bicarbonate-bearing environments. Experiments were performed in a culture of G975 Arthrobacter oxydans strain, herein referred to as G975, a soil bacterium previously isolated from Hanford Site soil. 91 mg of autunite powder and 50 mL of phosphorus-limiting sterile media were amended with bicarbonate ranging between 1-10 mM in glass reactor bottles and inoculated with G975 strain after the dissolution of autunite was at steady state. SEM observations indicated G975 formed a biofilm on the autunite surface and penetrated the mineral cleavages. The mineral surface colonization by bacteria tended to increase concomitantly with bicarbonate concentrations. Additionally, a sterile cultureware with inserts was used in non-contact bioleaching experiments where autunite and bacteria cells were kept separately. The data suggest the G975 bacteria is able to enhance U(VI) leaching from autunite without the direct contact with the mineral. In the presence of bicarbonate, the damage to bacterial cells caused by U(VI) toxicity was reduced, yielding similar values for total organic carbon (TOC) degradation and cell density compared to U(VI)-free controls. The presence of active bacterial cells greatly enhanced the U(VI) bioleaching from autunite in bicarbonate-amended media.

  9. Proteomics in biomarker discovery and drug development

    OpenAIRE

    He, Q.; Chiu, J

    2003-01-01

    Proteomics is a research field aiming to characterize molecular and cellular dynamics in protein expression and function on a global level. The introduction of proteomics has been greatly broadening our view and accelerating our path in various medical researches. The most significant advantage of proteomics is its ability to examine a whole proteome or sub-proteome in a single experiment so that the protein alterations corresponding to a pathological or biochemical condition at a given time ...

  10. Proteomic Biomarkers of Atherosclerosis

    Directory of Open Access Journals (Sweden)

    Natacha Diaz-Prieto

    2008-01-01

    Full Text Available Biomarkers provide a powerful approach to understanding the spectrum of cardiovascular diseases. They have application in screening, diagnostic, prognostication, prediction of recurrences and monitoring of therapy. The “omics” tool are becoming very useful in the development of new biomarkers in cardiovascular diseases. Among them, proteomics is especially fitted to look for new proteins in health and disease and is playing a significant role in the development of new diagnostic tools in cardiovascular diagnosis and prognosis. This review provides an overview of progress in applying proteomics to atherosclerosis. First, we describe novel proteins identified analysing atherosclerotic plaques directly. Careful analysis of proteins within the atherosclerotic vascular tissue can provide a repertoire of proteins involved in vascular remodelling and atherogenesis. Second, we discuss recent data concerning proteins secreted by atherosclerotic plaques. The definition of the atheroma plaque secretome resides in that proteins secreted by arteries can be very good candidates of novel biomarkers. Finally we describe proteins that have been differentially expressed (versus controls by individual cells which constitute atheroma plaques (endothelial cells, vascular smooth muscle cells, macrophages and foam cells as well as by circulating cells (monocytes, platelets or novel biomarkers present in plasma.

  11. Proteomic Biomarkers of Atherosclerosis.

    Science.gov (United States)

    Vivanco, F; Padial, L R; Darde, V M; de la Cuesta, F; Alvarez-Llamas, G; Diaz-Prieto, Natacha; Barderas, M G

    2008-01-01

    SUMMARY: Biomarkers provide a powerful approach to understanding the spectrum of cardiovascular diseases. They have application in screening, diagnostic, prognostication, prediction of recurrences and monitoring of therapy. The "omics" tool are becoming very useful in the development of new biomarkers in cardiovascular diseases. Among them, proteomics is especially fitted to look for new proteins in health and disease and is playing a significant role in the development of new diagnostic tools in cardiovascular diagnosis and prognosis. This review provides an overview of progress in applying proteomics to atherosclerosis. First, we describe novel proteins identified analysing atherosclerotic plaques directly. Careful analysis of proteins within the atherosclerotic vascular tissue can provide a repertoire of proteins involved in vascular remodelling and atherogenesis. Second, we discuss recent data concerning proteins secreted by atherosclerotic plaques. The definition of the atheroma plaque secretome resides in that proteins secreted by arteries can be very good candidates of novel biomarkers. Finally we describe proteins that have been differentially expressed (versus controls) by individual cells which constitute atheroma plaques (endothelial cells, vascular smooth muscle cells, macrophages and foam cells) as well as by circulating cells (monocytes, platelets) or novel biomarkers present in plasma. PMID:19578499

  12. Characterization of the porcine synovial fluid proteome and a comparison to the plasma proteome

    Directory of Open Access Journals (Sweden)

    Tue Bjerg Bennike

    2015-12-01

    In addition, we analyzed the proteome of human plasma, and compared the proteomes to the obtained porcine synovial fluid proteome. The proteome of the two body fluids were found highly similar, underlining the detected plasma derived nature of many synovial fluid components. The healthy porcine synovial fluid proteomics data, human rheumatoid arthritis synovial fluid proteomics data used in the method optimization, human plasma proteomics data, and search results, have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD000935.

  13. Ovarian Cancer Proteomic, Phosphoproteomic, and Glycoproteomic Data Released - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) scientists have just released a comprehensive dataset of the proteomic analysis of high grade serous ovarian tumor samples,

  14. Analysis of Peanut Leaf Proteome

    DEFF Research Database (Denmark)

    Ramesh, R.; Suravajhala, Prashanth; Pechan, T.

    2010-01-01

    approach to define function of their associated genes. Proteome analysis linked to genome sequence information is critical for functional genomics. However, the available protein expression data is extremely inadequate. Proteome analysis of peanut leaf was conducted using two-dimensional gel....... Furthermore, the leaf proteome map will lead to development of protein markers for cultivar identification at seedling stage of the plant. Overall, this study will contribute to improve our understanding of plant genetics and metabolism, and overall assist in the selection and breeding programs geared toward...

  15. Proteomics in Pancreatic Cancer Research

    Science.gov (United States)

    Geng, Ruihui; Li, Zhaoshen; Li, Shude; Gao, Jun

    2011-01-01

    Pancreatic cancer is a highly aggressive malignancy with a poor prognosis and deeply affects the life of people. Therefore, the earlier diagnosis and better treatments are urgently needed. In recent years, the proteomic technologies are well established and growing rapidly and have been widely applied in clinical applications, especially in pancreatic cancer research. In this paper, we attempt to discuss the development of current proteomic technologies and the application of proteomics to the field of pancreatic cancer research. This will explore the potential perspective in revealing pathogenesis, making the diagnosis earlier and treatment. PMID:22084685

  16. Analyzing shotgun proteomic data with PatternLab for proteomics

    OpenAIRE

    Carvalho, Paulo C; Yates, John R.; Barbosa, Valmir C

    2010-01-01

    PatternLab for proteomics is a one-stop-shop computational environment for analyzing shotgun proteomic data. Its modules provide means to pinpoint proteins / peptides that are differentially expressed, those that are unique to a state, and can also cluster the ones that share similar expression profiles in time-course experiments as well as help in interpreting results according to Gene Ontology. PatternLab is user-friendly, simple, and provides a graphical user interface.

  17. Characterization of an exo-inulinase from Arthrobacter: a novel NaCl-tolerant exo-inulinase with high molecular mass.

    Science.gov (United States)

    Shen, Jidong; Zhang, Rui; Li, Junjun; Tang, Xianghua; Li, Ruixian; Wang, Min; Huang, Zunxi; Zhou, Junpei

    2015-01-01

    A glycoside hydrolase family 32 exo-inulinase gene was cloned from Arthrobacter sp. HJ7 isolated from saline soil located in Heijing town. The gene encodes an 892-residue polypeptide with a calculated mass of 95.1 kDa and a high total frequency of amino acid residues G, A, and V (30.0%). Escherichia coli BL21 (DE3) cells were used as hosts to express the exo-inulinase gene. The recombinant exo-inulinase (rInuAHJ7) showed an apparently maximal activity at pH 5.0-5.5 and 40-45°C. The addition of 1.0 and 10.0 mM Zn(2+) and Pb(2+) had little or no effect on the enzyme activity. rInuAHJ7 exhibited good salt tolerance, retaining more than 98% inulinase activity at a concentration of 3.0%-20.0% (w/v) NaCl. Fructose was the main product of inulin, levan, and Jerusalem artichoke tubers hydrolyzed by the enzyme. The present study is the first to report the identification and characterization of an Arthrobacter sp exo-inulinase showing a high molecular mass of 95.1 kDa and NaCl tolerance. These results suggest that the exo-inulinase might be an alternative material for potential applications in processing seafood and other foods with high saline contents, such as marine algae, pickles, and sauces. PMID:25695343

  18. Evaluation of chromate reductase activity in the cell-free culture filtrate of Arthrobacter sp. SUK 1201 isolated from chromite mine overburden.

    Science.gov (United States)

    Dey, Satarupa; Paul, A K

    2016-08-01

    Arthrobacter sp. SUK 1201, a chromate resistant and reducing bacterium isolated from chromite mine overburden of Sukinda valley, Odisha, India has been evaluated for its hexavalent chromium [Cr(VI)] reduction potential using cell-free culture filtrate as extracellular chromate reductase enzyme. Production of the enzyme was enhanced in presence of Cr(VI) and its reducing efficiency was increased with increasing concentration of Cr(VI). The Michaelis-Menten constant (Km) and the maximum specific velocity (Vmax) of the extracellular Cr(VI) reductase were calculated to be 54.03 μM Cr(VI) and 5.803 U mg(-1) of protein respectively showing high affinity towards Cr(VI). The reducing activity of the enzyme was maximum at pH 6.5-7.5 and at a temperature of 35 °C and was dependent on NADH. The enzyme was tolerant to different metals such as Mn(II), Mg(II) and Fe(III) and was able to reduce Cr(VI) present in chromite mine seepage. These findings suggest that the extracellular chromate reductase of Arthrobacter sp. SUK 1201 has a great promise for use in Cr(VI) detoxification under different environmental conditions, particularly in the mining waste water treatment systems. PMID:27176938

  19. The human proteomics initiative (HPI).

    Science.gov (United States)

    O'Donovan, C; Apweiler, R; Bairoch, A

    2001-05-01

    The availability of the human genome sequence has enabled the exploration and exploitation of the human genome and proteome to begin. Research has now focussed on the annotation of the genome and in particular of the proteome. With expert annotation extracted from the literature by biologists as the foundation, it has been possible to expand into the areas of data mining and automatic annotation. With further development and integration of pattern recognition methods and the application of alignments clustering, proteome analysis can now be provided in a meaningful way. These various approaches have been integrated to attach, extract and combine as much relevant information as possible to the proteome. This resource should be valuable to users from both research and industry. PMID:11301130

  20. Spectral library searching in proteomics.

    Science.gov (United States)

    Griss, Johannes

    2016-03-01

    Spectral library searching has become a mature method to identify tandem mass spectra in proteomics data analysis. This review provides a comprehensive overview of available spectral library search engines and highlights their distinct features. Additionally, resources providing spectral libraries are summarized and tools presented that extend experimental spectral libraries by simulating spectra. Finally, spectrum clustering algorithms are discussed that utilize the same spectrum-to-spectrum matching algorithms as spectral library search engines and allow novel methods to analyse proteomics data. PMID:26616598

  1. Perfluorooctanoic Acid for Shotgun Proteomics

    OpenAIRE

    Kadiyala, Chandra Sekhar Rao; Tomechko, Sara E.; Miyagi, Masaru

    2010-01-01

    Here, we describe the novel use of a volatile surfactant, perfluorooctanoic acid (PFOA), for shotgun proteomics. PFOA was found to solubilize membrane proteins as effectively as sodium dodecyl sulfate (SDS). PFOA concentrations up to 0.5% (w/v) did not significantly inhibit trypsin activity. The unique features of PFOA allowed us to develop a single-tube shotgun proteomics method that used all volatile chemicals that could easily be removed by evaporation prior to mass spectrometry analysis. ...

  2. The Chordate Proteome History Database

    OpenAIRE

    Anthony Levasseur; Julien Paganini; Jacques Dainat; Thompson, Julie D; Olivier Poch; Pierre Pontarotti; Philippe Gouret

    2012-01-01

    The chordate proteome history database (http://ioda.univ-provence.fr) comprises some 20,000 evolutionary analyses of proteins from chordate species. Our main objective was to characterize and study the evolutionary histories of the chordate proteome, and in particular to detect genomic events and automatic functional searches. Firstly, phylogenetic analyses based on high quality multiple sequence alignments and a robust phylogenetic pipeline were performed for the whole protein and for each i...

  3. Quality Assessment for Clinical Proteomics

    OpenAIRE

    Tabb, David L.

    2012-01-01

    Proteomics has emerged from the labs of technologists to enter widespread application in clinical contexts. This transition, however, has been hindered by overstated early claims of accuracy, concerns about reproducibility, and the challenges of handling batch effects properly. New efforts have produced sets of performance metrics and measurements of variability that establish sound expectations for experiments in clinical proteomics. As researchers begin incorporating these metrics in a qual...

  4. Plant biology through quantitative proteomics

    OpenAIRE

    Bygdell, Joakim

    2013-01-01

    Over the last decade the field of mass spectrometry based proteomics has advanced from qualitative, analyses leading to publications revolving around lists of identified proteins and peptides, to addressing more biologically relevant issues requiring measurement of the abundance of identified proteins and hence quantitive mass spectrometry. The work described in this thesis addresses problems with quantitive proteomics in plant sciences, particularly complications caused by the complexity...

  5. Proteomics of human mitochondria

    DEFF Research Database (Denmark)

    Palmfeldt, Johan; Bross, Peter

    2016-01-01

    Proteomics have passed through a tremendous development in the recent years by the development of ever more sensitive, fast and precise mass spectrometry methods. The dramatically increased research in the biology of mitochondria and their prominent involvement in all kinds of diseases and ageing...... sensitivity of mass spectrometry technology aids in lowering this hurdle and new approaches like generation of induced pluripotent cells from somatic cells allow to produce patient-specific cellular disease models with great potential. We describe which human sample types are accessible, review the status of...... the catalog of human mitochondrial proteins and discuss proteins with dual localization in mitochondria and other cellular compartments. We describe the status and developments of pertinent mass spectrometric strategies, and the use of databases and bioinformatics. Using selected illustrative examples...

  6. The Succinated Proteome

    Energy Technology Data Exchange (ETDEWEB)

    Merkley, Eric D.; Metz, Thomas O.; Smith, Richard D.; Baynes, John; Frizell, Norma

    2014-03-30

    Succination is a chemical modification of cysteine in protein by the Krebs cycle intermediate, fumarate, yielding S-(2-succino)cysteine (2SC). Intracellular fumarate concentration and succination of proteins are increased by hyperpolarization of the inner mitochondrial membrane, in concert with mitochondrial, endoplasmic reticulum (ER) and oxidative stress in adipocytes grown in high glucose medium and in adipose tissue in obesity and diabetes. Increased succination of proteins is also detected in the kidney of a fumarase conditional knock-out mouse which develops renal tumors. Keap1, the gatekeeper of the antioxidant response, was identified as a major succinated protein in renal cancer cells, suggesting that succination may play a role in activation of the antioxidant response. A wide range of proteins is subject to succination, including enzymes, adipokines, cytoskeletal proteins and ER chaperones with functional cysteine residues. There is also significant overlap between succinated and glutathionylated proteins, and with proteins containing cysteine residues that are readily oxidized to the sulfenic (cysteic) acid. Succination of adipocyte proteins is inhibited by uncouplers, which discharge the mitochondrial membrane potential (Δψm) and by ER stress inhibitors. 2SC serves as a biomarker of mitochondrial stress or dysfunction in chronic diseases, such as obesity, diabetes and cancer, and recent studies suggest that succination is a mechanistic link between mitochondrial dysfunction, oxidative and ER stress, and cellular progression toward apoptosis. In this article, we review the history of the succinated proteome and the challenges associated with measuring this non-enzymatic post-translational modification of proteins by proteomics approaches.

  7. PLASMID-ENCODED PHTHALATE CATABOLIC PATHWAY IN ARTHROBACTER KEYSERI 12B: BIOTRANSFORMATIONS OF 2-SUBSTITUTED BENZOATES AND THEIR USE IN CLONING AND CHARACTERIZATION OF PHTHALATE CATABOLISM GENES AND GENE PRODUCTS

    Science.gov (United States)

    Several 2-substituted benzoates (including 2-trifluoromethyl-, 2-chloro-, 2-bromo-, 2-iodo-, 2-nitro-, 2-methoxy-, and 2-acetyl-benzoates) were converted by phthalate-grown Arthrobacter keyseri 12B to the corresponding 2-substituted 3,4-dihydroxybenzoates (protocatechuates)...

  8. Structural proteomics by NMR spectroscopy.

    Science.gov (United States)

    Shin, Joon; Lee, Woonghee; Lee, Weontae

    2008-08-01

    Structural proteomics is one of the powerful research areas in the postgenomic era, elucidating structure-function relationships of uncharacterized gene products based on the 3D protein structure. It proposes biochemical and cellular functions of unannotated proteins and thereby identifies potential drug design and protein engineering targets. Recently, a number of pioneering groups in structural proteomics research have achieved proof of structural proteomic theory by predicting the 3D structures of hypothetical proteins that successfully identified the biological functions of those proteins. The pioneering groups made use of a number of techniques, including NMR spectroscopy, which has been applied successfully to structural proteomics studies over the past 10 years. In addition, advances in hardware design, data acquisition methods, sample preparation and automation of data analysis have been developed and successfully applied to high-throughput structure determination techniques. These efforts ensure that NMR spectroscopy will become an important methodology for performing structural proteomics research on a genomic scale. NMR-based structural proteomics together with x-ray crystallography will provide a comprehensive structural database to predict the basic biological functions of hypothetical proteins identified by the genome projects. PMID:18761469

  9. Low temperature reduction of hexavalent chromium by a microbial enrichment consortium and a novel strain of Arthrobacter aurescens

    Directory of Open Access Journals (Sweden)

    Thompson Vicki S

    2006-01-01

    Full Text Available Abstract Background Chromium is a transition metal most commonly found in the environment in its trivalent [Cr(III] and hexavalent [Cr(VI] forms. The EPA maximum total chromium contaminant level for drinking water is 0.1 mg/l (0.1 ppm. Many water sources, especially underground sources, are at low temperatures (less than or equal to 15 Centigrade year round. It is important to evaluate the possibility of microbial remediation of Cr(VI contamination using microorganisms adapted to these low temperatures (psychrophiles. Results Core samples obtained from a Cr(VI contaminated aquifer at the Hanford facility in Washington were enriched in Vogel Bonner medium at 10 Centigrade with 0, 25, 50, 100, 200, 400 and 1000 mg/l Cr(VI. The extent of Cr(VI reduction was evaluated using the diphenyl carbazide assay. Resistance to Cr(VI up to and including 1000 mg/l Cr(VI was observed in the consortium experiments. Reduction was slow or not observed at and above 100 mg/l Cr(VI using the enrichment consortium. Average time to complete reduction of Cr(VI in the 30 and 60 mg/l Cr(VI cultures of the consortium was 8 and 17 days, respectively at 10 Centigrade. Lyophilized consortium cells did not demonstrate adsorption of Cr(VI over a 24 hour period. Successful isolation of a Cr(VI reducing organism (designated P4 from the consortium was confirmed by 16S rDNA amplification and sequencing. Average time to complete reduction of Cr(VI at 10 Centigrade in the 25 and 50 mg/l Cr(VI cultures of the isolate P4 was 3 and 5 days, respectively. The 16S rDNA sequence from isolate P4 identified this organism as a strain of Arthrobacter aurescens, a species that has not previously been shown to be capable of low temperature Cr(VI reduction. Conclusion A. aurescens, indigenous to the subsurface, has the potential to be a predominant metal reducer in enhanced, in situ subsurface bioremediation efforts involving Cr(VI and possibly other heavy metals and radionuclides.

  10. Increased iron-stress resilience of maize through inoculation of siderophore-producing Arthrobacter globiformis from mine.

    Science.gov (United States)

    Sharma, Meenakshi; Mishra, Vandana; Rau, Nupur; Sharma, Radhey Shyam

    2016-07-01

    Iron deficiency is common among graminaceous crops. Ecologically successful wild grasses from iron-limiting habitats are likely to harbour bacteria which secrete efficient high-affinity iron-chelating molecules (siderophores) to solubilize and mobilize iron. Such siderophore-producing rhizobacteria may increase the iron-stress resilience of graminaceous crops. Considering this, 51 rhizobacterial isolates of Dichanthium annulatum from iron-limiting abandoned mine (∼84% biologically unavailable iron) were purified and tested for siderophore production; and efficacy of Arthrobacter globiformis inoculation to increase iron-stress resilience of maize and wheat was also evaluated. 16S rRNA sequence analyses demonstrated that siderophore-producing bacteria were taxonomically diverse (seven genera, nineteen species). Among these, Gram-positive Bacillus (eleven species) was prevalent (76.92%). A. globiformis, a commonly found rhizobacterium of graminaceous crops was investigated in detail. Its siderophore has high iron-chelation capacity (ICC: 13.0 ± 2.4 μM) and effectively dissolutes diverse iron-complexes (FeCl3 : 256.13 ± 26.56 μM/ml; Fe2 O3 red: 84.3 ± 4.74 μM/ml; mine spoil: 123.84 ± 4.38 μM/ml). Siderophore production (ICC) of A. globiformis BGDa404 also varied with supplementation of different iron complexes. In plant bioassay with iron-deficiency sensitive species maize, A. globiformis inoculation triggered stress-associated traits (peroxidase and proline) in roots, enhanced plant biomass, uptake of iron and phosphate, and protein and chlorophyll contents. However, in iron deficiency tolerant species wheat, growth improvement was marginal. The present study illustrates: (i) rhizosphere of D. annulatum colonizing abandoned mine as a "hotspot" of siderophore-producing bacteria; and (ii) potential of A. globiformis BGDa404 inoculation to increase iron-stress resilience in maize. A. globiformis BGDa404 has the potential to develop as

  11. Cell death proteomics database: consolidating proteomics data on cell death.

    Science.gov (United States)

    Arntzen, Magnus Ø; Bull, Vibeke H; Thiede, Bernd

    2013-05-01

    Programmed cell death is a ubiquitous process of utmost importance for the development and maintenance of multicellular organisms. More than 10 different types of programmed cell death forms have been discovered. Several proteomics analyses have been performed to gain insight in proteins involved in the different forms of programmed cell death. To consolidate these studies, we have developed the cell death proteomics (CDP) database, which comprehends data from apoptosis, autophagy, cytotoxic granule-mediated cell death, excitotoxicity, mitotic catastrophe, paraptosis, pyroptosis, and Wallerian degeneration. The CDP database is available as a web-based database to compare protein identifications and quantitative information across different experimental setups. The proteomics data of 73 publications were integrated and unified with protein annotations from UniProt-KB and gene ontology (GO). Currently, more than 6,500 records of more than 3,700 proteins are included in the CDP. Comparing apoptosis and autophagy using overrepresentation analysis of GO terms, the majority of enriched processes were found in both, but also some clear differences were perceived. Furthermore, the analysis revealed differences and similarities of the proteome between autophagosomal and overall autophagy. The CDP database represents a useful tool to consolidate data from proteome analyses of programmed cell death and is available at http://celldeathproteomics.uio.no. PMID:23537399

  12. Proteomics in evolutionary ecology.

    Science.gov (United States)

    Baer, B; Millar, A H

    2016-03-01

    Evolutionary ecologists are traditionally gene-focused, as genes propagate phenotypic traits across generations and mutations and recombination in the DNA generate genetic diversity required for evolutionary processes. As a consequence, the inheritance of changed DNA provides a molecular explanation for the functional changes associated with natural selection. A direct focus on proteins on the other hand, the actual molecular agents responsible for the expression of a phenotypic trait, receives far less interest from ecologists and evolutionary biologists. This is partially due to the central dogma of molecular biology that appears to define proteins as the 'dead-end of molecular information flow' as well as technical limitations in identifying and studying proteins and their diversity in the field and in many of the more exotic genera often favored in ecological studies. Here we provide an overview of a newly forming field of research that we refer to as 'Evolutionary Proteomics'. We point out that the origins of cellular function are related to the properties of polypeptide and RNA and their interactions with the environment, rather than DNA descent, and that the critical role of horizontal gene transfer in evolution is more about coopting new proteins to impact cellular processes than it is about modifying gene function. Furthermore, post-transcriptional and post-translational processes generate a remarkable diversity of mature proteins from a single gene, and the properties of these mature proteins can also influence inheritance through genetic and perhaps epigenetic mechanisms. The influence of post-transcriptional diversification on evolutionary processes could provide a novel mechanistic underpinning for elements of rapid, directed evolutionary changes and adaptations as observed for a variety of evolutionary processes. Modern state-of the art technologies based on mass spectrometry are now available to identify and quantify peptides, proteins, protein

  13. Proteomics Study of Cotton Fiber Cells

    Institute of Scientific and Technical Information of China (English)

    LIU Jin-yuan

    2008-01-01

    @@ A comparative proteomic analysis was applied to explore the mechanism of fiber cell development in cotton.Initially,an efficient protein preparation method was established for proteomic analysis of developing cotton fibers by two-dimensional gel electrophoresis,and a microwave enhanced ink staining technique also was created for fast and sensitive protein quantification in proteomic studies.

  14. Proteomic Biomarkers for Spontaneous Preterm Birth

    DEFF Research Database (Denmark)

    Kacerovsky, Marian; Lenco, Juraj; Musilova, Ivana;

    2014-01-01

    This review aimed to identify, synthesize, and analyze the findings of studies on proteomic biomarkers for spontaneous preterm birth (PTB). Three electronic databases (Medline, Embase, and Scopus) were searched for studies in any language reporting the use of proteomic biomarkers for PTB published...... literature, there are no specific proteomic biomarkers capable of accurately predicting PTB....

  15. Proteomic insights into floral biology.

    Science.gov (United States)

    Li, Xiaobai; Jackson, Aaron; Xie, Ming; Wu, Dianxing; Tsai, Wen-Chieh; Zhang, Sheng

    2016-08-01

    The flower is the most important biological structure for ensuring angiosperms reproductive success. Not only does the flower contain critical reproductive organs, but the wide variation in morphology, color, and scent has evolved to entice specialized pollinators, and arguably mankind in many cases, to ensure the successful propagation of its species. Recent proteomic approaches have identified protein candidates related to these flower traits, which has shed light on a number of previously unknown mechanisms underlying these traits. This review article provides a comprehensive overview of the latest advances in proteomic research in floral biology according to the order of flower structure, from corolla to male and female reproductive organs. It summarizes mainstream proteomic methods for plant research and recent improvements on two dimensional gel electrophoresis and gel-free workflows for both peptide level and protein level analysis. The recent advances in sequencing technologies provide a new paradigm for the ever-increasing genome and transcriptome information on many organisms. It is now possible to integrate genomic and transcriptomic data with proteomic results for large-scale protein characterization, so that a global understanding of the complex molecular networks in flower biology can be readily achieved. This article is part of a Special Issue entitled: Plant Proteomics - a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock. PMID:26945514

  16. Platelet proteomics in cardiovascular diseases

    Directory of Open Access Journals (Sweden)

    Paula Vélez

    2015-06-01

    Full Text Available In recent years, platelet proteomics has been applied successfully to the study of cardiovascular diseases (CVDs. It is very well known that platelets play a pivotal role in the pathophysiological mechanisms underlying many CVDs, especially acute coronary syndromes (ACSs, since they are implied in thrombus formation after atheroma plaque rupture. This is the reason why molecules involved in platelet activation and aggregation are primary targets for treatment of ACSs. Many efforts are aimed at finding drugs that inhibit platelet activation; however it is difficult to separate the therapeutic benefits from harmful effects because pathological and physiological functions of platelets are due to the same mechanisms. Given that platelets lack a nucleus, proteomics is regarded as an ideal method to approach their biochemistry. Current platelet proteomic studies are focusing on the identification of platelet molecular and functional changes in normal and pathological states, enriching the comprehension of platelet biological function, and screening for new biomarkers and antiplatelet agents. In the present article, we introduce the reader to platelet biology and function, and revise recent advances in platelet proteomics applied to the study of CVDs, including a special emphasis on sample preparation requirements for proteome analysis of platelet clinical samples.

  17. Proteomic approaches to bacterial differentiation

    Energy Technology Data Exchange (ETDEWEB)

    Norbeck, Angela D.; Callister, Stephen J.; Monroe, Matthew E.; Jaitly, Navdeep; Elias, Dwayne A.; Lipton, Mary S.; Smith, Richard D.

    2006-12-01

    While genomic approaches have been applied for the detection and identification of individual bacteria within microbial communities, analogous proteomics approaches have been effectively precluded due to their inherent complexity. An in silico assessment of peptides that could potentially be present in the proteomes of artificial simple and complex communities was performed to evaluate the effect of proteome complexity on species detection. A mass spectrometry-based proteomics approach was employed to experimentally detect and validate the predicted tryptic peptides initially identified as distinctive within the simple community. An assessment of peptide distinctiveness and the potential for mapping to a particular bacterium within a community was made throughout each step of the study. A second in silico assessment of peptide distinctiveness for a complex community of 25 microorganisms was conducted to investigate the levels of instrumental performance that would be required to experimentally detect these peptides, as well as how performance varied with complexity (e.g., the number of different microorganisms). The experimental data for a simple community showed that it is feasible to predict, observe, and to quantify distinctive peptides from one organism in the presence of at least a 100-fold greater abundance of another, thus yielding putative markers for identifying a bacterium of interest. This work represents a first step towards quantitative proteomic characterization of complex microbial communities and the possible development of community wide markers of perturbations to such communities.

  18. Proteome of Hydra Nematocyst*

    Science.gov (United States)

    Balasubramanian, Prakash G.; Beckmann, Anna; Warnken, Uwe; Schnölzer, Martina; Schüler, Andreas; Bornberg-Bauer, Erich; Holstein, Thomas W.; Özbek, Suat

    2012-01-01

    Stinging cells or nematocytes of jellyfish and other cnidarians represent one of the most poisonous and sophisticated cellular inventions in animal evolution. This ancient cell type is unique in containing a giant secretory vesicle derived from the Golgi apparatus. The organelle structure within the vesicle comprises an elastically stretched capsule (nematocyst) to which a long tubule is attached. During exocytosis, the barbed part of the tubule is accelerated with >5 million g in <700 ns, enabling a harpoon-like discharge (Nüchter, T., Benoit, M., Engel, U., Ozbek, S., and Holstein, T. W. (2006) Curr. Biol. 16, R316–R318). Hitherto, the molecular components responsible for the organelle's biomechanical properties were largely unknown. Here, we describe the proteome of nematocysts from the freshwater polyp Hydra magnipapillata. Our analysis revealed an unexpectedly complex secretome of 410 proteins with venomous and lytic but also adhesive or fibrous properties. In particular, the insoluble fraction of the nematocyst represents a functional extracellular matrix structure of collagenous and elastic nature. This finding suggests an evolutionary scenario in which exocytic vesicles harboring a venomous secretome assembled a sophisticated predatory structure from extracellular matrix motif proteins. PMID:22291027

  19. Structural Proteomics of Herpesviruses.

    Science.gov (United States)

    Leroy, Baptiste; Gillet, Laurent; Vanderplasschen, Alain; Wattiez, Ruddy

    2016-01-01

    Herpesviruses are highly prevalent viruses associated with numerous pathologies both in animal and human populations. Until now, most of the strategies used to prevent or to cure these infections have been unsuccessful because these viruses have developed numerous immune evasion mechanisms. Therefore, a better understanding of their complex lifecycle is needed. In particular, while the genome of numerous herpesviruses has been sequenced, the exact composition of virions remains unknown for most of them. Mass spectrometry has recently emerged as a central method and has permitted fundamental discoveries in virology. Here, we review mass spectrometry-based approaches that have recently allowed a better understanding of the composition of the herpesvirus virion. In particular, we describe strategies commonly used for proper sample preparation and fractionation to allow protein localization inside the particle but also to avoid contamination by nonstructural proteins. A collection of other important data regarding post-translational modifications or the relative abundance of structural proteins is also described. This review also discusses the poorly studied importance of host proteins in herpesvirus structural proteins and the necessity to develop a quantitative workflow to better understand the dynamics of the structural proteome. In the future, we hope that this collaborative effort will assist in the development of new strategies to fight these infections. PMID:26907323

  20. Production of β -cyclodextrin from pH and thermo stable Cyclodextrin Glycosyl Transferase, obtained from Arthrobacter mysorens and its evaluation as a drug carrier for Irbesartan.

    Science.gov (United States)

    Rajesh, Y; Narayanan, K; Reddy, M Sreenivasa; Bhaskar, Vijaya K; Shenoy, G Gautham; Subrahmanyam, V M; Rao, J Venkata

    2015-01-01

    Cyclodextrins (CDs) are carrier molecules produced by cyclization of α-1,4-glucans by Cyclodextrin Glycosyl Transferase (CGTase). These torus shaped molecules have hydrophobic cavity and hydrophilic shell making them useful in pharmaceutical, food, textile, pesticide and cosmetic industries. In this study, culture conditions for the production of CGTase by organism belonging to Arthrobacter genus obtained from a paddy field soil were optimized by single parameter mode. Soluble starch, yeast extract and magnesium sulphate played an important role in CGTase production. Percentage increase in CGTase yield under optimized conditions was 396.77%. The enzyme precipitated by 60% ammonium sulphate was purified using DEAE-sepharose. The molecular weight of the purified protein as determined by SDS-PAGE was 75 kDa. Purified CGTase was thermostable and stable over a wide pH range. Dissolution studies on β -cyclodextrin-Irbesartan complex revealed that β -CDs formed were useful in preparing immediate release oral dosage forms. PMID:25901452

  1. Monitoring Arthrobacter protophormiae RKJ100 in a 'tag and chase' method during p-nitrophenol bio-remediation in soil microcosms.

    Science.gov (United States)

    Pandey, Gunjan; Pandey, Janmejay; Jain, Rakesh K

    2006-05-01

    Monitoring of micro-organisms released deliberately into the environment is essential to assess their movement during the bio-remediation process. During the last few years, DNA-based genetic methods have emerged as the preferred method for such monitoring; however, their use is restricted in cases where organisms used for bio-remediation are not well characterized or where the public domain databases do not provide sufficient information regarding their sequence. For monitoring of such micro-organisms, alternate approaches have to be undertaken. In this study, we have specifically monitored a p-nitrophenol (PNP)-degrading organism, Arthrobacter protophormiae RKJ100, using molecular methods during PNP degradation in soil microcosm. Cells were tagged with a transposon-based foreign DNA sequence prior to their introduction into PNP-contaminated microcosms. Later, this artificially introduced DNA sequence was PCR-amplified to distinguish the bio-augmented organism from the indigenous microflora during PNP bio-remediation. PMID:16205921

  2. A new cold-adapted β-D-galactosidase from the Antarctic Arthrobacter sp. 32c – gene cloning, overexpression, purification and properties

    Directory of Open Access Journals (Sweden)

    Kur Józef

    2009-07-01

    Full Text Available Abstract Background The development of a new cold-active β-D-galactosidases and microorganisms that efficiently ferment lactose is of high biotechnological interest, particularly for lactose removal in milk and dairy products at low temperatures and for cheese whey bioremediation processes with simultaneous bio-ethanol production. Results In this article, we present a new β-D-galactosidase as a candidate to be applied in the above mentioned biotechnological processes. The gene encoding this β-D-galactosidase has been isolated from the genomic DNA library of Antarctic bacterium Arthrobacter sp. 32c, sequenced, cloned, expressed in Escherichia coli and Pichia pastoris, purified and characterized. 27 mg of β-D-galactosidase was purified from 1 L of culture with the use of an intracellular E. coli expression system. The protein was also produced extracellularly by P. pastoris in high amounts giving approximately 137 mg and 97 mg of purified enzyme from 1 L of P. pastoris culture for the AOX1 and a constitutive system, respectively. The enzyme was purified to electrophoretic homogeneity by using either one step- or a fast two step- procedure including protein precipitation and affinity chromatography. The enzyme was found to be active as a homotrimeric protein consisting of 695 amino acid residues in each monomer. Although, the maximum activity of the enzyme was determined at pH 6.5 and 50°C, 60% of the maximum activity of the enzyme was determined at 25°C and 15% of the maximum activity was detected at 0°C. Conclusion The properties of Arthrobacter sp. 32cβ-D-galactosidase suggest that this enzyme could be useful for low-cost, industrial conversion of lactose into galactose and glucose in milk products and could be an interesting alternative for the production of ethanol from lactose-based feedstock.

  3. Advances of Proteomic Sciences in Dentistry

    Science.gov (United States)

    Khurshid, Zohaib; Zohaib, Sana; Najeeb, Shariq; Zafar, Muhammad Sohail; Rehman, Rabia; Rehman, Ihtesham Ur

    2016-01-01

    Applications of proteomics tools revolutionized various biomedical disciplines such as genetics, molecular biology, medicine, and dentistry. The aim of this review is to highlight the major milestones in proteomics in dentistry during the last fifteen years. Human oral cavity contains hard and soft tissues and various biofluids including saliva and crevicular fluid. Proteomics has brought revolution in dentistry by helping in the early diagnosis of various diseases identified by the detection of numerous biomarkers present in the oral fluids. This paper covers the role of proteomics tools for the analysis of oral tissues. In addition, dental materials proteomics and their future directions are discussed. PMID:27187379

  4. Proteomic classification of breast cancer.

    LENUS (Irish Health Repository)

    Kamel, Dalia

    2012-11-01

    Being a significant health problem that affects patients in various age groups, breast cancer has been extensively studied to date. Recently, molecular breast cancer classification has advanced significantly with the availability of genomic profiling technologies. Proteomic technologies have also advanced from traditional protein assays including enzyme-linked immunosorbent assay, immunoblotting and immunohistochemistry to more comprehensive approaches including mass spectrometry and reverse phase protein lysate arrays (RPPA). The purpose of this manuscript is to review the current protein markers that influence breast cancer prediction and prognosis and to focus on novel advances in proteomic classification of breast cancer.

  5. Proteomics Funding Opportunity - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    To expand the understanding of how cells sense and respond to changes in their physical environment, the NCI is seeking to perform proteomic assays on the panel of cell lines grown on a variety of substrates. These assays will provide insight into changes in protein levels or phosphorylation changes that could reflect the activity of mechano-transduction pathways.

  6. Database independent proteomics analysis of the ostrich and human proteome.

    NARCIS (Netherlands)

    Altelaar, A.F.; Navarro, D.; Boekhorst, J.; Breukelen, B. van; Snel, B.; Mohammed, S.; Heck, A.J.R. van

    2012-01-01

    Mass spectrometry (MS)-based proteome analysis relies heavily on the presence of complete protein databases. Such a strategy is extremely powerful, albeit not adequate in the analysis of unpredicted postgenome events, such as posttranslational modifications, which exponentially increase the search s

  7. Effects of Cd (Ⅱ) on the physico-biochemical behaviors of Arthrobacter sp.and Bacillus sp.%镉胁迫对节杆菌(Arthrobacter sp.)和芽孢杆菌(Bacillus sp.)生理生化特性的影响

    Institute of Scientific and Technical Information of China (English)

    杜瑞英

    2012-01-01

    将节杆菌和芽孢杆菌分别暴露于不同质量比的镉溶液中,进行不同暴露时间的急性毒性试验.结果表明,20 mg/kg的Cd(Ⅱ)处理会使节杆菌中还原型谷胱甘肽(GSH)质量浓度显著降低,细胞膜脂质过氧化产物——硫代巴比妥酸活性物质(TBARS)浓度显著升高;0.2mg/kg的Cd(Ⅱ)处理会使芽孢杆菌中GSH质量浓度、过氧化氢酶(CAT)活性显著降低.节杆菌的可溶性蛋白、可溶性糖质量浓度随暴露时间延长而减少,GSH质量浓度、CAT和超氧化物歧化酶(SOD)活性随暴露时间延长而增加,TBARS浓度呈先减后增的变化趋势;芽孢杆菌的可溶性蛋白质量浓度、CAT活性和TBARS浓度呈先增后减的变化趋势,可溶性糖、GSH质量浓度和SOD活性呈先减后增的变化趋势.镉处理对节杆菌和芽孢杆菌具有一定的胁迫作用,两种菌通过启动不同的抗性系统来抵抗外界胁迫.%This paper is engaged in the study of the effects of Cd(II) on the physico-biochemical behaviors of Arthrobacter sp. through tox-icity testing. The toxicity test has been arranged by putting the an-tioxidant system of Arthrobacter sp. and Bacillus sp. under the exposure to different concentrations of Cd(II) for different lengths of testing time. The results of our testing show that Cd(II) has a strong impact on the antioxidant system of Arthrobacter sp. and Bacillus sp. . However, it is possible to reduce GSH content and increase TBARS content of Arthrobacter sp. significantly by letting Cd(II) treated with 20 mg/kg. Our testing proves that it is possible to reduce the GSH content and CAT activity of Bacillus sp. significantly by treating Cd(II) with 0.2 mg/kg, for the Arthrobacter sp. , the soluble protein and soluble sugar content can be reduced through prolonging the time of exposure. On the contrary, it is also possible to increase the GSH content and the CAT & SOD activity by means of prolonging the exposure, with the TBARS content

  8. Proteomics of foodborne bacterial pathogens

    Science.gov (United States)

    This chapter focuses on recent research on foodborne bacterial pathogens that use mass spectrometry-based proteomic techniques as well as protein microarrays. Mass spectrometry ionization techniques (e.g. electrospray ionization and matrix-assisted laser desorption/ionization), analyzers (e.g. ion ...

  9. The potato tuber mitochondrial proteome

    DEFF Research Database (Denmark)

    Møller, Ian Max; Salvato, Fernanda; Havelund, Jesper;

    ) and in silico-predicted mitochondrial proteins (2000-3000). Thus, before starting to look for oxidized peptides, we wanted to expand the current compendium of plant mitochondrial proteins while obtaining what could be termed the "baseline proteome" from our model organelle, the potato tuber...

  10. Quantitative proteomics of Chlorobaculum tepidum

    DEFF Research Database (Denmark)

    Falkenby, Lasse Gaarde; Szymanska, Monika; Holkenbrink, Carina;

    2011-01-01

    Chlorobaculum (Cba.) tepidum is a green sulfur bacterium that oxidizes sulfide, elemental sulfur, and thiosulfate for photosynthetic growth. To gain insight into the sulfur metabolism, the proteome of Cba. tepidum cells sampled under different growth conditions has been quantified using a rapid gel...

  11. Proteomic interrogation of human chromatin.

    Directory of Open Access Journals (Sweden)

    Mariana P Torrente

    Full Text Available Chromatin proteins provide a scaffold for DNA packaging and a basis for epigenetic regulation and genomic maintenance. Despite understanding its functional roles, mapping the chromatin proteome (i.e. the "Chromatome" is still a continuing process. Here, we assess the biological specificity and proteomic extent of three distinct chromatin preparations by identifying proteins in selected chromatin-enriched fractions using mass spectrometry-based proteomics. These experiments allowed us to produce a chromatin catalog, including several proteins ranging from highly abundant histone proteins to less abundant members of different chromatin machinery complexes. Using a Normalized Spectral Abundance Factor approach, we quantified relative abundances of the proteins across the chromatin enriched fractions giving a glimpse into their chromosomal abundance. The large-scale data sets also allowed for the discovery of a variety of novel post-translational modifications on the identified chromatin proteins. With these comparisons, we find one of the probed methods to be qualitatively superior in specificity for chromatin proteins, but inferior in proteomic extent, evidencing a compromise that must be made between biological specificity and broadness of characterization. Additionally, we attempt to identify proteins in eu- and heterochromatin, verifying the enrichments by characterizing the post-translational modifications detected on histone proteins from these chromatin regions. In summary, our results provide insights into the value of different methods to extract chromatin-associated proteins and provide starting points to study the factors that may be involved in directing gene expression and other chromatin-related processes.

  12. At a glance: Proteomics in China

    Institute of Scientific and Technical Information of China (English)

    HE FuChu

    2011-01-01

    Proteomics is a new science that focuses on the comprehensive analysis of proteins in intact organisms or in molecule machineries,organelles,cells,tissues,or organs.It has become an important area of interests in life sciences and has propelled the rapid development of cutting-edge biotechnology in the 21st century.In response to this,the Human Proteome Organization (HUPO) was launched in 2001.The mission of HUPO is to advocate and promote proteomics worldwide and to initiate the Human Proteome Project (HPP) to decode the human genome and to establish the proteomic basis of human physiology and pathology.Eleven projects including the Human Liver Proteome Project (HLPP) led by China are under way.Governments,multinational companies,particularly pharmaceutical and analytical instrument companies,as well as the genomic company Celera Genomics,have invested heavily,hoping to seize the huge potential of proteomics.=He Fuchu,PhD,is a Member of the Chinese Academy of Sciences,a Member of the Academy of Sciences for the Developing World,and is currently the Director of the State Key Laboratory of Proteomics.He is the President of the Beijing Proteome Research Center and a Professor at the Beijing Institute of Radiation Medicine.He Fuchu is a council member of the Human Proteome Organization (HUPO),co-chair (inaugural chair) of the HUPO Human Liver Proteome Project (HLPP),the vice-president of AOHUPO,and the president of CNHUPO.He received his B.S.degree in genetics from Fudan University,Shanghai,in 1982 and earned his M.S.degree in biochemistry and his PhD in cell biology from the Beijing Institute of Radiation Medicine.His major fields of research are proteomics,genomics,bioinformatics and systems biology,with a special interest in liver physiology and pathology.He is a senior editor of Proteomics and Proteomics-Clinical Application and is an editorial board member of Molecular & Cellular Proteomics and the Journal of Proteome Research and an executive editor of the

  13. Cloning, sequencing, expression, and regulation of the structural gene for the copper/topa quinone-containing methylamine oxidase from Arthrobacter strain P1, a gram-positive facultative methylotroph.

    OpenAIRE

    Zhang, X.; Fuller, J.H.; McIntire, W. S.

    1993-01-01

    Deoxyoligonucleotides corresponding to amino acid sequences of methylamine oxidase and polyclonal anti-methylamine oxidase antibodies were used to probe Arthrobacter strain P1 plasmid and chromosomal DNA libraries. Two open reading frames, maoxI and maoxII, which are greater than 99% homologous, were cloned from the chromosomal library. The deduced amino acid sequences of the coding regions are identical except for two residues near the C termini. On the other hand, the 5'- and 3'-flanking re...

  14. NCI Launches Proteomics Assay Portal - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    In a paper recently published by the journal Nature Methods, Investigators from the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (NCI-CPTAC) announced the launch of a proteomics Assay Portal for multiple reaction monitoring-mass

  15. CPTAC Releases Largest-Ever Breast Cancer Proteome Dataset - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) scientists have released a dataset of proteins and phophorylated phosphopeptides identified through deep proteomic and phosphoproteomic analysis of breast tumor samples, previously genomically analyzed by The Cancer Genome Atlas (TCGA).

  16. Breast Cancer Proteomic and Phosphoproteomic Data Released - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) scientists have released a dataset of proteins and phophorylated phosphopeptides identified through deep proteomic and phosphoproteomic analysis of breast tumor samples, previously genomically analyzed by The Cancer Genome Atlas (TCGA).

  17. Proteomics Data on UCSC Genome Browser - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium scientists are working together with the University of California, Santa Cruz (UCSC) Genomics Institute to provide public access to cancer proteomics data.

  18. Proteomic Analysis of Chinese Hamster Ovary Cells

    DEFF Research Database (Denmark)

    Baycin-Hizal, Deniz; Tabb, David L.; Chaerkady, Raghothama; Chen, Lily; Lewis, Nathan; Nagarajan, Harish; Sarkaria, Vishaldeep; Kumar, Amit; Wolozny, Daniel; Colao, Joe; Jacobson, Elena; Tian, Yuan; O’Meally, Robert N.; Krag, Sharon S.; Cole, Robert N.; Palsson, Bernhard; Zhang, Hui; Betenbaugh, Michael

    2012-01-01

    this analysis, the CHO codon frequency was determined and found to be distinct from humans, which will facilitate expression of human proteins in CHO cells. Analysis of the combined proteomic and mRNA data sets indicated the enrichment of a number of pathways including protein processing and apoptosis......To complement the recent genomic sequencing of Chinese hamster ovary (CHO) cells, proteomic analysis was performed on CHO cells including the cellular proteome, secretome, and glycoproteome using tandem mass spectrometry (MS/MS) of multiple fractions obtained from gel electrophoresis...... identified from both glycoproteome and proteome analysis, representing an 8-fold increase in the number of proteins currently identified in the CHO proteome. Furthermore, this is the first proteomic study done using the CHO genome exclusively, which provides for more accurate identification of proteins. From...

  19. Proteome-Wide Quantitation by SILAC

    DEFF Research Database (Denmark)

    Rigbolt, Kristoffer T G; Blagoev, Blagoy

    2010-01-01

    Ongoing improvements in instrumentation, fractionation techniques, and enrichment procedures have dramatically increased the coverage of the proteome achievable via LC-MS/MS-based methodologies, opening the call for approaches to quantitatively assess differences at a proteome-wide scale. Stable...... isotope labeling by amino acids in cell culture (SILAC) has emerged as a powerful and versatile approach for proteome-wide quantitation by mass spectrometry. SILAC utilizes the cells' own metabolism to incorporate isotopically labeled amino acids into its proteome which can be mixed with the proteome of...... detailed procedure for performing SILAC-based experiment for proteome-wide quantitation, including a protocol for optimizing SILAC labeling. We also provide an update on the most recent developments of this technique....

  20. Proteomics in Discovery of Hepatocellular Carcinoma Biomarkers

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Objective: To discover new proteomic biomarkers of hepatocellular carcinoma. Methods: Surface enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry was used to discover biomarkers for differentiating hepatocellular carcinoma and chronic liver disease. A population of 50 patients with hepatocellular carcinoma and 33 patients with chronic liver disease was studied. Results: Twelve proteomic biomarkers of hepatocellular carcinoma were detected in this study. Three proteomic biomarkers were highly expressed in hepatocellular carcinoma and nine proteomic biomarkers were highly expressed in chronic liver disease. The most valuable proteomic biomarker with m/z=11498 had no similar diagnostic value as α-fetoprotein. Conclusion:Some of the twelve proteomic biomarkers may become new biomarkers of hepatocellular carcinoma.

  1. Proteomic Analysis of Human Tooth Pulp: Proteomics of Human Tooth

    Czech Academy of Sciences Publication Activity Database

    Eckhardt, Adam; Jágr, Michal; Pataridis, Statis; Mikšík, Ivan

    2014-01-01

    Roč. 40, č. 12 (2014), s. 1961-1966. ISSN 0099-2399 R&D Projects: GA ČR(CZ) GA13-17224S; GA ČR(CZ) GAP206/12/0453; GA MZd(CZ) NT14324 Institutional support: RVO:67985823 Keywords : dentin * human pulp * tandem mass spectrometry * tooth proteome * 2-dimensional gel electrophoresis Subject RIV: FF - HEENT, Dentistry Impact factor: 3.375, year: 2014

  2. Characterization of the porcine synovial fluid proteome and a comparison to the plasma proteome.

    Science.gov (United States)

    Bennike, Tue Bjerg; Barnaby, Omar; Steen, Hanno; Stensballe, Allan

    2015-12-01

    Synovial fluid is present in all joint cavities, and protects the articular cartilage surfaces in large by lubricating the joint, thus reducing friction. Several studies have described changes in the protein composition of synovial fluid in patients with joint disease. However, the protein concentration, content, and synovial fluid volume change dramatically during active joint diseases and inflammation, and the proteome composition of healthy synovial fluid is incompletely characterized. We performed a normative proteomics analysis of porcine synovial fluid, and report data from optimizing proteomic methods to investigate the proteome of healthy porcine synovial fluid (Bennike et al., 2014 [1]). We included an evaluation of different proteolytic sample preparation techniques, and an analysis of posttranslational modifications with a focus on glycosylation. We used pig (Sus Scrofa) as a model organism, as the porcine immune system is highly similar to human and the pig genome is sequenced. Furthermore, porcine model systems are commonly used large animal models to study several human diseases. In addition, we analyzed the proteome of human plasma, and compared the proteomes to the obtained porcine synovial fluid proteome. The proteome of the two body fluids were found highly similar, underlining the detected plasma derived nature of many synovial fluid components. The healthy porcine synovial fluid proteomics data, human rheumatoid arthritis synovial fluid proteomics data used in the method optimization, human plasma proteomics data, and search results, have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD000935. PMID:26543887

  3. Database independent proteomics analysis of the ostrich and human proteome.

    Science.gov (United States)

    Altelaar, A F Maarten; Navarro, Danny; Boekhorst, Jos; van Breukelen, Bas; Snel, Berend; Mohammed, Shabaz; Heck, Albert J R

    2012-01-10

    Mass spectrometry (MS)-based proteome analysis relies heavily on the presence of complete protein databases. Such a strategy is extremely powerful, albeit not adequate in the analysis of unpredicted postgenome events, such as posttranslational modifications, which exponentially increase the search space. Therefore, it is of interest to explore "database-free" approaches. Here, we sampled the ostrich and human proteomes with a method facilitating de novo sequencing, utilizing the protease Lys-N in combination with electron transfer dissociation. By implementing several validation steps, including the combined use of collision-induced dissociation/electron transfer dissociation data and a cross-validation with conventional database search strategies, we identified approximately 2,500 unique de novo peptide sequences from the ostrich sample with over 900 peptides generating full backbone sequence coverage. This dataset allowed the appropriate positioning of ostrich in the evolutionary tree. The described database-free sequencing approach is generically applicable and has great potential in important proteomics applications such as in the analysis of variable parts of endogenous antibodies or proteins modified by a plethora of complex posttranslational modifications. PMID:22198768

  4. Evolutionary conservation of the mature oocyte proteome

    Directory of Open Access Journals (Sweden)

    Tamar Lotan

    2014-06-01

    Significance: The current study provides the first proteomic profile of an oocyte of a cnidarian organism the starlet sea anemone N. vectensis and gives new insights on the ancient origin of an oocyte proteome template. The comparative analysis with a chordate oocyte suggests that the oocyte proteome predates the divergence of the cnidarian and bilaterian lineages. In addition, the data generated in the study will serve as a valuable resource for further developmental and evolutional studies.

  5. Biospecimen Solicitation - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    A funding opportunity in support of the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) seeks to prospectively procure tumor samples, collected for proteomics investigation.

  6. Quantitative Proteomic Analysis of the Human Nucleolus.

    Science.gov (United States)

    Bensaddek, Dalila; Nicolas, Armel; Lamond, Angus I

    2016-01-01

    Recent years have witnessed spectacular progress in the field of mass spectrometry (MS)-based quantitative proteomics, including advances in instrumentation, chromatography, sample preparation methods, and experimental design for multidimensional analyses. It is now possible not only to identify most of the protein components of a cell proteome in a single experiment, but also to describe additional proteome dimensions, such as protein turnover rates, posttranslational modifications, and subcellular localization. Furthermore, by comparing the proteome at different time points, it is possible to create a "time-lapse" view of proteome dynamics. By combining high-throughput quantitative proteomics with detailed subcellular fractionation protocols and data analysis techniques it is also now possible to characterize in detail the proteomes of specific subcellular organelles, providing important insights into cell regulatory mechanisms and physiological responses. In this chapter we present a reliable workflow and protocol for MS-based analysis and quantitation of the proteome of nucleoli isolated from human cells. The protocol presented is based on a SILAC analysis of human MCF10A-Src-ER cells with analysis performed on a Q-Exactive Plus Orbitrap MS instrument (Thermo Fisher Scientific). The subsequent chapter describes how to process the resulting raw MS files from this experiment using MaxQuant software and data analysis procedures to evaluate the nucleolar proteome using customized R scripts. PMID:27576725

  7. Farm animal proteomics - A review

    DEFF Research Database (Denmark)

    Bendixen, Emøke; Danielsen, Marianne; Hollung, Kristin;

    2011-01-01

    In agricultural sciences as in all other areas of life science, the implementation of proteomics and other post-genomic tools is an important step towards more detailed understanding of the complex biological systems that control physiology and pathology of living beings. Farm animals are raised...... in large-scale operations, with the aim to obtain animal products for human consumption. Hence, understanding the biological traits that impact yield and quality of these products is the specific aim of much biological experimentation. However, most of the data gathered from experiments on e.g. swine...... and cattle are relevant not only for farm animal sciences, but also for adding to our understanding of complex biological mechanisms of health and disease in humans. The aim of this review is to present an overview of the specific topics of interest within farm animal proteomics, and to highlight some...

  8. The Potato Tuber Mitochondrial Proteome

    DEFF Research Database (Denmark)

    Salvato, Fernanda; Havelund, Jesper F; Chen, Mingjie;

    2014-01-01

    Mitochondria are called the powerhouses of the cell. To better understand the role of mitochondria in maintaining and regulating metabolism in storage tissues, highly purified mitochondria were isolated from dormant potato tubers (Solanum tuberosum ‘Folva’) and their proteome investigated. Proteins...... that more than 50% of the identified proteins harbor at least one modification. The most prominently observed class of posttranslational modifications was oxidative modifications. This study reveals approximately 500 new or previously unconfirmed plant mitochondrial proteins and outlines a facile strategy...

  9. Mass Spectrometry Instrumentation in Proteomics

    DEFF Research Database (Denmark)

    Sprenger, Richard Remko; Roepstorff, Peter

    2012-01-01

    Mass spectrometry has evolved into a crucial technology for the field of proteomics, enabling the comprehensive study of proteins in biological systems. Innovative developments have yielded flexible and versatile mass spectrometric tools, including quadrupole time-of-flight, linear ion trap......, Orbitrap and ion mobility instruments. Together they offer various and complementary capabilities in terms of ionization, sensitivity, speed, resolution, mass accuracy, dynamic range and methods of fragmentation. Mass spectrometers can acquire qualitative and quantitative information on a large scale...

  10. Platelet proteomics in cardiovascular diseases

    OpenAIRE

    Paula Vélez; Ángel García

    2015-01-01

    In recent years, platelet proteomics has been applied successfully to the study of cardiovascular diseases (CVDs). It is very well known that platelets play a pivotal role in the pathophysiological mechanisms underlying many CVDs, especially acute coronary syndromes (ACSs), since they are implied in thrombus formation after atheroma plaque rupture. This is the reason why molecules involved in platelet activation and aggregation are primary targets for treatment of ACSs. Many efforts are aimed...

  11. Cell wall proteomics of crops

    OpenAIRE

    Komatsu, Setsuko; Yanagawa, Yuki

    2013-01-01

    Cell wall proteins play key roles in cell structure and metabolism, cell enlargement, signal transduction, responses to environmental stress, and many other physiological events. Agricultural crops are often used for investigating stress tolerance because cultivars with differing degrees of tolerance are available. Abiotic and biotic stress factors markedly influence the geographical distribution and yields of many crop species. Crop cell wall proteomics is of particular importance for improv...

  12. Proteomics of Rice Seed Germination

    Directory of Open Access Journals (Sweden)

    Dongli eHe

    2013-07-01

    Full Text Available Seed is a condensed form of plant. Under suitable environmental conditions, it can resume the metabolic activity from physiological quiescent status, and mobilize the reserves, biosynthesize new proteins, regenerate organelles and cell membrane, eventually protrude the radicle and enter into seedling establishment. So far, how these activities are regulated in a coordinated and sequential manner is largely unknown. With the availability of more and more genome sequence information and the development of mass spectrometry (MS technology, proteomics has been widely applied in analyzing the mechanisms of different biological processes, and proved to be very powerful. Regulation of rice seed germination is critical for rice cultivation. In recent years, a lot of proteomic studies have been conducted in exploring the gene expression regulation, reserves mobilization and metabolisms reactivation, which brings us new insights on the mechanisms of metabolism regulation during this process. Nevertheless, it also invokes a lot of questions. In this mini-review, we summarized the progress in the proteomic studies of rice seed germination. The current challenges and future perspectives were also discussed, which might be helpful for the following studies.

  13. Proteomic Investigations into Hemodialysis Therapy

    Directory of Open Access Journals (Sweden)

    Mario Bonomini

    2015-12-01

    Full Text Available The retention of a number of solutes that may cause adverse biochemical/biological effects, called uremic toxins, characterizes uremic syndrome. Uremia therapy is based on renal replacement therapy, hemodialysis being the most commonly used modality. The membrane contained in the hemodialyzer represents the ultimate determinant of the success and quality of hemodialysis therapy. Membrane’s performance can be evaluated in terms of removal efficiency for unwanted solutes and excess fluid, and minimization of negative interactions between the membrane material and blood components that define the membrane’s bio(incompatibility. Given the high concentration of plasma proteins and the complexity of structural functional relationships of this class of molecules, the performance of a membrane is highly influenced by its interaction with the plasma protein repertoire. Proteomic investigations have been increasingly applied to describe the protein uremic milieu, to compare the blood purification efficiency of different dialyzer membranes or different extracorporeal techniques, and to evaluate the adsorption of plasma proteins onto hemodialysis membranes. In this article, we aim to highlight investigations in the hemodialysis setting making use of recent developments in proteomic technologies. Examples are presented of why proteomics may be helpful to nephrology and may possibly affect future directions in renal research.

  14. Human saliva proteome: an overview

    Science.gov (United States)

    Griffin, Timothy J.

    2014-06-01

    Human saliva contains a rich mixture of biomolecules. Proteins are a major component of this mixture. Given their role as the molecular effectors within biological systems, ranging from catalysis to transport to structure, proteins have great potential as biomarkers of health and disease. The ability to collect these salivary biomarkers easily using non-invasive means makes saliva proteins even more attractive for diagnostic applications. Thousands of proteins are now to be known to be present in human saliva - discovered using proteomic technologies. Emerging technologies are now making it possible to go beyond large-scale cataloging of salivary proteins. These include approaches to catalog protein contributions from the community of microorganisms residing in the oral cavity (metaproteomics) that may reflect the health state of the human host. New mass spectrometry-based proteomics methods are also emerging, shifting the emphasis from large-scale discovery experiments to hypothesis-driven assays for profiling proteins of interest within saliva, enabling validation of their association with specific health conditions. This paper provides a brief overview of efforts to catalog the proteome of human saliva. Recent developments making possible characterization of the metaproteome of human saliva will be discussed, and technologies driving new mass spectrometry-based assays for targeted analysis of proteins within complex samples, such as saliva.

  15. The Proteome Analysis database: a tool for the in silico analysis of whole proteomes.

    Science.gov (United States)

    Pruess, Manuela; Fleischmann, Wolfgang; Kanapin, Alexander; Karavidopoulou, Youla; Kersey, Paul; Kriventseva, Evgenia; Mittard, Virginie; Mulder, Nicola; Phan, Isabelle; Servant, Florence; Apweiler, Rolf

    2003-01-01

    The Proteome Analysis database (http://www.ebi.ac.uk/proteome/) has been developed by the Sequence Database Group at EBI utilizing existing resources and providing comparative analysis of the predicted protein coding sequences of the complete genomes of bacteria, archeae and eukaryotes. Three main projects are used, InterPro, CluSTr and GO Slim, to give an overview on families, domains, sites, and functions of the proteins from each of the complete genomes. Complete proteome analysis is available for a total of 89 proteome sets. A specifically designed application enables InterPro proteome comparisons for any one proteome against any other one or more of the proteomes in the database. PMID:12520037

  16. Levan fructotransferase from Arthrobacter oxydans J17-21 catalyzes the formation of the di-D-fructose dianhydride IV from levan.

    Science.gov (United States)

    Jang, Ki-Hyo; Ryu, Eun-Ja; Park, Buem-Seek; Song, Ki-Bang; Kang, Soon Ah; Kim, Chul Ho; Uhm, Tai-Boong; Park, Yong-Il; Rhee, Sang-Ki

    2003-04-23

    A new levan fructotransferase (LFTase) isolated from Arthrobacter oxydans J17-21 was characterized for the production of difructose dianhydride IV (DFA IV). LFTase was purified to apparent homogeneity by Q-Sepharose ion exchange chromatography, Mono-Q HR 5/5 column chromatography, and gel permeation chromatography. The enzyme had an apparent molecular mass of 54000 Da. The optimum pH for the enzyme-catalyzed reaction was pH 6.5, and the optimum temperature was observed at 45 degrees C. The LFTase was activated by the presence of CaCl(2) and EDTA-2Na but inhibited strongly by MnCl(2) and CuSO(4) at 1 mM and completely by FeSO(4) and Ag(2)SO(4) at 1 mM. A bacterial levan from Zymomonas mobilis was incubated with an LFTase; final conversion yield from the levan to DFA IV was 35%. Neither inulin, levanbiose, sucrose, dextran, nor starch was hydrolyzed by LFTase. DFA IV was very stable at acidic pH and high temperature, thus indicating that DFA IV may be suitable for the food industry and related areas. PMID:12696949

  17. Cloning, nucleotide sequence and expression of a new L-N-carbamoylase gene from Arthrobacter aurescens DSM 3747 in E. coli.

    Science.gov (United States)

    Wilms, B; Wiese, A; Syldatk, C; Mattes, R; Altenbuchner, J; Pietzsch, M

    1999-02-19

    An L-N-carbamoyl amino acid amidohydrolase (L-N-carbamoylase) from Arthrobacter aurescens DSM 3747 was cloned in E. coli and the nucleotide sequence was determined. After expression of the gene in E. coli the enzyme was purified to homogeneity and characterized. The enzyme was shown to be strictly L-specific and exhibited the highest activity in the hydrolysis of beta-aryl substituted N alpha-carbamoyl-alanines as e.g. N-carbamoyl-tryptophan. Carbamoyl derivatives of beta-alanine and charged aliphatic amino acids were not accepted as substrates. The N-carbamoylase of A. aurescens DSM 3747 differs from all known enzymes with respect to its substrate specificity although amino acid sequence identity scores of 35-38% to other N-carbamoylases have been detected. The enzyme consists of two subunits of 44,000 Da, and has an isoelectric point of 4.3. The optima of temperature and pH were determined to be 50 degrees C and pH 8.5 respectively. At 37 degrees C the enzyme was completely stable for several days. PMID:10194852

  18. Toxicity screening of soils from different mine areas—A contribution to track the sensitivity and variability of Arthrobacter globiformis assay

    Energy Technology Data Exchange (ETDEWEB)

    Marques, Catarina R., E-mail: crmarques@ua.pt [Departamento de Biologia and CESAM (Centro de Estudos do Ambiente e do Mar), Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro (Portugal); Caetano, Ana L. [Departamento de Biologia and CESAM (Centro de Estudos do Ambiente e do Mar), Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro (Portugal); Haller, Andreas [ECT Oekotoxikologie GmbH, Böttgerstraße 2–14, D-65439 Flörsheim a. M. (Germany); Gonçalves, Fernando [Departamento de Biologia and CESAM (Centro de Estudos do Ambiente e do Mar), Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro (Portugal); Pereira, Ruth [Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto (Portugal); Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), Universidade do Porto, Rua dos Bragas 289, P 4050-123 Porto (Portugal); Römbke, Jörg [ECT Oekotoxikologie GmbH, Böttgerstraße 2–14, D-65439 Flörsheim a. M. (Germany)

    2014-06-01

    Highlights: • The assay gave rapid and feasible discrimination of toxic soils to A. globiformis. • Sensitive and low variability response to soils from different regions. • Soil properties may interfere with metal toxicity and fluorescence measurements. • Proposal of a toxicity threshold for the contact assay regarding soils. • A. globiformis assay should be included in the Tier I of risk assessment frameworks. - Abstract: This study used the Arthrobacter globiformis solid-contact test for assessing the quality of soils collected in areas subjected to past and present mine activities in Europe (uranium mine, Portugal) and North Africa (phosphogypsum pile, Tunisia; iron mine, Morocco). As to discriminate the influence of soils natural variability from the effect of contaminants, toxicity thresholds were derived for this test, based on the dataset of each study area. Furthermore, the test sensitivity and variability was also evaluated. As a result, soils that inhibited A. globiformis dehydrogenase activity above 45% or 50% relatively to the control, were considered to be toxic. Despite the soil metal content determined, the properties of soils seemed to influence dehydrogenase activity. Overall, the contact test provided a coherent outcome comparing to other more time-consuming and effort-demanding ecotoxicological assays. Our results strengthened the feasibility and ecological relevance of this assay, which variability was quite reduced hence suggesting its potential integration within the test battery of tier 1 of soil risk assessment schemes.

  19. Characteristics of an organic solvent-tolerant β-fructofuranosidase from Arthrobacter arilaitensis NJEM01 and efficient synthesis of prebiotic kestose.

    Science.gov (United States)

    Chu, Jianlin; Wu, Xueming; Wu, Bin; Wang, Rui; He, Bingfang

    2014-06-18

    An organic solvent-tolerant β-fructofuranosidase (β-FFase) from Arthrobacter arilaitensis NJEM01 was purified, characterized, cloned, and overexpressed in Escherichia coli. The mature β-FFase contained 495 amino acid residues with an estimated molecular mass of 55 kDa. The purified β-FFase from strain NJEM01 was very stable in the buffer systems (pH 5.0-9.5) and showed high stability below 45 °C. Furthermore, the enzyme exhibited relatively high solvent stability in various aqueous organic mixtures and retained nearly 100% of its initial activity after incubation for 10 days in 20% (v/v) DMSO. In addition, the β-FFase exhibited high transfructosylation activity, synthesized prebiotic products of mainly 6-kestose (up to 476 g/L), and showed fructosyl receptor specificity to C-glucosyl flavone. A relatively high yield of FOS was achieved by the β-FFase from bacterium with a high concentration of sucrose. It made the β-FFase an exploitable biocatalyst for the production of glycosides of natural products and prebiotic kestose. PMID:24854707

  20. Global Proteome Analysis of Leptospira interrogans

    Science.gov (United States)

    Comparative global proteome analyses were performed on Leptospira interrogans serovar Copenhageni grown under conventional in vitro conditions and those mimicking in vivo conditions (iron limitation and serum presence). Proteomic analyses were conducted using iTRAQ and LC-ESI-tandem mass spectrometr...

  1. Modification-specific proteomics in plant biology

    DEFF Research Database (Denmark)

    Ytterberg, A Jimmy; Jensen, Ole N

    2010-01-01

    and proteomics. In general, methods for PTM characterization are developed to study yeast and mammalian biology and later adopted to investigate plants. Our point of view is that it is advantageous to enrich for PTMs on the peptide level as part of a quantitative proteomics strategy to not only identify the PTM...

  2. Statistical data processing in clinical proteomics

    NARCIS (Netherlands)

    S. Smit

    2009-01-01

    The subject of this thesis is the analysis of data in clinical proteomics studies aimed at the discovery of biomarkers. The data sets produced in proteomics studies are huge, characterized by a small number of samples in which many proteins and peptides are measured. The studies described in this th

  3. Centennial Paper: Proteomics in animal science

    Science.gov (United States)

    Proteomics holds significant promise as a method for advancing animal science research. The use of this technology in animal science is still in its infancy. The ability of proteomics to simultaneously identify and quantify potentially thousands of proteins is unparalleled. In this review, we wil...

  4. The promise of proteomics in animal science

    Science.gov (United States)

    Proteomics hold significant promise as a method for advancing animal science research. The use of this technology in animal science is still in its infancy. The ability of proteomics to simultaneously identify and quantify potentially thousands of proteins is unparalleled. In this review, we will...

  5. Intestinal proteome changes during infant necrotizing enterocolitis

    DEFF Research Database (Denmark)

    Jiang, Pingping; Smith, Birgitte; Qvist, Niels;

    2013-01-01

    Background: Changes in the intestinal and colonic proteome in patients with necrotizing enterocolitis (NEC) may help to characterize the disease pathology and identify new biomarkers and treatment targets for NEC. Methods: Using gel-based proteomics, proteins in NEC-affected intestinal and coloni...

  6. Applications of proteomics in hepatic diseases research

    Institute of Scientific and Technical Information of China (English)

    SUN; Wei; HE; Fuchu

    2004-01-01

    Proteomics has become an important part in the leading research area and been widely used in the disease-associated study. In hepatic research field, proteomics could be applied in study of hepatic diseases including liver cancer, cirrhosis and hepatotoxicities, etc. Significant proteins could be identified as biomarkers, drug targets and clues for pathogenesis illumination.

  7. Proteomics: Protein Identification Using Online Databases

    Science.gov (United States)

    Eurich, Chris; Fields, Peter A.; Rice, Elizabeth

    2012-01-01

    Proteomics is an emerging area of systems biology that allows simultaneous study of thousands of proteins expressed in cells, tissues, or whole organisms. We have developed this activity to enable high school or college students to explore proteomic databases using mass spectrometry data files generated from yeast proteins in a college laboratory…

  8. Synchrotron radiation and structural proteomics

    CERN Document Server

    Pechkova, Eugenia

    2011-01-01

    This book presents an overview of the current state of research in both synchrotron radiation and structural proteomics from different laboratories worldwide. The book presents recent research results in the most advanced methods of synchrotron radiation analysis, protein micro- and nano crystallography, X-ray scattering and X-ray optics, coherent X-Ray diffraction, and laser cutting and contactless sample manipulation are described in details. The book focuses on biological applications and highlights important aspects such as radiation damage and molecular modeling.

  9. Guidelines for reporting the use of gel electrophoresis in proteomics.

    OpenAIRE

    Gibson, Frank; Anderson, Leigh; Babnigg, Gyorgy; Baker, Mark; Berth, Matthias; Binz, Pierre-Alain; Borthwick, Andy; Cash, Phil; Day, Billy W.; Friedman, David B; Garland, Donita; Gutstein, Howard B.; Hoogland, Christine; Jones, Neil A.; Khan, Alamgir

    2008-01-01

    the MIAPE Gel Electrophoresis (MIAPE-GE) guidelines specify the minimum information that should be provided when reporting the use of n-dimensional gel electrophoresis in a proteomics experiment. Developed through a joint effort between the gel-based analysis working group of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO-PSI; http://www.psidev.info/) and the wider proteomics community, they constitute one part of the overall Minimum Information about a Proteomics Exp...

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

    OpenAIRE

    Rabilloud, Thierry

    2014-01-01

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

  11. Proteomic analysis of Chinese hamster ovary cells.

    Science.gov (United States)

    Baycin-Hizal, Deniz; Tabb, David L; Chaerkady, Raghothama; Chen, Lily; Lewis, Nathan E; Nagarajan, Harish; Sarkaria, Vishaldeep; Kumar, Amit; Wolozny, Daniel; Colao, Joe; Jacobson, Elena; Tian, Yuan; O'Meally, Robert N; Krag, Sharon S; Cole, Robert N; Palsson, Bernhard O; Zhang, Hui; Betenbaugh, Michael

    2012-11-01

    To complement the recent genomic sequencing of Chinese hamster ovary (CHO) cells, proteomic analysis was performed on CHO cells including the cellular proteome, secretome, and glycoproteome using tandem mass spectrometry (MS/MS) of multiple fractions obtained from gel electrophoresis, multidimensional liquid chromatography, and solid phase extraction of glycopeptides (SPEG). From the 120 different mass spectrometry analyses generating 682,097 MS/MS spectra, 93,548 unique peptide sequences were identified with at most 0.02 false discovery rate (FDR). A total of 6164 grouped proteins were identified from both glycoproteome and proteome analysis, representing an 8-fold increase in the number of proteins currently identified in the CHO proteome. Furthermore, this is the first proteomic study done using the CHO genome exclusively, which provides for more accurate identification of proteins. From this analysis, the CHO codon frequency was determined and found to be distinct from humans, which will facilitate expression of human proteins in CHO cells. Analysis of the combined proteomic and mRNA data sets indicated the enrichment of a number of pathways including protein processing and apoptosis but depletion of proteins involved in steroid hormone and glycosphingolipid metabolism. Five-hundred four of the detected proteins included N-acetylation modifications, and 1292 different proteins were observed to be N-glycosylated. This first large-scale proteomic analysis will enhance the knowledge base about CHO capabilities for recombinant expression and provide information useful in cell engineering efforts aimed at modifying CHO cellular functions. PMID:22971049

  12. Visualizing Meta-Features in Proteomic Maps

    Directory of Open Access Journals (Sweden)

    Lepouras George

    2011-07-01

    Full Text Available Abstract Background The steps of a high-throughput proteomics experiment include the separation, differential expression and mass spectrometry-based identification of proteins. However, the last and more challenging step is inferring the biological role of the identified proteins through their association with interaction networks, biological pathways, analysis of the effect of post-translational modifications, and other protein-related information. Results In this paper, we present an integrative visualization methodology that allows combining experimentally produced proteomic features with protein meta-features, typically coming from meta-analysis tools and databases, in synthetic Proteomic Feature Maps. Using three proteomics analysis scenarios, we show that the proposed visualization approach is effective in filtering, navigating and interacting with the proteomics data in order to address visually challenging biological questions. The novelty of our approach lies in the ease of integration of any user-defined proteomic features in easy-to-comprehend visual representations that resemble the familiar 2D-gel images, and can be adapted to the user's needs. The main capabilities of the developed VIP software, which implements the presented visualization methodology, are also highlighted and discussed. Conclusions By using this visualization and the associated VIP software, researchers can explore a complex heterogeneous proteomics dataset from different perspectives in order to address visually important biological queries and formulate new hypotheses for further investigation. VIP is freely available at http://pelopas.uop.gr/~egian/VIP/index.html.

  13. Legume proteomics: Progress, prospects, and challenges.

    Science.gov (United States)

    Rathi, Divya; Gayen, Dipak; Gayali, Saurabh; Chakraborty, Subhra; Chakraborty, Niranjan

    2016-01-01

    Legumes are the major sources of food and fodder with strong commercial relevance, and are essential components of agricultural ecosystems owing to their ability to carry out endosymbiotic nitrogen fixation. In recent years, legumes have become one of the major choices of plant research. The legume proteomics is currently represented by more than 100 reference maps and an equal number of stress-responsive proteomes. Among the 48 legumes in the protein databases, most proteomic studies have been accomplished in two model legumes, soybean, and barrel medic. This review highlights recent contributions in the field of legume proteomics to comprehend the defence and regulatory mechanisms during development and adaptation to climatic changes. Here, we attempted to provide a concise overview of the progress in legume proteomics and discuss future developments in three broad perspectives: (i) proteome of organs/tissues; (ii) subcellular compartments; and (iii) spatiotemporal changes in response to stress. Such data mining may aid in discovering potential biomarkers for plant growth, in general, apart from essential components involved in stress tolerance. The prospect of integrating proteome data with genome information from legumes will provide exciting opportunities for plant biologists to achieve long-term goals of crop improvement and sustainable agriculture. PMID:26563903

  14. Network-based analysis of proteomic profiles

    KAUST Repository

    Wong, Limsoon

    2016-01-26

    Mass spectrometry (MS)-based proteomics is a widely used and powerful tool for profiling systems-wide protein expression changes. It can be applied for various purposes, e.g. biomarker discovery in diseases and study of drug responses. Although RNA-based high-throughput methods have been useful in providing glimpses into the underlying molecular processes, the evidences they provide are indirect. Furthermore, RNA and corresponding protein levels have been known to have poor correlation. On the other hand, MS-based proteomics tend to have consistency issues (poor reproducibility and inter-sample agreement) and coverage issues (inability to detect the entire proteome) that need to be urgently addressed. In this talk, I will discuss how these issues can be addressed by proteomic profile analysis techniques that use biological networks (especially protein complexes) as the biological context. In particular, I will describe several techniques that we have been developing for network-based analysis of proteomics profile. And I will present evidence that these techniques are useful in identifying proteomics-profile analysis results that are more consistent, more reproducible, and more biologically coherent, and that these techniques allow expansion of the detected proteome to uncover and/or discover novel proteins.

  15. Proteomics and the Inner Ear

    Directory of Open Access Journals (Sweden)

    Isolde Thalmann

    2001-01-01

    Full Text Available The inner ear, one of the most complex organs, contains within its bony shell three sensory systems, the evolutionary oldest gravity receptor system, the three semicircular canals for the detection of angular acceleration, and the auditory system - unrivaled in sensitivity and frequency discrimination. All three systems are susceptible to a host of afflictions affecting the quality of life for all of us. In the first part of this review we present an introduction to the milestones of inner ear research to pave the way for understanding the complexities of a proteomics approach to the ear. Minute sensory structures, surrounded by large fluid spaces and a hard bony shell, pose extreme challenges to the ear researcher. In spite of these obstacles, a powerful preparatory technique was developed, whereby precisely defined microscopic tissue elements can be isolated and analyzed, while maintaining the biochemical state representative of the in vivo conditions. The second part consists of a discussion of proteomics as a tool in the elucidation of basic and pathologic mechanisms, diagnosis of disease, as well as treatment. Examples are the organ of Corti proteins OCP1 and OCP2, oncomodulin, a highly specific calcium-binding protein, and several disease entities, Meniere's disease, benign paroxysmal positional vertigo, and perilymphatic fistula.

  16. Neural Stem Cells (NSCs) and Proteomics.

    Science.gov (United States)

    Shoemaker, Lorelei D; Kornblum, Harley I

    2016-02-01

    Neural stem cells (NSCs) can self-renew and give rise to the major cell types of the CNS. Studies of NSCs include the investigation of primary, CNS-derived cells as well as animal and human embryonic stem cell (ESC)-derived and induced pluripotent stem cell (iPSC)-derived sources. NSCs provide a means with which to study normal neural development, neurodegeneration, and neurological disease and are clinically relevant sources for cellular repair to the damaged and diseased CNS. Proteomics studies of NSCs have the potential to delineate molecules and pathways critical for NSC biology and the means by which NSCs can participate in neural repair. In this review, we provide a background to NSC biology, including the means to obtain them and the caveats to these processes. We then focus on advances in the proteomic interrogation of NSCs. This includes the analysis of posttranslational modifications (PTMs); approaches to analyzing different proteomic compartments, such the secretome; as well as approaches to analyzing temporal differences in the proteome to elucidate mechanisms of differentiation. We also discuss some of the methods that will undoubtedly be useful in the investigation of NSCs but which have not yet been applied to the field. While many proteomics studies of NSCs have largely catalogued the proteome or posttranslational modifications of specific cellular states, without delving into specific functions, some have led to understandings of functional processes or identified markers that could not have been identified via other means. Many challenges remain in the field, including the precise identification and standardization of NSCs used for proteomic analyses, as well as how to translate fundamental proteomics studies to functional biology. The next level of investigation will require interdisciplinary approaches, combining the skills of those interested in the biochemistry of proteomics with those interested in modulating NSC function. PMID:26494823

  17. Neural Stem Cells (NSCs) and Proteomics*

    Science.gov (United States)

    Shoemaker, Lorelei D.; Kornblum, Harley I.

    2016-01-01

    Neural stem cells (NSCs) can self-renew and give rise to the major cell types of the CNS. Studies of NSCs include the investigation of primary, CNS-derived cells as well as animal and human embryonic stem cell (ESC)-derived and induced pluripotent stem cell (iPSC)-derived sources. NSCs provide a means with which to study normal neural development, neurodegeneration, and neurological disease and are clinically relevant sources for cellular repair to the damaged and diseased CNS. Proteomics studies of NSCs have the potential to delineate molecules and pathways critical for NSC biology and the means by which NSCs can participate in neural repair. In this review, we provide a background to NSC biology, including the means to obtain them and the caveats to these processes. We then focus on advances in the proteomic interrogation of NSCs. This includes the analysis of posttranslational modifications (PTMs); approaches to analyzing different proteomic compartments, such the secretome; as well as approaches to analyzing temporal differences in the proteome to elucidate mechanisms of differentiation. We also discuss some of the methods that will undoubtedly be useful in the investigation of NSCs but which have not yet been applied to the field. While many proteomics studies of NSCs have largely catalogued the proteome or posttranslational modifications of specific cellular states, without delving into specific functions, some have led to understandings of functional processes or identified markers that could not have been identified via other means. Many challenges remain in the field, including the precise identification and standardization of NSCs used for proteomic analyses, as well as how to translate fundamental proteomics studies to functional biology. The next level of investigation will require interdisciplinary approaches, combining the skills of those interested in the biochemistry of proteomics with those interested in modulating NSC function. PMID:26494823

  18. Characterization of the porcine synovial fluid proteome and a comparison to the plasma proteome

    DEFF Research Database (Denmark)

    Bennike, Tue Bjerg; Barnaby, Omar; Steen, Hanno;

    2015-01-01

    Synovial fluid is present in all joint cavities, and protects the articular cartilage surfaces in large by lubricating the joint, thus reducing friction. Several studies have described changes in the protein composition of synovial fluid in patients with joint disease. However, the protein concen...... proteomics data used in the method optimization, human plasma proteomics data, and search results, have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD000935....

  19. The Proteome Analysis database: a tool for the in silico analysis of whole proteomes

    OpenAIRE

    Pruess, Manuela; Fleischmann, Wolfgang; Kanapin, Alexander; Karavidopoulou, Youla; Kersey, Paul; Kriventseva, Evgenia; Mittard, Virginie; Mulder, Nicola; Phan, Isabelle; Servant, Florence; Apweiler, Rolf

    2003-01-01

    The Proteome Analysis database (http://www.ebi.ac.uk/proteome/) has been developed by the Sequence Database Group at EBI utilizing existing resources and providing comparative analysis of the predicted protein coding sequences of the complete genomes of bacteria, archeae and eukaryotes. Three main projects are used, InterPro, CluSTr and GO Slim, to give an overview on families, domains, sites, and functions of the proteins from each of the complete genomes. Complete proteome analysis is avail...

  20. Virion Proteomics of Large DNA Viruses

    Institute of Scientific and Technical Information of China (English)

    Ran-ran WANG; Zhi-hong HU; Hua-lin WANG; Fei DENG

    2009-01-01

    Large DNA viruses normally have complex structures with many of protein components derived from both viral and host origins. The development in proteomics, especially mass spectrometry identification techniques provide powerful tools for analyzing large viruses. In this review, we have summarized the recent achievements on proteomic studies of large DNA viruses, such as herpesvirus, poxvirus, nimavirus and baculoviruse. The proteomics of baculovirus occlusion-derived virions (ODV) were emphasized. Different mass spectrometry techniques used on ,carious baculoviruses were introduced, and the identified structurally associated proteins of baculoviruses are summarized.

  1. Analysis of mass spectrometry data in proteomics

    DEFF Research Database (Denmark)

    Matthiesen, Rune; Jensen, Ole N

    2008-01-01

    The systematic study of proteins and protein networks, that is, proteomics, calls for qualitative and quantitative analysis of proteins and peptides. Mass spectrometry (MS) is a key analytical technology in current proteomics and modern mass spectrometers generate large amounts of high-quality data...... that in turn allow protein identification, annotation of secondary modifications, and determination of the absolute or relative abundance of individual proteins. Advances in mass spectrometry-driven proteomics rely on robust bioinformatics tools that enable large-scale data analysis. This chapter...

  2. Affinity Proteomics in the mountains: Alpbach 2015.

    Science.gov (United States)

    Taussig, Michael J

    2016-09-25

    The 2015 Alpbach Workshop on Affinity Proteomics, organised by the EU AFFINOMICS consortium, was the 7th workshop in this series. As in previous years, the focus of the event was the current state of affinity methods for proteome analysis, including complementarity with mass spectrometry, progress in recombinant binder production methods, alternatives to classical antibodies as affinity reagents, analysis of proteome targets, industry focus on biomarkers, and diagnostic and clinical applications. The combination of excellent science with Austrian mountain scenery and winter sports engender an atmosphere that makes this series of workshops exceptional. The articles in this Special Issue represent a cross-section of the presentations at the 2015 meeting. PMID:27118167

  3. Proteomics and the dynamic plasma membrane

    DEFF Research Database (Denmark)

    Sprenger, Richard R; Jensen, Ole Nørregaard

    2010-01-01

    plasma membrane is of particular interest, by not only serving as a barrier between the "cell interior" and the external environment, but moreover by organizing and clustering essential components to enable dynamic responses to internal and external stimuli. Defining and characterizing the dynamic plasma...... the challenges in functional proteomic studies of the plasma membrane. We review the recent progress in MS-based plasma membrane proteomics by presenting key examples from eukaryotic systems, including mammals, yeast and plants. We highlight the importance of enrichment and quantification technologies...... required for detailed functional and comparative analysis of the dynamic plasma membrane proteome....

  4. Identification of a Novel Di-D-Fructofuranose 1,2’:2,3’ Dianhydride (DFA III) Hydrolysis Enzyme from Arthrobacter aurescens SK8.001

    Science.gov (United States)

    Yu, Shuhuai; Wang, Xiao; Zhang, Tao; Stressler, Timo; Fischer, Lutz; Jiang, Bo; Mu, Wanmeng

    2015-01-01

    Previously, a di-D-fructofuranose 1,2’:2,3’ dianhydride (DFA III)-producing strain, Arthrobacter aurescens SK8.001, was isolated from soil, and the gene cloning and characterization of the DFA III-forming enzyme was studied. In this study, a DFA III hydrolysis enzyme (DFA IIIase)-encoding gene was obtained from the same strain, and the DFA IIIase gene was cloned and expressed in Escherichia coli. The SDS-PAGE and gel filtration results indicated that the purified enzyme was a homotrimer holoenzyme of 145 kDa composed of subunits of 49 kDa. The enzyme displayed the highest catalytic activity for DFA III at pH 5.5 and 55°C, with specific activity of 232 U mg-1. Km and Vmax for DFA III were 30.7 ± 4.3 mM and 1.2 ± 0.1 mM min-1, respectively. Interestingly, DFA III-forming enzymes and DFA IIIases are highly homologous in amino acid sequence. The molecular modeling and docking of DFA IIIase were first studied, using DFA III-forming enzyme from Bacillus sp. snu-7 as a template. It was suggested that A. aurescens DFA IIIase shared a similar three-dimensional structure with the reported DFA III-forming enzyme from Bacillus sp. snu-7. Furthermore, their catalytic sites may occupy the same position on the proteins. Based on molecular docking analysis and site-directed mutagenesis, it was shown that D207 and E218 were two potential critical residues for the catalysis of A. aurescens DFA IIIase. PMID:26555784

  5. Sakshat Labs: India's Virtual Proteomics Initiative

    OpenAIRE

    Sandipan Ray; Nicole R Koshy; Shyam Diwakar; Bipin Nair; Sanjeeva Srivastava

    2012-01-01

    The first Virtual Proteomics Lab of India has been developed at the IIT Bombay as a part of the “Sakshat” Lab Project, established to develop openly accessible, high-quality educational materials on science and technology.

  6. Proteome Regulation during Olea europaea Fruit Development

    DEFF Research Database (Denmark)

    Bianco, Linda; Alagna, Fiammetta; Baldoni, Luciana;

    2013-01-01

    the biosynthesis of compounds affecting the quality of the drupes as well as the final composition of the olive oil. Proteomics offers the possibility to dig deeper into the major changes during fruit development, including the important phase of ripening, and to classify temporal patterns of protein...... accumulation occurring during these complex physiological processes. Methodology/Principal Findings: In this work, we started monitoring the proteome variations associated with olive fruit development by using comparative proteomics coupled to mass spectrometry. Proteins extracted from drupes at three...... evaluate if changes observed at the protein level were consistent with changes of mRNAs, proteomic data produced in the present work were compared with transcriptomic data elaborated during previous studies. Conclusions/Significance: This study identifies a number of proteins responsible for quality traits...

  7. Analysis of soybean seed proteins using proteomics

    Science.gov (United States)

    This editorial elaborates on investigations consisting of different proteomics technologies and their application to biological sciences. In addition, different classes of soybean seed proteins are discussed. This information will be useful to scientists in obtaining a greater understanding of the...

  8. The proteomics in prostate cancer biomarker discovery

    Directory of Open Access Journals (Sweden)

    V. E. Shevchenko

    2015-06-01

    Full Text Available Prostate cancer (PC represents the second most frequent type of tumor in men worldwide. Proteomics represents a promising approach for the discovery of new biomarkers able to improve the management of PC patients. Markers more specific and sensitive than prostate-specific antigen are needed for PC diagnosis, prognosis and response to treatment. Moreover, proteomics could represent an important tool to identify new molecular targets for PC tailored therapy. Now several possible PC biomarkers sources, each with advantages and limitations, are under investigation, including tissues, urine, serum, plasma and prostatic fluids. Innovative high-throughput proteomic platforms are now identifying and quantifying new specific and sensitive biomarkers for PC detection, stratification and treatment. Nevertheless, many putative biomarkers are still far from being applied in clinical practice.This review aims to discuss the recent advances in PC proteomics, emphasizing biomarker discovery and their application to clinical utility for diagnosis and patient stratification.

  9. Proteomics of aluminum tolerance in plants.

    Science.gov (United States)

    Zheng, Lu; Lan, Ping; Shen, Ren Fang; Li, Wen Feng

    2014-03-01

    Aluminum (Al) toxicity is a major constraint for plant root development and growth as well as crop yield in acidic soils, which constitute approximately 40% of the potentially arable lands worldwide. The mechanisms of Al tolerance in plants are not well understood. As a whole systems approach, proteomic techniques have proven to be crucial as a complementary strategy to explore the mechanism in Al toxicity. Review here focuses on the potential of proteomics to unravel the common and plant species-specific changes at proteome level under Al stress, via comparative analysis of the Al-responsive proteins uncovered by recent proteomic studies using 2DE. Understanding the mechanisms of Al tolerance in plants is critical to generate Al resistance crops for developing sustainable agriculture practices, thereby contributing to food security worldwide. PMID:24339160

  10. The Clinical Proteomic Technologies for Cancer | About

    Science.gov (United States)

    An objective of the Reagents and Resources component of NCI's Clinical Proteomic Technologies for Cancer Initiative is to generate highly characterized monoclonal antibodies to human proteins associated with cancer.

  11. The Clinical Proteomic Technologies for Cancer | Partners

    Science.gov (United States)

    An objective of the Reagents and Resources component of NCI's Clinical Proteomic Technologies for Cancer Initiative is to generate highly characterized monoclonal antibodies to human proteins associated with cancer.

  12. Characterization of individual mouse cerebrospinal fluid proteomes

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Jeffrey S.; Angel, Thomas E.; Chavkin, Charles; Orton, Daniel J.; Moore, Ronald J.; Smith, Richard D.

    2014-03-20

    Analysis of cerebrospinal fluid (CSF) offers key insight into the status of the central nervous system. Characterization of murine CSF proteomes can provide a valuable resource for studying central nervous system injury and disease in animal models. However, the small volume of CSF in mice has thus far limited individual mouse proteome characterization. Through non-terminal CSF extractions in C57Bl/6 mice and high-resolution liquid chromatography-mass spectrometry analysis of individual murine samples, we report the most comprehensive proteome characterization of individual murine CSF to date. Utilizing stringent protein inclusion criteria that required the identification of at least two unique peptides (1% false discovery rate at the peptide level) we identified a total of 566 unique proteins, including 128 proteins from three individual CSF samples that have been previously identified in brain tissue. Our methods and analysis provide a mechanism for individual murine CSF proteome analysis.

  13. Statistical data processing in clinical proteomics

    OpenAIRE

    Smit, S.

    2009-01-01

    The subject of this thesis is the analysis of data in clinical proteomics studies aimed at the discovery of biomarkers. The data sets produced in proteomics studies are huge, characterized by a small number of samples in which many proteins and peptides are measured. The studies described in this thesis compare different patient groups (recovering vs. relapsing patients) or a group of patients with a group of healthy controls. The size of the data and the size of the differences between the g...

  14. Collaboration - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    Despite great strides in proteomics and the growing number of articles citing the discovery of potential biomarkers, the actual rate of introduction of Food and Drug Administration (FDA) approved protein analytes has been relatively unchanged over the past 10 years. One of reasons for the lack of new protein-based biomarkers approved has been a lack of information and understanding by the proteomics research community to the regulatory process used by the FDA.

  15. Simple sequence proteins in prokaryotic proteomes

    OpenAIRE

    Ramachandran Srinivasan; Gnanamani Muthiah; Subramanyam Mekapati

    2006-01-01

    Abstract Background The structural and functional features associated with Simple Sequence Proteins (SSPs) are non-globularity, disease states, signaling and post-translational modification. SSPs are also an important source of genetic and possibly phenotypic variation. Analysis of 249 prokaryotic proteomes offers a new opportunity to examine the genomic properties of SSPs. Results SSPs are a minority but they grow with proteome size. This relationship is exhibited across species varying in g...

  16. Bayesian methods for proteomic biomarker development

    Directory of Open Access Journals (Sweden)

    Belinda Hernández

    2015-12-01

    In this review we provide an introduction to Bayesian inference and demonstrate some of the advantages of using a Bayesian framework. We summarize how Bayesian methods have been used previously in proteomics and other areas of bioinformatics. Finally, we describe some popular and emerging Bayesian models from the statistical literature and provide a worked tutorial including code snippets to show how these methods may be applied for the evaluation of proteomic biomarkers.

  17. Proteomics methods applied to malaria: Plasmodium falciparum

    International Nuclear Information System (INIS)

    Malaria is a parasitic disease that has a high impact on public health in developing countries. The sequencing of the plasmodium falciparum genome and the development of proteomics have enabled a breakthrough in understanding the biology of the parasite. Proteomics have allowed to characterize qualitatively and quantitatively the parasite s expression of proteins and has provided information on protein expression under conditions of stress induced by antimalarial. Given the complexity of their life cycle, this takes place in the vertebrate host and mosquito vector. It has proven difficult to characterize the protein expression during each stage throughout the infection process in order to determine the proteome that mediates several metabolic, physiological and energetic processes. Two dimensional electrophoresis, liquid chromatography and mass spectrometry have been useful to assess the effects of antimalarial on parasite protein expression and to characterize the proteomic profile of different p. falciparum stages and organelles. The purpose of this review is to present state of the art tools and advances in proteomics applied to the study of malaria, and to present different experimental strategies used to study the parasite's proteome in order to show the advantages and disadvantages of each one.

  18. Proteomics of survival structures of fungal pathogens.

    Science.gov (United States)

    Loginov, Dmitry; Šebela, Marek

    2016-09-25

    Fungal pathogens are causal agents of numerous human, animal, and plant diseases. They employ various infection modes to overcome host defense systems. Infection mechanisms of different fungi have been subjected to many comprehensive studies. These investigations have been facilitated by the development of various '-omics' techniques, and proteomics has one of the leading roles in this regard. Fungal conidia and sclerotia could be considered the most important structures for pathogenesis as their germination is one of the first steps towards a host infection. They represent interesting objects for proteomic studies because of the presence of unique proteins with unexplored biotechnological potential required for pathogen viability, development and the subsequent host infection. Proteomic peculiarities of survival structures of different fungi, including those of biotechnological significance (e.g., Asperillus fumigatus, A. nidulans, Metarhizium anisopliae), in a dormant state, as well as changes in the protein production during early stages of fungal development are the subjects of the present review. We focused on biological aspects of proteomic studies of fungal survival structures rather than on an evaluation of proteomic approaches. For that reason, proteins that have been identified in this context are discussed from the point of view of their involvement in different biological processes and possible functions assigned to them. This is the first review paper summarizing recent advances in proteomics of fungal survival structures. PMID:26777984

  19. Proteogenomics Dashboard for the Human Proteome Project.

    Science.gov (United States)

    Tabas-Madrid, Daniel; Alves-Cruzeiro, Joao; Segura, Victor; Guruceaga, Elizabeth; Vialas, Vital; Prieto, Gorka; García, Carlos; Corrales, Fernando J; Albar, Juan Pablo; Pascual-Montano, Alberto

    2015-09-01

    dasHPPboard is a novel proteomics-based dashboard that collects and reports the experiments produced by the Spanish Human Proteome Project consortium (SpHPP) and aims to help HPP to map the entire human proteome. We have followed the strategy of analog genomics projects like the Encyclopedia of DNA Elements (ENCODE), which provides a vast amount of data on human cell lines experiments. The dashboard includes results of shotgun and selected reaction monitoring proteomics experiments, post-translational modifications information, as well as proteogenomics studies. We have also processed the transcriptomics data from the ENCODE and Human Body Map (HBM) projects for the identification of specific gene expression patterns in different cell lines and tissues, taking special interest in those genes having little proteomic evidence available (missing proteins). Peptide databases have been built using single nucleotide variants and novel junctions derived from RNA-Seq data that can be used in search engines for sample-specific protein identifications on the same cell lines or tissues. The dasHPPboard has been designed as a tool that can be used to share and visualize a combination of proteomic and transcriptomic data, providing at the same time easy access to resources for proteogenomics analyses. The dasHPPboard can be freely accessed at: http://sphppdashboard.cnb.csic.es. PMID:26144527

  20. Proteome map of the human hippocampus.

    Science.gov (United States)

    Edgar, P F; Douglas, J E; Knight, C; Cooper, G J; Faull, R L; Kydd, R

    1999-01-01

    The proteins expressed by a genome have been termed the proteome. By comparing the proteome of a disease-affected tissue with the proteome of an unaffected tissue it is possible to identify proteins that play a role in a disease process. The hippocampus is involved in the processing of short-term memory and is affected in Alzheimer's disease. Any comparative proteome analysis that can identify proteins important in a disease affecting the hippocampus requires the characterization of the normal hippocampal proteome. Therefore, we homogenised normal hippocampal tissue and separated the proteins by two-dimensional polyacrylamide gel electrophoresis (2DE). Seventy-two unique protein spots were collected from Coomassie blue-stained 2DE gels and subjected to in-gel digestion with trypsin, reversed-phase high-pressure liquid chromatography peptide separation, and N-terminal protein sequencing. Sufficient protein sequence was obtained to successfully characterize 66 of the 72 protein spots chosen (92%). Three of the 66 proteins were not present in any database (4.5%). The characterized proteins comprised two dominant functional groups, i.e., enzymes involved in intermediary cellular metabolism (40%), and proteins associated with the cytoskeleton (15%). The identity, molecular mass, isoelectric point, and relative concentration of the characterized proteins are described and constitute a partial proteome map of the normal human hippocampus. PMID:10641757

  1. The core proteome and pan proteome of Salmonella Paratyphi A epidemic strains.

    Directory of Open Access Journals (Sweden)

    Li Zhang

    Full Text Available Comparative proteomics of the multiple strains within the same species can reveal the genetic variation and relationships among strains without the need to assess the genomic data. Similar to comparative genomics, core proteome and pan proteome can also be obtained within multiple strains under the same culture conditions. In this study we present the core proteome and pan proteome of four epidemic Salmonella Paratyphi A strains cultured under laboratory culture conditions. The proteomic information was obtained using a Two-dimensional gel electrophoresis (2-DE technique. The expression profiles of these strains were conservative, similar to the monomorphic genome of S. Paratyphi A. Few strain-specific proteins were found in these strains. Interestingly, non-core proteins were found in similar categories as core proteins. However, significant fluctuations in the abundance of some core proteins were also observed, suggesting that there is elaborate regulation of core proteins in the different strains even when they are cultured in the same environment. Therefore, core proteome and pan proteome analysis of the multiple strains can demonstrate the core pathways of metabolism of the species under specific culture conditions, and further the specific responses and adaptations of the strains to the growth environment.

  2. The 3rd Central and Eastern European Proteomic Conference

    Czech Academy of Sciences Publication Activity Database

    Gadher, S. J.; Martinková, Jiřina; Drahoš, L.; Vékey, K.; Allmaier, G.; Kovářová, Hana

    2010-01-01

    Roč. 7, č. 1 (2010), s. 15-17. ISSN 1478-9450 Institutional research plan: CEZ:AV0Z50450515 Keywords : proteomics * proteome research * biomarkers Subject RIV: CE - Biochemistry Impact factor: 4.406, year: 2010

  3. Iron overload in human hepatoma cells - proteomic analysis

    Czech Academy of Sciences Publication Activity Database

    Petrák, J.; Myslivcová, D.; Man, Petr; Babušiak, M.; Vyoral, D.

    Lednice, 2005, s. 38-38. [Czech Proteomic Conference /2./. Lednice (CZ), 17.10.2005-20.10.2005] Institutional research plan: CEZ:AV0Z50200510 Keywords : iron * proteomic analysis Subject RIV: EE - Microbiology, Virology

  4. Progress through Collaboration - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The National Cancer Institute (NCI), through the Office of Cancer Clinical Proteomics Research (OCCPR), has signed two Memorandums of Understanding (MOUs) in the areas of sharing proteomics reagents and protocols and also in regulatory science.

  5. Letter from the Director - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The NCI’s Clinical Proteomic Technologies for Cancer (CPTC) initiative is focused on developing a better understanding of cancer biology through the proteomic interrogation of genomically characterized tumors from sources such as The Cancer Genome Atlas.

  6. Director's Update - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (NCI-CPTAC) has recently begun the proteomic interrogation of genomically-characterized tumors from The Cancer Genome Atlas.

  7. Proteomics: an efficient tool to analyze nematode proteins

    Science.gov (United States)

    Proteomic technologies have been successfully used to analyze proteins structure and characterization in plants, animals, microbes and humans. We used proteomics methodologies to separate and characterize soybean cyst nematode (SCN) proteins. Optimizing the quantity of proteins required to separat...

  8. Defining an Open Metadata Framework for Proteomics: The PROMIS Project

    OpenAIRE

    MacMullen, W. John; Parmelee, Mary C.; Fenstermacher, David A.; Hemminger, Bradley M.

    2002-01-01

    This presentation describes the PROMIS project under development at UNC Chapel Hill. PROMIS (Proteomics Metadata Interchange Schema) is a proof-of-concept prototype of an open metadata standard for compositional proteomics.

  9. Role of Proteomics in the Development of Personalized Medicine.

    Science.gov (United States)

    Jain, Kewal K

    2016-01-01

    Advances in proteomic technologies have made import contribution to the development of personalized medicine by facilitating detection of protein biomarkers, proteomics-based molecular diagnostics, as well as protein biochips and pharmacoproteomics. Application of nanobiotechnology in proteomics, nanoproteomics, has further enhanced applications in personalized medicine. Proteomics-based molecular diagnostics will have an important role in the diagnosis of certain conditions and understanding the pathomechanism of disease. Proteomics will be a good bridge between diagnostics and therapeutics; the integration of these will be important for advancing personalized medicine. Use of proteomic biomarkers and combination of pharmacoproteomics with pharmacogenomics will enable stratification of clinical trials and improve monitoring of patients for development of personalized therapies. Proteomics is an important component of several interacting technologies used for development of personalized medicine, which is depicted graphically. Finally, cancer is a good example of applications of proteomic technologies for personalized management of cancer. PMID:26827601

  10. Global analysis of predicted proteomes: Functional adaptation of physical properties

    OpenAIRE

    Knight, Christopher G.; Kassen, Rees; Hebestreit, Holger; Rainey, Paul B.

    2004-01-01

    The physical characteristics of proteins are fundamentally important in organismal function. We used the complete predicted proteomes of >100 organisms spanning the three domains of life to investigate the comparative biology and evolution of proteomes. Theoretical 2D gels were constructed with axes of protein mass and charge (pI) and converted to density estimates comparable across all types and sizes of proteome. We asked whether we could detect general patterns of proteome conservation and...

  11. Advances take stage - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    Regulatory advances in proteomics will be taking center stage at a Symposia scheduled to occur at the 2011 American Association for Clinical Chemistry (AACC) Annual Meeting. The symposium entitled "Enabling Translational Proteomics with NCI's Clinical Proteomic Technologies for Cancer" is scheduled for July 25, 2011 at AACC's annual Meeting.

  12. Tumor Cold Ischemia - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    In a recently published manuscript in the journal of Molecular and Cellular Proteomics, researchers from the National Cancer Institutes (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) investigated the effect of cold ischemia on the proteome of fresh frozen tumors.

  13. Role of the proteome in phytohormonal signaling.

    Science.gov (United States)

    Černý, Martin; Novák, Jan; Habánová, Hana; Cerna, Hana; Brzobohatý, Břetislav

    2016-08-01

    Phytohormones are orchestrators of plant growth and development. A lot of time and effort has been invested in attempting to comprehend their complex signaling pathways but despite success in elucidating some key components, molecular mechanisms in the transduction pathways are far from being resolved. The last decade has seen a boom in the analysis of phytohormone-responsive proteins. Abscisic acid, auxin, brassinosteroids, cytokinin, ethylene, gibberellins, nitric oxide, oxylipins, strigolactones, salicylic acid - all have been analyzed to various degrees. For this review, we collected data from proteome-wide analyses resulting in a list of over 2000 annotated proteins from Arabidopsis proteomics and nearly 500 manually filtered protein families merged from all the data available from different species. We present the currently accepted model of phytohormone signaling, highlight the contributions made by proteomic-based research and describe the key nodes in phytohormone signaling networks, as revealed by proteome analysis. These include ubiquitination and proteasome mediated degradation, calcium ion signaling, redox homeostasis, and phosphoproteome dynamics. Finally, we discuss potential pitfalls and future perspectives in the field. This article is part of a Special Issue entitled: Plant Proteomics - a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock. PMID:26721743

  14. Mass spectrometry in food proteomics: a tutorial.

    Science.gov (United States)

    Cunsolo, Vincenzo; Muccilli, Vera; Saletti, Rosaria; Foti, Salvatore

    2014-09-01

    In the last decades, the continuous and rapid evolution of proteomic approaches has provided an efficient platform for the characterization of food-derived proteins. Particularly, the impressive increasing in performance and versatility of the MS instrumentation has contributed to the development of new analytical strategies for proteins, evidencing how MS arguably represents an indispensable tool in food proteomics. Investigation of protein composition in foodstuffs is helpful for understanding the relationship between the protein content and the nutritional and technological properties of foods, the production of methods for food traceability, the assessment of food quality and safety, including the detection of allergens and microbial contaminants in foods, or even the characterization of genetically modified products. Given the high variety of the food-derived proteins and considering their differences in chemical and physical properties, a single proteomic strategy for all purposes does not exist. Rather, proteomic approaches need to be adapted to each analytical problem, and development of new strategies is necessary in order to obtain always the best results. In this tutorial, the most relevant aspects of MS-based methodologies in food proteomics will be examined, and their advantages and drawbacks will be discussed. PMID:25230173

  15. Urine proteomic profiling of uranium nephrotoxicity

    Energy Technology Data Exchange (ETDEWEB)

    Malard, V.; Gaillard, J.C.; Sage, N. [CEA, DSV, IBEB, SBTN, Laboratoire de Biochimie des Systemes Perturbes (LBSP), Bagnols-sur-Ceze, F-30207 (France); Berenguer, F. [CEA, DSV, IBEB, SBTN, Laboratoire d' Etude des Proteines Cibles (LEPC), Bagnols-sur-Ceze, F-30207 (France); Quemeneur, E. [CEA, DSV, IBEB, SBTN, Bagnols-sur-Ceze, F-30207 (France)

    2009-07-01

    Uranium is used in many chemical forms in civilian and military industries and is a known nephro-toxicant. A key issue in monitoring occupational exposure is to be able to evaluate the potential damage to the body, particularly the kidney. In this study we used innovative proteomic techniques to analyse urinary protein modulation associated with acute uranium exposure in rats. Given that the rat urinary proteome has rarely been studied, we first identified 102 different proteins in normal urine, expanding the current proteome data set for this central animal in toxicology. Rats were exposed intravenously to uranyl nitrate at 2.5 and 5 mg/kg and samples were collected 24 h later. Using two complementary proteomic methods, a classic 2-DE approach and semi-quantitative SDS-PAGE-LC-MS/MS, 14 modulated proteins (7 with increased levels and 7 with decreased levels) were identified in urine after uranium exposure. Modulation of three of them was confirmed by western blot. Some of the modulated proteins corresponded to proteins already described in case of nephrotoxicity, and indicated a loss of glomerular permeability (albumin, alpha-1-anti-proteinase, sero-transferrin). Others revealed tubular damage, such as EGF and vitamin D-binding protein. A third category included proteins never described in urine as being associated with metal stress, such as ceruloplasmin. Urinary proteomics is thus a valuable tool to profile uranium toxicity non-invasively and could be very useful in follow-up in case of accidental exposure to uranium. (authors)

  16. Making proteomics data accessible and reusable: current state of proteomics databases and repositories.

    Science.gov (United States)

    Perez-Riverol, Yasset; Alpi, Emanuele; Wang, Rui; Hermjakob, Henning; Vizcaíno, Juan Antonio

    2015-03-01

    Compared to other data-intensive disciplines such as genomics, public deposition and storage of MS-based proteomics, data are still less developed due to, among other reasons, the inherent complexity of the data and the variety of data types and experimental workflows. In order to address this need, several public repositories for MS proteomics experiments have been developed, each with different purposes in mind. The most established resources are the Global Proteome Machine Database (GPMDB), PeptideAtlas, and the PRIDE database. Additionally, there are other useful (in many cases recently developed) resources such as ProteomicsDB, Mass Spectrometry Interactive Virtual Environment (MassIVE), Chorus, MaxQB, PeptideAtlas SRM Experiment Library (PASSEL), Model Organism Protein Expression Database (MOPED), and the Human Proteinpedia. In addition, the ProteomeXchange consortium has been recently developed to enable better integration of public repositories and the coordinated sharing of proteomics information, maximizing its benefit to the scientific community. Here, we will review each of the major proteomics resources independently and some tools that enable the integration, mining and reuse of the data. We will also discuss some of the major challenges and current pitfalls in the integration and sharing of the data. PMID:25158685

  17. Proteomics: Analysis of Spectral Data

    Directory of Open Access Journals (Sweden)

    Harry B Burke

    2005-01-01

    Full Text Available Abstract: The goal of disease-related proteogenomic research is a complete description of the unfolding of the disease process from its origin to its cure. With a properly selected patient cohort and correctly collected, processed, analyzed data, large scale proteomic spectra may be able to provide much of the information necessary for achieving this goal. Protein spectra, which are one way of representing protein expression, can be extremely useful clinically since they can be generated from blood rather than from diseased tissue. At the same time, the analysis of circulating proteins in blood presents unique challenges because of their heterogeneity, blood contains a large number of different abundance proteins generated by tissues throughout the body. Another challenge is that protein spectra are massively parallel information. One can choose to perform top-down analysis, where the entire spectra is examined and candidate peaks are selected for further assessment. Or one can choose a bottom-up analysis, where, via hypothesis testing, individual proteins are identified in the spectra and related to the disease process. Each approach has advantages and disadvantages that must be understood if protein spectral data are to be properly analyzed. With either approach, several levels of information must be integrated into a predictive model. This model will allow us to detect disease and it will allow us to discover therapeutic interventions that reduce the risk of disease in at-risk individuals and effectively treat newly diagnosed disease.

  18. Proteomic Analysis of Hair Follicles

    Science.gov (United States)

    Ishioka, Noriaki; Terada, Masahiro; Yamada, Shin; Seki, Masaya; Takahashi, Rika; Majima, Hideyuki J.; Higashibata, Akira; Mukai, Chiaki

    2013-02-01

    Hair root cells actively divide in a hair follicle, and they sensitively reflect physical conditions. By analyzing the human hair, we can know stress levels on the human body and metabolic conditions caused by microgravity environment and cosmic radiation. The Japan Aerospace Exploration Agency (JAXA) has initiated a human research study to investigate the effects of long-term space flight on gene expression and mineral metabolism by analyzing hair samples of astronauts who stayed in the International Space Station (ISS) for 6 months. During long-term flights, the physiological effects on astronauts include muscle atrophy and bone calcium loss. Furthermore, radiation and psychological effects are important issue to consider. Therefore, an understanding of the effects of the space environment is important for developing countermeasures against the effects experienced by astronauts. In this experiment, we identify functionally important target proteins that integrate transcriptome, mineral metabolism and proteome profiles from human hair. To compare the protein expression data with the gene expression data from hair roots, we developed the protein processing method. We extracted the protein from five strands of hair using ISOGEN reagents. Then, these extracted proteins were analyzed by LC-MS/MS. These collected profiles will give us useful physiological information to examine the effect of space flight.

  19. Proteomic landscape in Central and Eastern Europe: the 9th Central and Eastern European Proteomic Conference, Poznan, Poland

    Czech Academy of Sciences Publication Activity Database

    Gadher, S. J.; Marczak, L.; Luczak, M.; Stobiecki, M.; Widlak, P.; Kovářová, Hana

    2016-01-01

    Roč. 13, č. 1 (2016), s. 5-7. ISSN 1478-9450. [Central and Eastern European Proteomic Conference (CEEPC) /9./. Poznaň, 15.06.2015-18.06.2015] Institutional support: RVO:67985904 Keywords : Central and Eastern Proteomic Conference * proteomics * mass spectrometry imaging Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.896, year: 2014

  20. Proteome analysis of developing mice diastema region

    Directory of Open Access Journals (Sweden)

    Young-Mi Chae1, Young-Joo Jin1, Hyeng-Soo Kim2, Gi-Jeong Gwon1, Wern-Joo Sohn1,2, Sung-Hyun Kim3, Myoung-Ok Kim4, Sanggyu Lee2, Jo-Young Suh5 & Jae-Young Kim1*

    2012-06-01

    Full Text Available Different from humans, who have a continuous dentition ofteeth, mice have only three molars and one incisor separatedby a toothless region called the diastema in the hemimandibular arch. Although tooth buds form in the embryonicdiastema, they regress and do not develop into teeth. In thisstudy, we evaluated the proteins that modulate the diastemaformation through comparative analysis with molar-formingtissue by liquid chromatography-tandem mass spectroscopy(LC-MS/MS proteome analysis. From the comparative andsemi-quantitative proteome analysis, we identified 147 up- and173 down-regulated proteins in the diastema compared to themolar forming proteins. Based on this proteome analysis, weselected and evaluated two candidate proteins, EMERIN andRAB7A, as diastema tissue specific markers. This studyprovides the first list of proteins that were detected in themouse embryonic diastema region, which will be useful tounderstand the mechanisms of tooth development.

  1. Proteomic profiling of skeletal muscle plasticity.

    Science.gov (United States)

    Ohlendieck, Kay

    2011-10-01

    One of the most striking physiological features of skeletal muscle tissues are their enormous capacity to adapt to changed functional demands. Muscle plasticity has been extensively studied by histological, biochemical, physiological and genetic methods over the last few decades. With the recent emergence of high-throughput and large-scale proteomic techniques, mass spectrometry-based surveys have also been applied to the global analysis of the skeletal muscle protein complement during physiological modifications and pathophysiological alterations. This review outlines and discusses the impact of recent proteomic profiling studies of skeletal muscle transitions, including the effects of chronic electro-stimulation, physical exercise, denervation, disuse atrophy, hypoxia, myotonia, motor neuron disease and age-related fibre type shifting. This includes studies on the human skeletal muscle proteome, animal models of muscle plasticity and major neuromuscular pathologies. The biomedical importance of establishing reliable biomarker signatures for the various molecular and cellular transition phases involved in muscle transformation is critically examined. PMID:23738259

  2. Comparative proteomics and difference gel electrophoresis.

    Science.gov (United States)

    Minden, Jonathan

    2007-12-01

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

  3. Introduction to mass spectrometry-based proteomics

    DEFF Research Database (Denmark)

    Matthiesen, Rune; Bunkenborg, Jakob

    2013-01-01

    Mass spectrometry has been widely applied to study biomolecules and one rapidly developing field is the global analysis of proteins, proteomics. Understanding and handling mass spectrometry data is a multifaceted task that requires many decisions to be made to get the most comprehensive information...... from an experiment. Later chapters in this book deal in-depth with various aspects of the process and how different tools can be applied to the many analytical challenges. This introductory chapter is intended as a basic introduction to mass spectrometry (MS)-based proteomics to set the scene...... for newcomers and give pointers to reference material. There are many applications of mass spectrometry in proteomics and each application is associated with some analytical choices, instrumental limitations and data processing steps that depend on the aim of the study and means of conducting it. Different...

  4. Plant nuclear proteomics for unraveling physiological function.

    Science.gov (United States)

    Yin, Xiaojian; Komatsu, Setsuko

    2016-09-25

    The nucleus is the subcellular organelle that functions as the regulatory hub of the cell and is responsible for regulating several critical cellular functions, including cell proliferation, gene expression, and cell survival. Nuclear proteomics is a useful approach for investigating the mechanisms underlying plant responses to abiotic stresses, including protein-protein interactions, enzyme activities, and post-translational modifications. Among abiotic stresses, flooding is a major limiting factor for plant growth and yields, particularly for soybean. In this review, plant nuclei purification methods, modifications of plant nuclear proteins, and recent contributions to the field of plant nuclear proteomics are summarized. In addition, to reveal the upstream regulating mechanisms controlling soybean responses to flooding stress, the functions of flooding-responsive nuclear proteins are reviewed based on the results of nuclear proteomic analysis of soybean in the early stages of flooding stress. PMID:27004615

  5. Shaping Biological Knowledge: Applications in Proteomics

    Directory of Open Access Journals (Sweden)

    R. Appel

    2006-04-01

    Full Text Available The central dogma of molecular biology has provided a meaningful principle for data integration in the field of genomics. In this context, integration reflects the known transitions from a chromosome to a protein sequence: transcription, intron splicing, exon assembly and translation. There is no such clear principle for integrating proteomics data, since the laws governing protein folding and interactivity are not quite understood. In our effort to bring together independent pieces of information relative to proteins in a biologically meaningful way, we assess the bias of bioinformatics resources and consequent approximations in the framework of small-scale studies. We analyse proteomics data while following both a data-driven (focus on proteins smaller than 10 kDa and a hypothesis-driven (focus on whole bacterial proteomes approach. These applications are potentially the source of specialized complements to classical biological ontologies.

  6. A Review: Proteomics in Nasopharyngeal Carcinoma

    Directory of Open Access Journals (Sweden)

    Ze-Tan Chen

    2015-07-01

    Full Text Available Although radiotherapy is generally effective in the treatment of major nasopharyngeal carcinoma (NPC, this treatment still makes approximately 20% of patients radioresistant. Therefore, the identification of blood or biopsy biomarkers that can predict the treatment response to radioresistance and that can diagnosis early stages of NPC would be highly useful to improve this situation. Proteomics is widely used in NPC for searching biomarkers and comparing differentially expressed proteins. In this review, an overview of proteomics with different samples related to NPC and common proteomics methods was made. In conclusion, identical proteins are sorted as follows: Keratin is ranked the highest followed by such proteins as annexin, heat shock protein, 14-3-3σ, nm-23 protein, cathepsin, heterogeneous nuclear ribonucleoproteins, enolase, triosephosphate isomerase, stathmin, prohibitin, and vimentin. This ranking indicates that these proteins may be NPC-related proteins and have potential value for further studies.

  7. A comprehensive compilation of SUMO proteomics.

    Science.gov (United States)

    Hendriks, Ivo A; Vertegaal, Alfred C O

    2016-09-01

    Small ubiquitin-like modifiers (SUMOs) are essential for the regulation of several cellular processes and are potential therapeutic targets owing to their involvement in diseases such as cancer and Alzheimer disease. In the past decade, we have witnessed a rapid expansion of proteomic approaches for identifying sumoylated proteins, with recent advances in detecting site-specific sumoylation. In this Analysis, we combined all human SUMO proteomics data currently available into one cohesive database. We provide proteomic evidence for sumoylation of 3,617 proteins at 7,327 sumoylation sites, and insight into SUMO group modification by clustering the sumoylated proteins into functional networks. The data support sumoylation being a frequent protein modification (on par with other major protein modifications) with multiple nuclear functions, including in transcription, mRNA processing, DNA replication and the DNA-damage response. PMID:27435506

  8. Oxidative stress and bivalves: a proteomic approach

    Directory of Open Access Journals (Sweden)

    B McDonagh

    2008-09-01

    Full Text Available Bivalves are of major importance in aquatic ecology, aquaculture, are widely used as sentinel species in environmental toxicology and show remarkable plasticity to molecular oxygen. Excess reactive oxygen species (ROS arising from molecular oxygen can cause oxidative stress and this is also a consequence of exposure to many common environmental pollutants. Indices of oxidative stress have therefore found favor as biomarkers of exposure and effect in environmental toxicology. However, there is a growing body of literature on the use of discovery-led proteomics methods to detect oxidative stress in bivalves. This is because proteins absorb up to 70 % of ROS leading to complication of the proteome. This article explores the background to these developments and assesses the practice and future potential of proteomics in the study of oxidative stress in bivalves.

  9. Biomarkers in Transplantation-Proteomics and Metabolomics.

    Science.gov (United States)

    Christians, Uwe; Klawitter, Jelena; Klawitter, Jost

    2016-04-01

    Modern multianalyte "omics" technologies allow for the identification of molecular signatures that confer significantly more information than measurement of a single parameter as typically used in current medical diagnostics. Proteomics and metabolomics bioanalytical assays capture a large set of proteins and metabolites in body fluids, cells, or tissues and, complementing genomics, assess the phenome. Proteomics and metabolomics contribute to the development of novel predictive clinical biomarkers in transplantation in 2 ways: they can be used to generate a diagnostic fingerprint or they can be used to discover individual proteins and metabolites of diagnostic potential. Much fewer metabolomics than proteomics biomarker studies in transplant patients have been reported, and, in contrast to proteomics discovery studies, new lead metabolite markers have yet to emerge. Most clinical proteomics studies have been discovery studies. Several of these studies have assessed diagnostic sensitivity and specificity. Nevertheless, none of these newly discovered protein biomarkers have yet been implemented in clinical decision making in transplantation. The currently most advanced markers discovered in proteomics studies in transplant patients are the chemokines CXCL-9 and CXCL-10, which have successfully been validated in larger multicenter trials in kidney transplant patients. These chemokines can be measured using standard immunoassay platforms, which should facilitate clinical implementation. Based on the published evidence, it is reasonable to expect that these chemokine markers can help guiding and individualizing immunosuppressive regimens, may be able to predict acute and chronic T-cell-mediated and antibody-mediated rejection, and may be useful tools for risk stratification of kidney transplant patients. PMID:26418702

  10. An individual urinary proteome analysis in normal human beings to define the minimal sample number to represent the normal urinary proteome

    OpenAIRE

    Liu Xuejiao; Shao Chen; Wei Lilong; Duan Jindan; Wu Shuzhen; Li Xuewang; Li Mingxi; Sun Wei

    2012-01-01

    Abstract Background The urinary proteome has been widely used for biomarker discovery. A urinary proteome database from normal humans can provide a background for discovery proteomics and candidate proteins/peptides for targeted proteomics. Therefore, it is necessary to define the minimum number of individuals required for sampling to represent the normal urinary proteome. Methods In this study, inter-individual and inter-gender variations of urinary proteome were taken into consideration to ...

  11. New challenges for proteomics technologies: a mini perspective review

    Energy Technology Data Exchange (ETDEWEB)

    Shen, Yufeng; Pasa-Tolic, Ljiljana; Robinson, Errol W.; Adkins, Joshua N.; Smith, Richard D.

    2014-10-10

    Proteomics technologies have experienced rapid advances over the last decade to identify or quantify thousands of proteins per sample, typically in a few hours, enabling proteomics applications in environmental, biological, medical, and clinical research. A number of publications have reviewed advances in proteomic technologies and applications. This short review focuses first on a discussion of sensitivity in bottom-up (i.e. digested protein) proteomics and approaches for characterization of small cell populations, and secondly on protein separations for top-down (i.e. intact protein) proteomics including discussions of key technical challenges where recent advances are elucidating specific functions of proteins in biological processes.

  12. Influence of single-walled carbon nanotubes on the growth and phenol biodegradation characteristics of Arthrobacter sp.W1%单壁碳纳米管对Arthrobacter sp.W1生长及苯酚降解功能的影响

    Institute of Scientific and Technical Information of China (English)

    李端行; 王经伟; 沈文丽; 张照婧; 厉舒祯; 李会杰; 刘紫嫣; 马桥; 曲媛媛

    2015-01-01

    单壁碳纳米管(SWCNTs)对大肠杆菌等模式菌株的生长抑制作用明显,为了解SWCNTs对具有环境功能的菌株的作用,以苯酚降解菌Arthrobacter sp.Wl为对象,考察不同浓度SWCNTs下菌株W1的生长曲线和苯酚降解曲线,并通过扫描电镜观察、细胞凋亡检测、DNA泄漏量分析和活性氧产量分析考察作用机制.结果表明,特定浓度范围的SWCNTs (0.5-5.0 mg/L)会加快W1的苯酚降解速率,且1.5-2.0 mg/L SWCNTs不抑制Wl的生长.SWCNTs在溶液中形成团簇并吸附Wl细胞,且对Wl产生以物理穿刺为主的毒性作用,但在特定浓度范围的SWCNTS条件下,SWCNTs-菌株-苯酚体系增加了菌体与苯酚的接触机会,从而对Wl生长和苯酚降解产生明显的促进作用.本研究结果可为进一步揭示SWCNTs的环境微生物效应提供理论依据.

  13. Comprehensive proteomic analysis of human pancreatic juice

    DEFF Research Database (Denmark)

    Grønborg, Mads; Bunkenborg, Jakob; Kristiansen, Troels Zakarias;

    2004-01-01

    chromatography tandem mass spectrometry (LC-MS/MS). A total of 170 unique proteins were identified including known pancreatic cancer tumor markers (e.g., CEA, MUC1) and proteins overexpressed in pancreatic cancers (e.g., hepatocarcinoma-intestine-pancreas/pancreatitis-associated protein (HIP/PAP) and lipocalin 2......Proteomic technologies provide an excellent means for analysis of body fluids for cataloging protein constituents and identifying biomarkers for early detection of cancers. The biomarkers currently available for pancreatic cancer, such as CA19-9, lack adequate sensitivity and specificity...... in this study could be directly assessed for their potential as biomarkers for pancreatic cancer by quantitative proteomics methods or immunoassays....

  14. Unraveling pancreatic islet biology by quantitative proteomics

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Jianying; Dann, Geoffrey P.; Liew, Chong W.; Smith, Richard D.; Kulkarni, Rohit N.; Qian, Weijun

    2011-08-01

    The pancreatic islets of Langerhans play a critical role in maintaining blood glucose homeostasis by secreting insulin and several other important peptide hormones. Impaired insulin secretion due to islet dysfunction is linked to the pathogenesis underlying both Type 1 and Type 2 diabetes. Over the past 5 years, emerging proteomic technologies have been applied to dissect the signaling pathways that regulate islet functions and gain an understanding of the mechanisms of islet dysfunction relevant to diabetes. Herein, we briefly review some of the recent quantitative proteomic studies involving pancreatic islets geared towards gaining a better understanding of islet biology relevant to metabolic diseases.

  15. Proteomics of Rice Seed Germination

    Institute of Scientific and Technical Information of China (English)

    Dongli He; Chao Han; Xiaojian Yin; Hui Zhang; Pingfang Yang

    2012-01-01

    Seed germination is a complex physiological which starts from the uptake of water by the dry seeds and ends at the protrusion of the radicle.In order to elucidate the mechanism of rice seed germination,we have conducted a systematic proteomic analyses combining with 1-D via LC MS/MS,comparative 2-DE and iTRAQ techniques using the whole seed or dissected embryos and endosperm.During rice seed germination,the embryo and endosperm played different roles.The seed weight increased and complied by a triphasic model.Phase I accompanied with rapid seed water-up-take,the embryo produced gibberellic acid (GA) and diffused to aleurone and then prepared to initiate a signaling cascade to drive the reserves degradation in the starchy endosperm.Phase II is the most important stage for metabolic reactions reactivation,the reserves mobilization,cell construction respiration,cell wall loosening and coleoptile elongation,most of the metabolism related proteins sorted to different pathways were identified at 24 h after imbibition,but the metabolism of nucleotides was not active at this stage for few related proteins have been involved.The degradation of seed maturation and desiccation-associated proteins seemed to be earlier than that of the storage proteins and starch.The glycolysis was the main pathway for energy and substance providing.Phase III is another rapid water-uptake stage accompanying with TCA and aerobic respiration strengthening,cell division initiation and the radical protrusion.Interesting,both biosynthesis and degradation of the same macromolecule were concurrence even in the dry seed,which implied the sequentially matabolic and regulatory events triggered by water uptake during rice seed germination have been programmed during seed maturation.

  16. The proteome of Hypobaric Induced Hypoxic Lung: Insights from Temporal Proteomic Profiling for Biomarker Discovery

    OpenAIRE

    Ahmad, Yasmin; Sharma, Narendra K.; Ahmad, Mohammad Faiz; Sharma, Manish; Garg, Iti; Srivastava, Mousami; Bhargava, Kalpana

    2015-01-01

    Exposure to high altitude induces physiological responses due to hypoxia. Lungs being at the first level to face the alterations in oxygen levels are critical to counter and balance these changes. Studies have been done analysing pulmonary proteome alterations in response to exposure to hypobaric hypoxia. However, such studies have reported the alterations at specific time points and do not reflect the gradual proteomic changes. These studies also identify the various biochemical pathways and...

  17. Approaching clinical proteomics: current state and future fields of application in fluid proteomics

    OpenAIRE

    Apweiler, Rolf; Aslanidis, Charalampos; Deufel, Thomas; Gerstner, Andreas; Hansen, Jens; Hochstrasser, Dennis; Kellner, Roland; Kubicek, Markus; Lottspeich, Friedrich; Maser, Edmund; Mewes, Hans-Werner; Meyer, Helmut E.; Müllner, Stefan; Mutter, Wolfgang; Neumaier, Michael

    2009-01-01

    The field of clinical proteomics offers opportunities to identify new disease biomarkers in body fluids, cells and tissues. These biomarkers can be used in clinical applications for diagnosis, stratification of patients for specific treatment, or therapy monitoring. New protein array formats and improved spectrometry technologies have brought these analyses to a level with potential for use in clinical diagnostics. The nature of the human body fluid proteome with its large dynamic range of pr...

  18. Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline.

    Science.gov (United States)

    Slagel, Joseph; Mendoza, Luis; Shteynberg, David; Deutsch, Eric W; Moritz, Robert L

    2015-02-01

    Cloud computing, where scalable, on-demand compute cycles and storage are available as a service, has the potential to accelerate mass spectrometry-based proteomics research by providing simple, expandable, and affordable large-scale computing to all laboratories regardless of location or information technology expertise. We present new cloud computing functionality for the Trans-Proteomic Pipeline, a free and open-source suite of tools for the processing and analysis of tandem mass spectrometry datasets. Enabled with Amazon Web Services cloud computing, the Trans-Proteomic Pipeline now accesses large scale computing resources, limited only by the available Amazon Web Services infrastructure, for all users. The Trans-Proteomic Pipeline runs in an environment fully hosted on Amazon Web Services, where all software and data reside on cloud resources to tackle large search studies. In addition, it can also be run on a local computer with computationally intensive tasks launched onto the Amazon Elastic Compute Cloud service to greatly decrease analysis times. We describe the new Trans-Proteomic Pipeline cloud service components, compare the relative performance and costs of various Elastic Compute Cloud service instance types, and present on-line tutorials that enable users to learn how to deploy cloud computing technology rapidly with the Trans-Proteomic Pipeline. We provide tools for estimating the necessary computing resources and costs given the scale of a job and demonstrate the use of cloud enabled Trans-Proteomic Pipeline by performing over 1100 tandem mass spectrometry files through four proteomic search engines in 9 h and at a very low cost. PMID:25418363

  19. Pressurized Pepsin Digestion in Proteomics: An Automatable Alternative to Trypsin for Integrated Top-down Bottom-up Proteomics

    Energy Technology Data Exchange (ETDEWEB)

    Lopez-Ferrer, Daniel; Petritis, Konstantinos; Robinson, Errol W.; Hixson, Kim K.; Tian, Zhixin; Lee, Jung Hwa; Lee, Sang-Won; Tolic, Nikola; Weitz, Karl K.; Belov, Mikhail E.; Smith, Richard D.; Pasa-Tolic, Ljiljana

    2011-02-01

    Integrated top-down bottom-up proteomics combined with online digestion has great potential to improve the characterization of protein isoforms in biological systems and is amendable to highthroughput proteomics experiments. Bottom-up proteomics ultimately provides the peptide sequences derived from the tandem MS analyses of peptides after the proteome has been digested. Top-down proteomics conversely entails the MS analyses of intact proteins for more effective characterization of genetic variations and/or post-translational modifications (PTMs). Herein, we describe recent efforts towards efficient integration of bottom-up and top-down LCMS based proteomic strategies. Since most proteomic platforms (i.e. LC systems) operate in acidic environments, we exploited the compatibility of the pepsin (i.e. the enzyme’s natural acidic activity) for the integration of bottom-up and top-down proteomics. Pressure enhanced pepsin digestions were successfully performed and characterized with several standard proteins in either an offline mode using a Barocycler or an online mode using a modified high pressure LC system referred to as a fast online digestion system (FOLDS). FOLDS was tested using pepsin and a whole microbial proteome, and the results compared against traditional trypsin digestions on the same platform. Additionally, FOLDS was integrated with a RePlay configuration to demonstrate an ultra-rapid integrated bottom-up top-down proteomic strategy employing a standard mixture of proteins and a monkey pox virus proteome.

  20. Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation.

    Directory of Open Access Journals (Sweden)

    Chuming Chen

    Full Text Available The accelerating growth in the number of protein sequences taxes both the computational and manual resources needed to analyze them. One approach to dealing with this problem is to minimize the number of proteins subjected to such analysis in a way that minimizes loss of information. To this end we have developed a set of Representative Proteomes (RPs, each selected from a Representative Proteome Group (RPG containing similar proteomes calculated based on co-membership in UniRef50 clusters. A Representative Proteome is the proteome that can best represent all the proteomes in its group in terms of the majority of the sequence space and information. RPs at 75%, 55%, 35% and 15% co-membership threshold (CMT are provided to allow users to decrease or increase the granularity of the sequence space based on their requirements. We find that a CMT of 55% (RP55 most closely follows standard taxonomic classifications. Further analysis of this set reveals that sequence space is reduced by more than 80% relative to UniProtKB, while retaining both sequence diversity (over 95% of InterPro domains and annotation information (93% of experimentally characterized proteins. All sets can be browsed and are available for sequence similarity searches and download at http://www.proteininformationresource.org/rps, while the set of 637 RPs determined using a 55% CMT are also available for text searches. Potential applications include sequence similarity searches, protein classification and targeted protein annotation and characterization.

  1. Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation.

    Science.gov (United States)

    Chen, Chuming; Natale, Darren A; Finn, Robert D; Huang, Hongzhan; Zhang, Jian; Wu, Cathy H; Mazumder, Raja

    2011-01-01

    The accelerating growth in the number of protein sequences taxes both the computational and manual resources needed to analyze them. One approach to dealing with this problem is to minimize the number of proteins subjected to such analysis in a way that minimizes loss of information. To this end we have developed a set of Representative Proteomes (RPs), each selected from a Representative Proteome Group (RPG) containing similar proteomes calculated based on co-membership in UniRef50 clusters. A Representative Proteome is the proteome that can best represent all the proteomes in its group in terms of the majority of the sequence space and information. RPs at 75%, 55%, 35% and 15% co-membership threshold (CMT) are provided to allow users to decrease or increase the granularity of the sequence space based on their requirements. We find that a CMT of 55% (RP55) most closely follows standard taxonomic classifications. Further analysis of this set reveals that sequence space is reduced by more than 80% relative to UniProtKB, while retaining both sequence diversity (over 95% of InterPro domains) and annotation information (93% of experimentally characterized proteins). All sets can be browsed and are available for sequence similarity searches and download at http://www.proteininformationresource.org/rps, while the set of 637 RPs determined using a 55% CMT are also available for text searches. Potential applications include sequence similarity searches, protein classification and targeted protein annotation and characterization. PMID:21556138

  2. Mining the active proteome of Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Renier A. L. Van Der Hoorn

    2011-11-01

    Full Text Available Assigning functions to the >30.000 proteins encoded by the Arabidopsis genome is a challenging task of the Arabidopsis Functional Genomics Network. Although genome-wide technologies like proteomics and transcriptomics have generated a wealth of information that significantly accelerated gene annotation, protein activities are poorly predicted by transcript or protein levels as protein activities are post-translationally regulated. To directly display protein activities in Arabidopsis proteomes, we developed and applied Activity-based Protein Profiling (ABPP. ABPP is based on the use of small molecule probes that react with the catalytic residues of distinct protein classes in an activity-dependent manner. Labeled proteins are separated and detected from proteins gels and purified and identified by mass spectrometry. Using probes of six different chemotypes we have displayed of activities of 76 Arabidopsis proteins. These proteins represent over ten different protein classes that contain over 250 Arabidopsis proteins, including cysteine- serine- and metallo-proteases, lipases, acyltransferases, and the proteasome. We have developed methods for identification of in vivo labeled proteins using click-chemistry and for in vivo imaging with fluorescent probes. In vivo labeling has revealed novel protein activities and unexpected subcellular activities of the proteasome. Labeling of extracts displayed several differential activities e.g. of the proteasome during immune response and methylesterases during infection. These studies illustrate the power of ABPP to display the functional proteome and testify to a successful interdisciplinary collaboration involving chemical biology, organic chemistry and proteomics.

  3. The dynamic proteome of Lyme disease Borrelia.

    Science.gov (United States)

    Norris, Steven J

    2006-01-01

    The proteome of the spirochete bacterium Borrelia burgdorferi, the tick-borne agent of Lyme disease, has been characterized by two different approaches using mass spectrometry, providing a launching point for future studies on the dramatic changes in protein expression that occur during transmission of the bacterium between ticks and mammals. PMID:16563176

  4. The dynamic proteome of Lyme disease Borrelia

    OpenAIRE

    Norris, Steven J

    2006-01-01

    The proteome of the spirochete bacterium Borrelia burgdorferi, the tick-borne agent of Lyme disease, has been characterized by two different approaches using mass spectrometry, providing a launching point for future studies on the dramatic changes in protein expression that occur during transmission of the bacterium between ticks and mammals.

  5. A proteomic analysis of human bile

    DEFF Research Database (Denmark)

    Kristiansen, Troels Zakarias; Bunkenborg, Jakob; Gronborg, Mads; Molina, Henrik; Thuluvath, Paul J; Argani, Pedram; Goggins, Michael G; Maitra, Anirban; Pandey, Akhilesh

    2004-01-01

    We have carried out a comprehensive characterization of human bile to define the bile proteome. Our approach involved fractionation of bile by one-dimensional gel electrophoresis and lectin affinity chromatography followed by liquid chromatography tandem mass spectrometry. Overall, we identified ...

  6. Top Down proteomics: Facts and perspectives

    International Nuclear Information System (INIS)

    Highlights: • Top Down versus Bottom Up proteomics analysis. • Separations methods for Top Down proteomics. • Developments in mass spectrometry instrumentation and fragmentation. • Native mass spectrometry. - Abstract: The rise of the “Top Down” method in the field of mass spectrometry-based proteomics has ushered in a new age of promise and challenge for the characterization and identification of proteins. Injecting intact proteins into the mass spectrometer allows for better characterization of post-translational modifications and avoids several of the serious “inference” problems associated with peptide-based proteomics. However, successful implementation of a Top Down approach to endogenous or other biologically relevant samples often requires the use of one or more forms of separation prior to mass spectrometric analysis, which have only begun to mature for whole protein MS. Recent advances in instrumentation have been used in conjunction with new ion fragmentation using photons and electrons that allow for better (and often complete) protein characterization on cases simply not tractable even just a few years ago. Finally, the use of native electrospray mass spectrometry has shown great promise for the identification and characterization of whole protein complexes in the 100 kDa to 1 MDa regime, with prospects for complete compositional analysis for endogenous protein assemblies a viable goal over the coming few years

  7. Serum-proteomics in melanoma patients

    International Nuclear Information System (INIS)

    The project Serum-proteomics in melanoma patients funded by 'Programma Oncologico Italia-USA' Oncoproteomica has the general aim to collect serum samples from melanoma patients and to analyze the expression profile of several cytokines, in order to identify whether significant differences are evident between patients and controls, or among different patients subgroups with different staging or therapy

  8. GUHA Analysis of Proteomic Oncological Data

    Czech Academy of Sciences Publication Activity Database

    Coufal, David; Vydra, J.; Selicharová, Irena

    2007-01-01

    Roč. 17, č. 5 (2007), s. 447-457. ISSN 1210-0552 R&D Projects: GA MZd NR8323 Institutional research plan: CEZ:AV0Z10300504; CEZ:AV0Z40550506 Keywords : data mining * proteomic analysis * breast cancer Subject RIV: IN - Informatics, Computer Science Impact factor: 0.280, year: 2007

  9. The cell surface proteome of Staphylococcus aureus

    NARCIS (Netherlands)

    Dreisbach, Annette; van Dijl, Jan Maarten; Buist, Girbe

    2011-01-01

    The Gram-positive bacterium Staphylococcus aureus is a wide spread opportunistic pathogen that can cause a range of life-threatening diseases. To obtain a better understanding of the global mechanisms for pathogenesis and to identify novel targets for therapeutic interventions, the S. aureus proteom

  10. Shotgun Proteomic Analysis of Arabidopsis thaliana Leaves

    Science.gov (United States)

    Two shotgun tandem mass spectrometry proteomics approaches, Multidimensional Protein Identification Technology (MudPIT) and 1D-Gel-LC-MS/MS, were used to identify Arabidopsis thaliana leaf proteins. These methods utilize different protein/peptide separation strategies. Detergents not compatible wit...

  11. feature - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    "Cancer is a disease of the genome," noted Lynda Chin, M.D., professor of dermatology, Harvard Medical School and Dana-Farber Cancer Institute. "And understanding the impact of genomic changes in the proteome is critically important for converting genomic knowledge into something that a clinician can use on their patients."

  12. A proteomic analysis of human hemodialysis fluid

    DEFF Research Database (Denmark)

    Molina, Henrik; Bunkenborg, Jakob; Reddy, G Hanumanthu;

    2005-01-01

    The vascular compartment is an easily accessible compartment that provides an opportunity to measure analytes for diagnostic, prognostic, or therapeutic indications. Both serum and plasma have been analyzed extensively by proteomic approaches in an effort to catalog all proteins and polypeptides...

  13. JDIP Genomics, Antibodies, and Proteomics Core Update

    Science.gov (United States)

    The JDIP Genomics, Proteomics, and Antibodies Core has developed several resources that are available for use by JDIP researchers. Five tasks have been completed or are in progress: Task 1 – Transposon mutants: Nearly 24,000 gene disruption M. paratuberculosis mutants are now available for JDIP re...

  14. Proteomics of mastitis causing Escherichia coli

    Science.gov (United States)

    Mastitis remains the most prevalent disease in dairy cattle. The economic impact of mastitis on the dairy industry is estimated to be $2 billion per year. Mastitis involves a complex set of interactions between an invading pathogen and the host’s immune systems. Proteomics is a new tool used to s...

  15. Aluminum induced proteome changes in tomato cotyledons

    Science.gov (United States)

    Cotyledons of tomato seedlings that germinated in a 20 µM AlK(SO4)2 solution remained chlorotic while those germinated in an aluminum free medium were normal (green) in color. Previously, we have reported the effect of aluminum toxicity on root proteome in tomato seedlings (Zhou et al. J Exp Bot, 20...

  16. Proteomics of human teeth and saliva

    Czech Academy of Sciences Publication Activity Database

    Jágr, Michal; Eckhardt, Adam; Pataridis, Statis; Broukal, Z.; Dušková, J.; Mikšík, Ivan

    2014-01-01

    Roč. 63, Suppl.1 (2014), S141-S154. ISSN 0862-8408 R&D Projects: GA MZd(CZ) NT14324 Institutional support: RVO:67985823 Keywords : proteomics * tooth * dentin * enamel * pulp Subject RIV: FF - HEENT, Dentistry Impact factor: 1.293, year: 2014

  17. Functional proteomics within the genus Lactobacillus.

    Science.gov (United States)

    De Angelis, Maria; Calasso, Maria; Cavallo, Noemi; Di Cagno, Raffaella; Gobbetti, Marco

    2016-03-01

    Lactobacillus are mainly used for the manufacture of fermented dairy, sourdough, meat, and vegetable foods or used as probiotics. Under optimal processing conditions, Lactobacillus strains contribute to food functionality through their enzyme portfolio and the release of metabolites. An extensive genomic diversity analysis was conducted to elucidate the core features of the genus Lactobacillus, and to provide a better comprehension of niche adaptation of the strains. However, proteomics is an indispensable "omics" science to elucidate the proteome diversity, and the mechanisms of regulation and adaptation of Lactobacillus strains. This review focuses on the novel and comprehensive knowledge of functional proteomics and metaproteomics of Lactobacillus species. A large list of proteomic case studies of different Lactobacillus species is provided to illustrate the adaptability of the main metabolic pathways (e.g., carbohydrate transport and metabolism, pyruvate metabolism, proteolytic system, amino acid metabolism, and protein synthesis) to various life conditions. These investigations have highlighted that lactobacilli modulate the level of a complex panel of proteins to growth/survive in different ecological niches. In addition to the general regulation and stress response, specific metabolic pathways can be switched on and off, modifying the behavior of the strains. PMID:27001126

  18. An update on the mouse liver proteome

    Directory of Open Access Journals (Sweden)

    Borlak Jürgen

    2009-09-01

    Full Text Available Abstract Background Decoding of the liver proteome is subject of intense research, but hampered by methodological constraints. We recently developed an improved protocol for studying rat liver proteins based on 2-DE-MALDI-TOF-MS peptide mass finger printing. This methodology was now applied to develop a mouse liver protein database. Results Liver proteins were extracted by two different lysis buffers in sequence followed by a liquid-phase IEF pre-fractionation and separation of proteins by 2 DE at two different pH ranges, notably 5-8 and 7-10. Based on 9600 in gel digests a total of 643 mouse liver proteins with high sequence coverage (> 20 peptides per protein could be identified by MALDI-TOF-MS peptide mass finger printing. Notably, 255 proteins are novel and have not been reported so far by conventional two-dimensional electrophoresis proteome mapping. Additionally, the results of the present findings for mouse liver were compared to published data of the rat proteome to compile as many proteins as possible in a rodent liver database. Conclusion Based on 2-DE MALDI-TOF-MS a significantly improved proteome map of mouse liver was obtained. We discuss some prominent members of newly identified proteins for a better understanding of liver biology.

  19. Human maternal plasma proteomic changes with parturition

    Directory of Open Access Journals (Sweden)

    Robert J. Phillips

    2014-12-01

    Significance: Proteomic technology is constantly advancing, and the latest techniques enable gel-free analysis of minimally preprocessed, complex biological samples, enabling simultaneous identification and quantification of many hundreds of proteins. The technique of TMT labelling and Orbitrap mass spectrometry is applicable to the analysis of serial maternal plasma samples in order to identify potential markers of the onset of labour.

  20. The proteomic toolbox for studying cerebrospinal fluid

    NARCIS (Netherlands)

    Gool, A.J. van; Hendrickson, R.C.

    2012-01-01

    Cerebrospinal fluid (CSF) can be considered the most promising biosample for the discovery and analysis of biomarkers in neuroscience, an area of great medical need. CSF is a body fluid that surrounds the brain and provides a rich pool of biochemical markers, both proteomic and metabolomic, that ref

  1. Proteomic Approaches for Biomarker Panels in Cancer.

    Science.gov (United States)

    Tanase, Cristiana; Albulescu, Radu; Neagu, Monica

    2016-01-01

    Proteomic technologies remain the main backbone of biomarkers discovery in cancer. The continuous development of proteomic technologies also enlarges the bioinformatics domain, thus founding the main pillars of cancer therapy. The main source for diagnostic/prognostic/therapy monitoring biomarker panels are molecules that have a dual role, being both indicators of disease development and therapy targets. Proteomic technologies, such as mass-spectrometry approaches and protein array technologies, represent the main technologies that can depict these biomarkers. Herein, we will illustrate some of the most recent strategies for biomarker discovery in cancer, including the development of immune-markers and the use of cancer stem cells as target therapy. The challenges of proteomic biomarker discovery need new forms of cross-disciplinary conglomerates that will result in increased and tailored access to treatments for patients; diagnostic companies would benefit from the enhanced co-development of companion diagnostics and pharmaceutical companies. In the technology optimization in biomarkers, immune assays are the leaders of discovery machinery. PMID:26565430

  2. Introduction to mass spectrometry-based proteomics

    DEFF Research Database (Denmark)

    Matthiesen, R.; Bunkenborg, J.

    2013-01-01

    for newcomers and give pointers to reference material. There are many applications of mass spectrometry in proteomics and each application is associated with some analytical choices, instrumental limitations and data processing steps that depend on the aim of the study and means of conducting it. Different...

  3. Top Down proteomics: Facts and perspectives

    Energy Technology Data Exchange (ETDEWEB)

    Catherman, Adam D.; Skinner, Owen S.; Kelleher, Neil L., E-mail: n-kelleher@northwestern.edu

    2014-03-21

    Highlights: • Top Down versus Bottom Up proteomics analysis. • Separations methods for Top Down proteomics. • Developments in mass spectrometry instrumentation and fragmentation. • Native mass spectrometry. - Abstract: The rise of the “Top Down” method in the field of mass spectrometry-based proteomics has ushered in a new age of promise and challenge for the characterization and identification of proteins. Injecting intact proteins into the mass spectrometer allows for better characterization of post-translational modifications and avoids several of the serious “inference” problems associated with peptide-based proteomics. However, successful implementation of a Top Down approach to endogenous or other biologically relevant samples often requires the use of one or more forms of separation prior to mass spectrometric analysis, which have only begun to mature for whole protein MS. Recent advances in instrumentation have been used in conjunction with new ion fragmentation using photons and electrons that allow for better (and often complete) protein characterization on cases simply not tractable even just a few years ago. Finally, the use of native electrospray mass spectrometry has shown great promise for the identification and characterization of whole protein complexes in the 100 kDa to 1 MDa regime, with prospects for complete compositional analysis for endogenous protein assemblies a viable goal over the coming few years.

  4. Induced Sputum Proteome in Health and Asthma

    Science.gov (United States)

    Gharib, Sina A.; Nguyen, Elizabeth V.; Lai, Ying; Plampin, Jessica D.; Goodlett, David R.; Hallstrand, Teal S.

    2014-01-01

    Background Asthma is a heterogeneous disease characterized by abnormal airway pathophysiology and susceptibility to different stimuli, as exemplified by a subset of individuals with exercise-induced bronchoconstriction (EIB). Induced sputum provides a noninvasive method to sample airway biofluids that are enriched in proteins. Objective We hypothesized that novel mechanisms in the pathogenesis of asthma may be revealed by studying the patterns of protein expression in induced sputum. Methods We used shotgun proteomics to analyze induced sputum from 5 normal individuals and 10 asthmatics, including 5 with EIB. Differential protein expression between asthmatics, asthma subphenotypes and control subjects was determined using spectral counting and computational methods. Results Using Gene Ontology analysis, we defined the functional landscape of induced sputum proteome and applied network analysis to construct a protein interaction map for this airway compartment. Shotgun proteomics analysis identified a number of proteins whose differential enrichment or depletion robustly distinguishedasthmatics from normal controls, and captured the effects of exercise on induced sputum proteome. Functional and network analysis identified key processes, including proteolytic activity that are known contributors to airway remodeling. Importantly, this approach highlighted previously unrecognized roles for differentially expressed proteins in pathways implicated in asthma, such as modulation of phospholipase A2 by secretoglobin, a putative role for S100A8/9 in human asthma, and selective upregulation of complement 3a in response to exercise in asthmatics. Conclusion Computationally-intensive analysis of induced sputum proteome is a powerful approach to understand the pathophysiology of asthma and a promising methodology to investigate other diseases of the airways. PMID:21906793

  5. Proteome identification of the silkworm middle silk gland.

    Science.gov (United States)

    Li, Jian-Ying; Ye, Lu-Peng; Che, Jia-Qian; Song, Jia; You, Zheng-Ying; Wang, Shao-Hua; Zhong, Bo-Xiong

    2016-03-01

    To investigate the functional differentiation among the anterior (A), middle (M), and posterior (P) regions of silkworm middle silk gland (MSG), their proteomes were characterized by shotgun LC-MS/MS analysis with a LTQ-Orbitrap mass spectrometer. To get better proteome identification and quantification, triplicate replicates of mass spectrometry analysis were performed for each sample. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (Vizcaíno et al., 2014) [1] via the PRIDE partner repository (Vizcaino, 2013) [2] with the dataset identifier PXD003371. The peptide identifications that were further processed by PeptideProphet program in Trans-Proteomic Pipeline (TPP) after database search with Mascot software were also available in .XML format files. Data presented here are related to a research article published in Journal of Proteomics by Li et al. (2015) [3]. PMID:26937469

  6. Plasma Proteome Profiling to Assess Human Health and Disease.

    Science.gov (United States)

    Geyer, Philipp E; Kulak, Nils A; Pichler, Garwin; Holdt, Lesca M; Teupser, Daniel; Mann, Matthias

    2016-03-23

    Proteins in the circulatory system mirror an individual's physiology. In daily clinical practice, protein levels are generally determined using single-protein immunoassays. High-throughput, quantitative analysis using mass-spectrometry-based proteomics of blood, plasma, and serum would be advantageous but is challenging because of the high dynamic range of protein abundances. Here, we introduce a rapid and robust "plasma proteome profiling" pipeline. This single-run shotgun proteomic workflow does not require protein depletion and enables quantitative analysis of hundreds of plasma proteomes from 1 μl single finger pricks with 20 min gradients. The apolipoprotein family, inflammatory markers such as C-reactive protein, gender-related proteins, and >40 FDA-approved biomarkers are reproducibly quantified (CV proteome obtained by simple peptide pre-fractionation. Plasma proteome profiling delivers an informative portrait of a person's health state, and we envision its large-scale use in biomedicine. PMID:27135364

  7. Subcellular Proteomics of Soybean under Flooding Stress

    Institute of Scientific and Technical Information of China (English)

    Setsuko Komatsu

    2012-01-01

    Flooding is an environmental stress found worldwide and may increase in frequency due to changes in global climate,and causes significant reductions in the growth and yield of several crops.The application of proteomics techniques to clarify the molecular mechanisms underlying crop responses to flooding stress may facilitate the development of flood tolerant crops.To understand the response mechanism of soybean under flooding stress,proteomics analysis was carried out.Especially,subcellular proteomics studies have led to a better understanding of the mechanism of flooding stress tolerance in soybean.The effects of flooding stress on root plasma membrane were analyzed using an aqueous two-phase partitioning method in combination with gel-based and gel-free proteomics techniques.The results led to the following conclusions:proteins located in the cell wall were increased in the plasma membrane of flooded plants,indicating the contribution of plasma membrane to modification of the cell wall; superoxide dismutase was increased,indicating that the antioxidative system may play a crucial role in protecting cells from oxidative damage following exposure to flooding stress; heat shock cognate 70 kDa protein likely plays a significant role in protecting other proteins from denaturation and degradation during flooding stress; and signaling proteins might work cooperatively to regulate plasma membrane H +-ATPase and maintain ion homeostasis.Cell wall proteins were isolated from root of flooding stressed plants via sucrose gradient centrifugation and analyzed using gel-based proteomics technique.Cell wall proteins identified were related to lignification,and these results indicated that a decrease of lignification-related proteins is related to flooding decreased ROS and jasmonate biosynthesis.And also,lignin staining confirmed that lignification was suppressed in the roots of flooding stressed soybeans.Mitochondrial fractions were purified from root of flooding stressed

  8. Proteomics study revealed altered proteome of Dichogaster curgensis upon exposure to fly ash.

    Science.gov (United States)

    Markad, Vijaykumar L; Adav, Sunil S; Ghole, Vikram S; Sze, Siu Kwan; Kodam, Kisan M

    2016-10-01

    Fly ash is toxic and its escalating use as a soil amendment and disposal by dumping into environment is receiving alarming attention due to its impact on environment. Proteomics technology is being used for environmental studies since proteins respond rapidly when an organism is exposed to a toxicant, and hence soil engineers such as earthworms are used as model organisms to assess the toxic effects of soil toxicants. This study adopted proteomics technology and profiled proteome of earthworm Dichogaster curgensis that was exposed to fly ash, with main aim to elucidate fly ash effects on cellular and metabolic pathways. The functional classification of identified proteins revealed carbohydrate metabolism (14.36%), genetic information processing (15.02%), folding, sorting and degradation (10.83%), replication and repair (3.95%); environmental information processing (2.19%), signal transduction (9.61%), transport and catabolism (17.27%), energy metabolism (6.69%), etc. in the proteome. Proteomics data and functional assays revealed that the exposure of earthworm to fly ash induced protein synthesis, up-regulation of gluconeogenesis, disturbed energy metabolism, oxidative and cellular stress, and mis-folding of proteins. The regulation of ubiquitination, proteasome and modified alkaline comet assay in earthworm coelomocytes suggested DNA-protein cross link affecting chromatin remodeling and protein folding. PMID:27371791

  9. Plant fluid proteomics: Delving into the xylem sap, phloem sap and apoplastic fluid proteomes.

    Science.gov (United States)

    Rodríguez-Celma, Jorge; Ceballos-Laita, Laura; Grusak, Michael A; Abadía, Javier; López-Millán, Ana-Flor

    2016-08-01

    The phloem sap, xylem sap and apoplastic fluid play key roles in long and short distance transport of signals and nutrients, and act as a barrier against local and systemic pathogen infection. Among other components, these plant fluids contain proteins which are likely to be important players in their functionalities. However, detailed information about their proteomes is only starting to arise due to the difficulties inherent to the collection methods. This review compiles the proteomic information available to date in these three plant fluids, and compares the proteomes obtained in different plant species in order to shed light into conserved functions in each plant fluid. Inter-species comparisons indicate that all these fluids contain the protein machinery for self-maintenance and defense, including proteins related to cell wall metabolism, pathogen defense, proteolysis, and redox response. These analyses also revealed that proteins may play more relevant roles in signaling in the phloem sap and apoplastic fluid than in the xylem sap. A comparison of the proteomes of the three fluids indicates that although functional categories are somewhat similar, proteins involved are likely to be fluid-specific, except for a small group of proteins present in the three fluids, which may have a universal role, especially in cell wall maintenance and defense. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock. PMID:27033031

  10. An overview of stress response proteomes in Listeria monocytogenes

    OpenAIRE

    Soni, K A; Nannapaneni, R; Tasara, T

    2011-01-01

    Listeria monocytogenes adapts to diverse stress conditions including cold, osmotic, heat, acid, and alkali stresses encountered during food processing and preservation which is a serious food safety threat. In this review, we have presented the major findings on this bacterium’s stress response proteomes to date along with the different approaches used for its proteomic analysis. The key proteome findings on cold, heat shock, salt, acid, alkaline and HHP stresses illustrate that the cellular ...

  11. Yeast expression proteomics by high-resolution mass spectrometry

    DEFF Research Database (Denmark)

    Walther, Tobias C; Olsen, Jesper Velgaard; Mann, Matthias

    2010-01-01

    -translational controls contribute majorly to regulation of protein abundance, for example in heat shock stress response. The development of new sample preparation methods, high-resolution mass spectrometry and novel bioinfomatic tools close this gap and allow the global quantitation of the yeast proteome under different...... conditions. Here, we provide background information on proteomics by mass-spectrometry and describe the practice of a comprehensive yeast proteome analysis....

  12. Computational approaches to protein inference in shotgun proteomics

    OpenAIRE

    Li Yong; Radivojac Predrag

    2012-01-01

    Abstract Shotgun proteomics has recently emerged as a powerful approach to characterizing proteomes in biological samples. Its overall objective is to identify the form and quantity of each protein in a high-throughput manner by coupling liquid chromatography with tandem mass spectrometry. As a consequence of its high throughput nature, shotgun proteomics faces challenges with respect to the analysis and interpretation of experimental data. Among such challenges, the identification of protein...

  13. Mass Spectrometry-Based Label-Free Quantitative Proteomics

    OpenAIRE

    Chun-Ming Huang; Smith, Jeffrey W.; Wenhong Zhu

    2009-01-01

    In order to study the differential protein expression in complex biological samples, strategies for rapid, highly reproducible and accurate quantification are necessary. Isotope labeling and fluorescent labeling techniques have been widely used in quantitative proteomics research. However, researchers are increasingly turning to label-free shotgun proteomics techniques for faster, cleaner, and simpler results. Mass spectrometry-based label-free quantitative proteomics falls into two general c...

  14. Mass Spectrometry-Based Approaches Toward Absolute Quantitative Proteomics

    OpenAIRE

    Kito, Keiji; Ito, Takashi

    2008-01-01

    Mass spectrometry has served as a major tool for the discipline of proteomics to catalogue proteins in an unprecedented scale. With chemical and metabolic techniques for stable isotope labeling developed over the past decade, it is now routinely used as a method for relative quantification to provide valuable information on alteration of protein abundance in a proteome-wide scale. More recently, absolute or stoichiometric quantification of proteome is becoming feasible, in particular, with th...

  15. Mass spectrometry-based proteomics in cell biology

    OpenAIRE

    Walther, T. C.; Mann, M

    2010-01-01

    The global analysis of protein composition, modifications, and dynamics are important goals in cell biology. Mass spectrometry (MS)–based proteomics has matured into an attractive technology for this purpose. Particularly, high resolution MS methods have been extremely successful for quantitative analysis of cellular and organellar proteomes. Rapid advances in all areas of the proteomic workflow, including sample preparation, MS, and computational analysis, should make the technology more eas...

  16. Virtual Labs in proteomics: new E-learning tools.

    Science.gov (United States)

    Ray, Sandipan; Koshy, Nicole Rachel; Reddy, Panga Jaipal; Srivastava, Sanjeeva

    2012-05-17

    Web-based educational resources have gained enormous popularity recently and are increasingly becoming a part of modern educational systems. Virtual Labs are E-learning platforms where learners can gain the experience of practical experimentation without any direct physical involvement on real bench work. They use computerized simulations, models, videos, animations and other instructional technologies to create interactive content. Proteomics being one of the most rapidly growing fields of the biological sciences is now an important part of college and university curriculums. Consequently, many E-learning programs have started incorporating the theoretical and practical aspects of different proteomic techniques as an element of their course work in the form of Video Lectures and Virtual Labs. To this end, recently we have developed a Virtual Proteomics Lab at the Indian Institute of Technology Bombay, which demonstrates different proteomics techniques, including basic and advanced gel and MS-based protein separation and identification techniques, bioinformatics tools and molecular docking methods, and their applications in different biological samples. This Tutorial will discuss the prominent Virtual Labs featuring proteomics content, including the Virtual Proteomics Lab of IIT-Bombay, and E-resources available for proteomics study that are striving to make proteomic techniques and concepts available and accessible to the student and research community. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 14). Details can be found at: http://www.proteomicstutorials.org/. PMID:22484059

  17. Proteomic study of cancer cells response to anthracycline anticancer treatment

    Czech Academy of Sciences Publication Activity Database

    Tylečková, Jiřina; Hrabáková, Rita; Mairychová, Kateřina; Halada, Petr; Radová, L.; Džubák, P.; Hajduch, M.; Kovářová, Hana

    Berlin : Freie Universität Berlin, 2011. s. 225-225. [Proteomic Forum 2011. 3.4.2011-7.4.2011, Berlin] R&D Projects: GA MŠk LC07017; GA MŠk MSM6198959216 Institutional research plan: CEZ:AV0Z50450515; CEZ:AV0Z50200510 Keywords : anticancer research * anthracycline * proteomics Subject RIV: CE - Biochemistry http://www.proteomic-forum.de/images/stories/pics/proteomic%20forum%202011%20-%20abstract%20book.pdf

  18. From protein catalogues towards targeted proteomics approaches in cereal grains

    DEFF Research Database (Denmark)

    Finnie, Christine; Sultan, Abida; Grasser, Klaus D.

    2011-01-01

    Due to their importance for human nutrition, the protein content of cereal grains has been a subject of intense study for over a century and cereal grains were not surprisingly one of the earliest subjects for 2D-gel-based proteome analysis. Over the last two decades, countless cereal grain...... extraction, separation and identification of proteins and peptides is facilitating functional proteomics and analysis of sub-proteomes from small amounts of starting material, such as seed tissues. The combination of proteomics with structural and functional analysis is increasingly applied to target subsets...

  19. Proteomics and Its Application in Biomarker Discovery and Drug Development

    Institute of Scientific and Technical Information of China (English)

    He Qing-Yu; Chiu Jen-Fu

    2004-01-01

    Proteomics is a research field aiming to characterize molecular and cellular dynamics in protein expression and function on a global level. The introduction of proteomics has been greatly broadening our view and accelerating our path in various medical researches. The most significant advantage of proteomics is its ability to examine a whole proteome or sub-proteome in a single experiment so that the protein alterations corresponding to a pathological or biochemical condition at a given time can be considered in an integrated way. Proteomic technology has been extensively used to tackle a wide variety of medical subjects including biomarker discovery and drug development. By complement with other new technique advance in genomics and bioinformatics,proteomics has a great potential to make considerable contribution to biomarker identification and revolutionize drug development process. A brief overview of the proteomic technologies will be provided and the application of proteomics in biomarker discovery and drug development will be discussed using our current research projects as examples.

  20. Single Electron Transistor Platform for Microgravity Proteomics Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Proteomic studies in microgravity are crucial to understanding the health effects of spaceflight on astronauts. Unfortunately, existing tools for measuring protein,...

  1. Receptor tyrosine kinase signaling: a view from quantitative proteomics

    DEFF Research Database (Denmark)

    Dengjel, Joern; Kratchmarova, Irina; Blagoev, Blagoy

    2009-01-01

    signal transduction. Numerous new post-translational modification sites have been identified by quantitative mass spectrometry-based proteomics. In addition, plentiful new players in signal transduction have been identified underlining the complexity and the modular architecture of most signaling...... networks. In this review, we outline the principles of signal transduction via RTKs and highlight some of the new insights obtained from proteomic approaches such as protein microarrays and quantitative mass spectrometry....... RTKs. In recent years proteomic approaches have yielded detailed descriptions of cellular signaling events. Quantitative proteomics is able to characterize the exact position and strength of post-translational modifications (PTMs) providing essential information for understanding the molecular basis of...

  2. Comprehensive data analysis of human ureter proteome

    Directory of Open Access Journals (Sweden)

    Sameh Magdeldin

    2016-03-01

    Full Text Available Comprehensive human ureter proteome dataset was generated from OFFGel fractionated ureter samples. Our result showed that among 2217 non-redundant ureter proteins, 751 protein candidates (33.8% were detected in urine as urinary protein/polypeptide or exosomal protein. On the other hand, comparing ureter protein hits (48 that are not shown in corresponding databases to urinary bladder and prostate human protein atlas databases pinpointed 21 proteins that might be unique to ureter tissue. In conclusion, this finding offers future perspectives for possible identification of ureter disease-associated biomarkers such as ureter carcinoma. In addition, Cytoscape GO annotation was examined on the final ureter dataset to better understand proteins molecular function, biological processes, and cellular component. The ureter proteomic dataset published in this article will provide a valuable resource for researchers working in the field of urology and urine biomarker discovery.

  3. Application of Proteomics and Peptidomics to COPD

    Directory of Open Access Journals (Sweden)

    Girolamo Pelaia

    2014-01-01

    Full Text Available Chronic obstructive pulmonary disease (COPD is a complex disorder involving both airways and lung parenchyma, usually associated with progressive and poorly reversible airflow limitation. In order to better characterize the phenotypic heterogeneity and the prognosis of patients with COPD, there is currently an urgent need for discovery and validation of reliable disease biomarkers. Within this context, proteomic and peptidomic techniques are emerging as very valuable tools that can be applied to both systemic and pulmonary samples, including peripheral blood, induced sputum, exhaled breath condensate, bronchoalveolar lavage fluid, and lung tissues. Identification of COPD biomarkers by means of proteomic and peptidomic approaches can thus also lead to discovery of new molecular targets potentially useful to improve and personalize the therapeutic management of this widespread respiratory disease.

  4. Comprehensive data analysis of human ureter proteome

    Science.gov (United States)

    Magdeldin, Sameh; Hirao, Yoshitoshi; El Guoshy, Amr; Xu, Bo; Zhang, Ying; Fujinaka, Hidehiko; Yamamoto, Keiko; Yates, John R.; Yamamoto, Tadashi

    2016-01-01

    Comprehensive human ureter proteome dataset was generated from OFFGel fractionated ureter samples. Our result showed that among 2217 non-redundant ureter proteins, 751 protein candidates (33.8%) were detected in urine as urinary protein/polypeptide or exosomal protein. On the other hand, comparing ureter protein hits (48) that are not shown in corresponding databases to urinary bladder and prostate human protein atlas databases pinpointed 21 proteins that might be unique to ureter tissue. In conclusion, this finding offers future perspectives for possible identification of ureter disease-associated biomarkers such as ureter carcinoma. In addition, Cytoscape GO annotation was examined on the final ureter dataset to better understand proteins molecular function, biological processes, and cellular component. The ureter proteomic dataset published in this article will provide a valuable resource for researchers working in the field of urology and urine biomarker discovery. PMID:26937461

  5. Cancer Proteomics: The State of the Art

    Directory of Open Access Journals (Sweden)

    Paul C. Herrmann

    2001-01-01

    Full Text Available Now that the human genome has been determined, the field of proteomics is ramping up to tackle the vast protein networks that both control and are controlled by the information encoded by the genome. The study of proteomics should yield an unparalleled understanding of cancer as well as an invaluable new target for therapeutic intervention and markers for early detection. This rapidly expanding field attempts to track the protein interactions responsible for all cellular processes. By careful analysis of these systems, a detailed understanding of the molecular causes and consequences of cancer should emerge. A brief overview of some of the cutting edge technologies employed by this rapidly expanding field is given, along with specific examples of how these technologies are employed. Soon cellular protein networks will be understood at a level that will permit a totally new paradigm of diagnosis and will allow therapy tailored to individual patients and situations.

  6. Proteomic cornerstones of hematopoietic stem cell differentiation

    DEFF Research Database (Denmark)

    Klimmeck, Daniel; Hansson, Jenny; Raffel, Simon;

    2012-01-01

    Regenerative tissues such as the skin epidermis, the intestinal mucosa or the hematopoietic system are organized in a hierarchical manner with stem cells building the top of this hierarchy. Somatic stem cells harbor the highest self-renewal activity and generate a series of multipotent progenitors...... which differentiate into lineage committed progenitors and subsequently mature cells. In this report, we applied an in-depth quantitative proteomic approach to analyze and compare the full proteomes of ex vivo isolated and FACS-sorted populations highly enriched for either multipotent hematopoietic stem....../progenitor cells (HSPCs, Lin(neg)Sca-1(+)c-Kit(+)) or myeloid committed precursors (Lin(neg)Sca-1(-)c-Kit(+)). By employing stable isotope dimethyl labeling and high-resolution mass spectrometry, more than 5,000 proteins were quantified. From biological triplicate experiments subjected to rigorous statistical...

  7. Genomics and proteomics: Applications in autoimmune diseases

    Directory of Open Access Journals (Sweden)

    Wolfgang Hueber

    2009-08-01

    Full Text Available Wolfgang Hueber1,2,3, William H Robinson1,21VA Palo Alto Health Care System, Palo Alto, CA, USA; 2Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA; 3Novartis Institutes of Biomedical Research, Novartis, Basle, SwitzerlandAbstract: Tremendous progress has been made over the past decade in the development and refinement of genomic and proteomic technologies for the identification of novel drug targets and molecular signatures associated with clinically important disease states, disease subsets, or differential responses to therapies. The rapid progress in high-throughput technologies has been preceded and paralleled by the elucidation of cytokine networks, followed by the stepwise clinical development of pathway-specific biological therapies that revolutionized the treatment of autoimmune diseases. Together, these advances provide opportunities for a long-anticipated personalized medicine approach to the treatment of autoimmune disease. The ever-increasing numbers of novel, innovative therapies will need to be harnessed wisely to achieve optimal long-term outcomes in as many patients as possible while complying with the demands of health authorities and health care providers for evidence-based, economically sound prescription of these expensive drugs. Genomic and proteomic profiling of patients with autoimmune diseases holds great promise in two major clinical areas: (1 rapid identification of new targets for the development of innovative therapies and (2 identification of patients who will experience optimal benefit and minimal risk from a specific (targeted therapy. In this review, we attempt to capture important recent developments in the application of genomic and proteomic technologies to translational research by discussing informative examples covering a diversity of autoimmune diseases.Keywords: proteomics, genomics, autoimmune diseases, antigen microarrays, 2-Dih, rheumatoid arthritis

  8. Proteome analysis of developing mice diastema region

    OpenAIRE

    Young-Mi Chae1, Young-Joo Jin1, Hyeng-Soo Kim2, Gi-Jeong Gwon1, Wern-Joo Sohn1,2, Sung-Hyun Kim3, Myoung-Ok Kim4, Sanggyu Lee2, Jo-Young Suh5 & Jae-Young Kim1*

    2012-01-01

    Different from humans, who have a continuous dentition ofteeth, mice have only three molars and one incisor separatedby a toothless region called the diastema in the hemimandibular arch. Although tooth buds form in the embryonicdiastema, they regress and do not develop into teeth. In thisstudy, we evaluated the proteins that modulate the diastemaformation through comparative analysis with molar-formingtissue by liquid chromatography-tandem mass spectroscopy(LC-MS/MS) proteome analysis. From t...

  9. The pancreatic beta cell surface proteome

    OpenAIRE

    Stützer, I.; Esterházy, D.; Stoffel, M.

    2012-01-01

    The pancreatic beta cell is responsible for maintaining normoglycaemia by secreting an appropriate amount of insulin according to blood glucose levels. The accurate sensing of the beta cell extracellular environment is therefore crucial to this endocrine function and is transmitted via its cell surface proteome. Various surface proteins that mediate or affect beta cell endocrine function have been identified, including growth factor and cytokine receptors, transporters, ion channels and prote...

  10. Integrative Bioinformatics for Genomics and Proteomics

    OpenAIRE

    Wu, C.H.

    2011-01-01

    Systems integration is becoming the driving force for 21st century biology. Researchers are systematically tackling gene functions and complex regulatory processes by studying organisms at different levels of organization, from genomes and transcriptomes to proteomes and interactomes. To fully realize the value of such high-throughput data requires advanced bioinformatics for integration, mining, comparative analysis, and functional interpretation. We are developing a bioinformatics research ...

  11. Proteomics of CDK inhibition in cancer cells

    Czech Academy of Sciences Publication Activity Database

    Kovářová, Hana; Skalníková, Helena; Halada, Petr; Strnad, M.; Hajdúch, M.

    Olomouc: -, 2007, s. 1-1. [Symposium and Workshop on Molecular Pathology /3./. Olomouc (CZ), 04.05.2007-05.05.2007] R&D Projects: GA ČR GA301/05/0418; GA MŠk LC07017 Institutional research plan: CEZ:AV0Z50450515; CEZ:AV0Z50200510 Keywords : cyclin-dependent kinase inhibitors * cancer * proteomics Subject RIV: EB - Genetics ; Molecular Biology

  12. Comprehensive proteomic analysis of human dentin

    Czech Academy of Sciences Publication Activity Database

    Jágr, Michal; Eckhardt, Adam; Pataridis, Statis; Mikšík, Ivan

    2012-01-01

    Roč. 120, č. 4 (2012), s. 259-268. ISSN 0909-8836 R&D Projects: GA ČR(CZ) GA203/08/1428; GA ČR(CZ) GAP206/12/0453 Institutional research plan: CEZ:AV0Z50110509 Institutional support: RVO:67985823 Keywords : dentin * mass spectrometry * proteomics * tooth * two-dimensional gel electrophoresis Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 1.420, year: 2012

  13. Comparative proteomic analysis of Clostridium difficile

    OpenAIRE

    Chilton, Caroline Hazel

    2011-01-01

    The recent increase in availability of next generation sequencing methodologies has led to extensive analysis of the genome of Clostridium difficile. In contrast, protein expression analysis, crucial to the elucidation of mechanisms of disease, has severely lagged behind. In this study, in-depth proteomic analysis of three strains of varying virulence, demonstrated previously in an animal model, has been undertaken against a background of the sequenced genomes. Strain B-1 is ...

  14. Global MS-Based Proteomics Drug Profiling.

    Science.gov (United States)

    Carvalho, Ana Sofia; Matthiesen, Rune

    2016-01-01

    DNA-based technologies such as RNAi, chemical-genetic profiling, or gene expression profiling by DNA microarrays combined with other biochemical methods are established strategies for surveying drug mechanisms. Such approaches can provide mechanistic information on how drugs act and affect cellular pathways. By studying how cancer cells compensate for the drug treatment, novel targets used in a combined treatment can be designed. Furthermore, toxicity effects on cells not targeted can be obtained on a molecular level. For example, drug companies are particularly interested in studying the molecular side effects of drugs in the liver. In addition, experiments with the purpose of elucidating liver toxicity can be studied using samples obtained from animal models exposed to different concentrations of a drug over time. More recently considerable advances in mass spectrometry (MS) technologies and bioinformatics tools allows informative global drug profiling experiments to be performed at a cost comparable to other large-scale technologies such as DNA-based technologies. Moreover, MS-based proteomics provides an additional layer of information on the dynamic regulation of proteins translation and particularly protein degradation. MS-based proteomics approaches combined with other biochemical methods delivers information on regulatory networks, signaling cascades, and metabolic pathways upon drug treatment. Furthermore, MS-based proteomics can provide additional information on single amino acid polymorphisms, protein isoform distribution, posttranslational modifications, and subcellular localization. In this chapter, we will share our experience using MS based proteomics as a pharmacoproteomics strategy to characterize drug mechanisms of action in single drug therapy or in multidrug combination. Finally, the emergence of integrated proteogenomics analysis, such as "The Cancer Genome Atlas" program, opened interesting perspectives to extend this approach to drug target

  15. An update on the mouse liver proteome

    OpenAIRE

    Borlak Jürgen; Gazzana Giuseppe

    2009-01-01

    Abstract Background Decoding of the liver proteome is subject of intense research, but hampered by methodological constraints. We recently developed an improved protocol for studying rat liver proteins based on 2-DE-MALDI-TOF-MS peptide mass finger printing. This methodology was now applied to develop a mouse liver protein database. Results Liver proteins were extracted by two different lysis buffers in sequence followed by a liquid-phase IEF pre-fractionation and separation of proteins by 2 ...

  16. Is the unfoldome widespread in proteomes?

    OpenAIRE

    Deiana, Antonio; Giansanti, Andrea

    2010-01-01

    The term unfoldome has been recently used to indicate the universe of intrinsically disordered proteins. These proteins are characterized by an ensemble of high-flexible interchangeable conformations and therefore they can interact with many targets without requiring pre-existing stereo-chemical complementarity. It has been suggested that intrinsically disordered proteins are frequent in proteomes and disorder is widespread also in structured proteins. However, several studies raise some doub...

  17. Urinary Proteomics to Support Diagnosis of Stroke

    OpenAIRE

    Dawson, J.; Walters, M.; Delles, C.; Mischak, H.; Mullen, W

    2012-01-01

    Accurate diagnosis in suspected ischaemic stroke can be difficult. We explored the urinary proteome in patients with stroke (n = 69), compared to controls (n = 33), and developed a biomarker model for the diagnosis of stroke. We performed capillary electrophoresis online coupled to micro-time-of-flight mass spectrometry. Potentially disease-specific peptides were identified and a classifier based on these was generated using support vector machine-based software. Candidate biomarkers were seq...

  18. Proteomic profiling of skeletal muscle plasticity

    OpenAIRE

    Ohlendieck, Kay

    2012-01-01

    One of the most striking physiological features of skeletal muscle tissues are their enormous capacity to adapt to changed functional demands. Muscle plasticity has been extensively studied by histological, biochemical, physiological and genetic methods over the last few decades. With the recent emergence of high-throughput and large-scale proteomic techniques, mass spectrometry-based surveys have also been applied to the global analysis of the skeletal muscle protein complement during physio...

  19. Proteomics and syndrome of Chinese medicine

    OpenAIRE

    Lu, Chuan-li; Qv, Xiao-Ying; Jiang, Jian-Guo

    2010-01-01

    Abstract Syndrome of Chinese medicine is an understanding of the regularity of disease occurrence and development and its performance of symptoms. Syndrome is the key to recognize diseases and the foundation to treat them. However, because of the complexity of the concept and the limitation of present investigations, the research of syndrome is hard to go further. Proteomics has been received extensive attention in the area of medical diagnosis and drug development. In the holistic and system...

  20. A Review: Proteomics in Nasopharyngeal Carcinoma

    OpenAIRE

    Ze-Tan Chen; Zhong-Guo Liang; Xiao-Dong Zhu

    2015-01-01

    Although radiotherapy is generally effective in the treatment of major nasopharyngeal carcinoma (NPC), this treatment still makes approximately 20% of patients radioresistant. Therefore, the identification of blood or biopsy biomarkers that can predict the treatment response to radioresistance and that can diagnosis early stages of NPC would be highly useful to improve this situation. Proteomics is widely used in NPC for searching biomarkers and comparing differentially expressed proteins. In...

  1. Application of Proteomics to Cancer Molecular Diagnostics

    Institute of Scientific and Technical Information of China (English)

    Sam HANASH

    2009-01-01

    @@ Strategies to achieve personalized medicine and improve public health encompass assessment of an individual's risk for disease, early detection and molecular classification of disease resulting in an informed choice of the most appropriate treatment instituted at an early stage of disease develop- ment. A major contribution of proteomics in this field is the development of blood based tests to achieve the goals of personalized medicine.

  2. Proteomics of Aggregatibacter actinomycetemcomitans Outer Membrane Vesicles

    Science.gov (United States)

    Kieselbach, Thomas; Zijnge, Vincent; Granström, Elisabeth; Oscarsson, Jan

    2015-01-01

    Aggregatibacter actinomycetemcomitans is an oral and systemic pathogen associated with aggressive forms of periodontitis and with endocarditis. Outer membrane vesicles (OMVs) released by this species have been demonstrated to deliver effector proteins such as cytolethal distending toxin (CDT) and leukotoxin (LtxA) into human host cells and to act as triggers of innate immunity upon carriage of NOD1- and NOD2-active pathogen-associated molecular patterns (PAMPs). To improve our understanding of the pathogenicity-associated functions that A. actinomycetemcomitans exports via OMVs, we studied the proteome of density gradient-purified OMVs from a rough-colony type clinical isolate, strain 173 (serotype e) using liquid chromatography-tandem mass spectrometry (LC-MS/MS). This analysis yielded the identification of 151 proteins, which were found in at least three out of four independent experiments. Data are available via ProteomeXchange with identifier PXD002509. Through this study, we not only confirmed the vesicle-associated release of LtxA, and the presence of proteins, which are known to act as immunoreactive antigens in the human host, but we also identified numerous additional putative virulence-related proteins in the A. actinomycetemcomitans OMV proteome. The known and putative functions of these proteins include immune evasion, drug targeting, and iron/nutrient acquisition. In summary, our findings are consistent with an OMV-associated proteome that exhibits several offensive and defensive functions, and they provide a comprehensive basis to further disclose roles of A. actinomycetemcomitans OMVs in periodontal and systemic disease. PMID:26381655

  3. Sequence Scrambling in Shotgun Proteomics is Negligible

    Science.gov (United States)

    Goloborodko, Anton A.; Gorshkov, Mikhail V.; Good, David M.; Zubarev, Roman A.

    2011-07-01

    Analysis of 15,897 low-energy (CAD) and 10,878 higher-energy (HCD) collisional dissociation mass spectra of doubly protonated tryptic peptides taken with high resolution revealed that the rate of sequence scrambling due to b-ion cyclization is negligible (shotgun proteomics. On the other hand, there is significant presence of normal (non-scrambled) internal fragments in HCD, which should be taken into account by MS/MS search engines.

  4. Panorama: A Targeted Proteomics Knowledge Base

    OpenAIRE

    Sharma, Vagisha; Eckels, Josh; Taylor, Greg K.; Shulman, Nicholas J.; Stergachis, Andrew B.; Joyner, Shannon A.; Yan, Ping; Whiteaker, Jeffrey R.; Halusa, Goran N; Schilling, Birgit; Gibson, Bradford W.; Colangelo, Christopher M.; Paulovich, Amanda G.; Carr, Steven A.; Jaffe, Jacob D

    2014-01-01

    Panorama is a web application for storing, sharing, analyzing, and reusing targeted assays created and refined with Skyline,1 an increasingly popular Windows client software tool for targeted proteomics experiments. Panorama allows laboratories to store and organize curated results contained in Skyline documents with fine-grained permissions, which facilitates distributed collaboration and secure sharing of published and unpublished data via a web-browser interface. It is fully integrated wit...

  5. Combining Search Engines for Comparative Proteomics

    OpenAIRE

    Tabb, David

    2012-01-01

    Many proteomics laboratories have found spectral counting to be an ideal way to recognize biomarkers that differentiate cohorts of samples. This approach assumes that proteins that differ in quantity between samples will generate different numbers of identifiable tandem mass spectra. Increasingly, researchers are employing multiple search engines to maximize the identifications generated from data collections. This talk evaluates four strategies to combine information from multiple search eng...

  6. PROTEOMICS: AN EVOLVING TECHNOLOGY IN LABORATORY MEDICINE

    Directory of Open Access Journals (Sweden)

    Dr. D J Venter

    2010-01-01

    Full Text Available The rapid developments in both genomics and proteomics will allow scientists to define the molecular pathways in normal and diseased cells. With these models, researchers will have the ability to predict previously unknown interactions and verify such predictions experimentally. Novel proteins, cellular functions, and pathways will also be unravelled. It is hoped that understanding the connections between cellular pathways and the ability to identify their associated biomarkers will greatly reduce the suffering and loss of life due to diseases.

  7. Origin and evolution of the mitochondrial proteome

    OpenAIRE

    Kurland, Charles; Andersson, S. G. E.

    2000-01-01

    The endosymbiotic theory for the origin of mitochondria requires substantial modification. The three identifiable ancestral sources to the proteome of mitochondria are proteins descended from the ancestral alpha -proteobacteria symbiont, proteins with no homology to bacterial orthologs, and diverse proteins with bacterial affinities not derived from alpha -proteobacteria. Random mutations in the form of deletions large and small seem to have eliminated nonessential genes from the endosymbiont...

  8. In Silico Instrumental Response Correction Improves Precision of Label-free Proteomics and Accuracy of Proteomics-based Predictive Models*

    OpenAIRE

    Lyutvinskiy, Yaroslav; Yang, Hongqian; Rutishauser, Dorothea; Zubarev, Roman A.

    2013-01-01

    In the analysis of proteome changes arising during the early stages of a biological process (e.g. disease or drug treatment) or from the indirect influence of an important factor, the biological variations of interest are often small (∼10%). The corresponding requirements for the precision of proteomics analysis are high, and this often poses a challenge, especially when employing label-free quantification. One of the main contributors to the inaccuracy of label-free proteomics experiments is...

  9. Interaction Analysis through Proteomic Phage Display

    Directory of Open Access Journals (Sweden)

    Gustav N. Sundell

    2014-01-01

    Full Text Available Phage display is a powerful technique for profiling specificities of peptide binding domains. The method is suited for the identification of high-affinity ligands with inhibitor potential when using highly diverse combinatorial peptide phage libraries. Such experiments further provide consensus motifs for genome-wide scanning of ligands of potential biological relevance. A complementary but considerably less explored approach is to display expression products of genomic DNA, cDNA, open reading frames (ORFs, or oligonucleotide libraries designed to encode defined regions of a target proteome on phage particles. One of the main applications of such proteomic libraries has been the elucidation of antibody epitopes. This review is focused on the use of proteomic phage display to uncover protein-protein interactions of potential relevance for cellular function. The method is particularly suited for the discovery of interactions between peptide binding domains and their targets. We discuss the largely unexplored potential of this method in the discovery of domain-motif interactions of potential biological relevance.

  10. From genomes to vaccines via the proteome

    Directory of Open Access Journals (Sweden)

    R Alan Wilson

    2004-08-01

    Full Text Available An effective vaccine against schistosomiasis mansoni would be a valuable control tool and the high levels of protection elicited in rodents and primates by radiation-attenuated cercariae provide proof of principle. A major obstacle to vaccine development is the difficulty of identifying the antigens that mediate protection, not least because of the size of the genome at 280Mb DNA encoding 14,000 to 20,000 genes. The technologies collectively called proteomics, including 2D electrophoresis, liquid chromatography and mass spectrometry, now permit any protein to be identified provided there is extensive DNA data, and preferably a genome sequence. Applied to soluble (cytosolic proteins from schistosomes, proteomics reveals the great similarity in composition between life cycle stages, with several WHO vaccine candidates amongst the most abundant constituents. The proteomic approach has been successfully applied to identify the secretions used by cercaria to penetrate host skin, the gut secretions of adult worms and the proteins exposed on the tegument surface. Soluble proteins can also be separated by 2D electrophoresis before western blotting to identify the full range of antigenic targets present in a parasite preparation. The next step is to discover which target proteins represent the weak points in the worm's defences.

  11. The Clathrin-dependent Spindle Proteome.

    Science.gov (United States)

    Rao, Sushma R; Flores-Rodriguez, Neftali; Page, Scott L; Wong, Chin; Robinson, Phillip J; Chircop, Megan

    2016-08-01

    The mitotic spindle is required for chromosome congression and subsequent equal segregation of sister chromatids. These processes involve a complex network of signaling molecules located at the spindle. The endocytic protein, clathrin, has a "moonlighting" role during mitosis, whereby it stabilizes the mitotic spindle. The signaling pathways that clathrin participates in to achieve mitotic spindle stability are unknown. Here, we assessed the mitotic spindle proteome and phosphoproteome in clathrin-depleted cells using quantitative MS/MS (data are available via ProteomeXchange with identifier PXD001603). We report a spindle proteome that consists of 3046 proteins and a spindle phosphoproteome consisting of 5157 phosphosites in 1641 phosphoproteins. Of these, 2908 (95.4%) proteins and 1636 (99.7%) phosphoproteins are known or predicted spindle-associated proteins. Clathrin-depletion from spindles resulted in dysregulation of 121 proteins and perturbed signaling to 47 phosphosites. The majority of these proteins increased in mitotic spindle abundance and six of these were validated by immunofluorescence microscopy. Functional pathway analysis confirmed the reported role of clathrin in mitotic spindle stabilization for chromosome alignment and highlighted possible new mechanisms of clathrin action. The data also revealed a novel second mitotic role for clathrin in bipolar spindle formation. PMID:27174698

  12. Proteomics: a biotechnology tool for crop improvement.

    Science.gov (United States)

    Eldakak, Moustafa; Milad, Sanaa I M; Nawar, Ali I; Rohila, Jai S

    2013-01-01

    A sharp decline in the availability of arable land and sufficient supply of irrigation water along with a continuous steep increase in food demands have exerted a pressure on farmers to produce more with fewer resources. A viable solution to release this pressure is to speed up the plant breeding process by employing biotechnology in breeding programs. The majority of biotechnological applications rely on information generated from various -omic technologies. The latest outstanding improvements in proteomic platforms and many other but related advances in plant biotechnology techniques offer various new ways to encourage the usage of these technologies by plant scientists for crop improvement programs. A combinatorial approach of accelerated gene discovery through genomics, proteomics, and other associated -omic branches of biotechnology, as an applied approach, is proving to be an effective way to speed up the crop improvement programs worldwide. In the near future, swift improvements in -omic databases are becoming critical and demand immediate attention for the effective utilization of these techniques to produce next-generation crops for the progressive farmers. Here, we have reviewed the recent advances in proteomics, as tools of biotechnology, which are offering great promise and leading the path toward crop improvement for sustainable agriculture. PMID:23450788

  13. Proteomics in the Study of Bacterial Keratitis

    Directory of Open Access Journals (Sweden)

    Rachida Bouhenni

    2015-12-01

    Full Text Available Bacterial keratitis is a serious ocular infection that can cause severe visual loss if treatment is not initiated at an early stage. It is most commonly caused by Staphylococcus aureus, Pseudomonas aeruginosa, Streptococcus pneumoniae, or Serratia species. Depending on the invading organism, bacterial keratitis can progress rapidly, leading to corneal destruction and potential blindness. Common risk factors for bacterial keratitis include contact lens wear, ocular trauma, ocular surface disease, ocular surgery, lid deformity, chronic use of topical steroids, contaminated ocular medications or solutions, and systemic immunosuppression. The pathogenesis of bacterial keratitis, which depends on the bacterium-host interaction and the virulence of the invading bacterium, is complicated and not completely understood. This review highlights some of the proteomic technologies that have been used to identify virulence factors and the host response to infections of bacterial keratitis in order to understand the disease process and develop improved methods of diagnosis and treatment. Although work in this field is not abundant, proteomic technologies have provided valuable information toward our current knowledge of bacterial keratitis. More studies using global proteomic approaches are warranted because it is an important tool to identify novel targets for intervention and prevention of corneal damage caused by these virulent microorganisms.

  14. Proteomics: A Biotechnology Tool for Crop Improvement

    Directory of Open Access Journals (Sweden)

    Moustafa eEldakak

    2013-02-01

    Full Text Available A sharp decline in the availability of arable land and sufficient supply of irrigation water along with a continuous steep increase in food demands have exerted a pressure on farmers to produce more with fewer resources. A viable solution to release this pressure is to speed up the plant breeding process by employing biotechnology in breeding programs. The majority of biotechnological applications rely on information generated from various -omic technologies. The latest outstanding improvements in proteomic platforms and many other but related advances in plant biotechnology techniques offer various new ways to encourage the usage of these technologies by plant scientists for crop improvement programs. A combinatorial approach of accelerated gene discovery through genomics, proteomics, and other associated -omic branches of biotechnology, as an applied approach, is proving to be an effective way to speed up the crop improvement programs worldwide. In the near future, swift improvements in -omic databases are becoming critical and demand immediate attention for the effective utilization of these techniques to produce next-generation crops for the progressive farmers. Here, we have reviewed the recent advances in proteomics, as tools of biotechnology, which are offering great promise and leading the path towards crop improvement for sustainable agriculture.

  15. Proteomic evaluation of sheep serum proteins

    Directory of Open Access Journals (Sweden)

    Chiaradia Elisabetta

    2012-05-01

    Full Text Available Abstract Background The applications of proteomic strategies to ovine medicine remain limited. The definition of serum proteome may be a good tool to identify useful protein biomarkers for recognising sub-clinical conditions and overt disease in sheep. Findings from bovine species are often directly translated for use in ovine medicine. In order to characterize normal protein patterns and improve knowledge of molecular species-specific characteristics, we generated a two-dimensional reference map of sheep serum. The possible application of this approach was tested by analysing serum protein patterns in ewes with mild broncho-pulmonary disease, which is very common in sheep and in the peripartum period which is a stressful time, with a high incidence of infectious and parasitic diseases. Results This study generated the first reference 2-DE maps of sheep serum. Overall, 250 protein spots were analyzed, and 138 identified. Compared with healthy sheep, serum protein profiles of animals with rhino-tracheo-bronchitis showed a significant decrease in protein spots identified as transthyretin, apolipoprotein A1 and a significant increase in spots identified as haptoglobin, endopin 1b and alpha1B glycoprotein. In the peripartum period, haptoglobin, alpha-1-acid glycoprotein, apolipoprotein A1 levels rose, while transthyretin content dropped. Conclusions This study describes applications of proteomics in putative biomarker discovery for early diagnosis as well as for monitoring the physiological and metabolic situations critical for ovine welfare.

  16. Unveiling the Trypanosoma cruzi Nuclear Proteome.

    Directory of Open Access Journals (Sweden)

    Agenor de Castro Moreira dos Santos Júnior

    Full Text Available Replication of Trypanosoma cruzi, the etiological agent of Chagas disease, displays peculiar features, such as absence of chromosome condensation and closed mitosis. Although previous proteome and subproteome analyses of T. cruzi have been carried out, the nuclear subproteome of this protozoan has not been described. Here, we report, for the first time to the best of our knowledge, the isolation and proteome analysis of T. cruzi nuclear fraction. For that, T. cruzi epimastigote cells were lysed and subjected to cell fractionation using two steps of sucrose density gradient centrifugation. The purity of the nuclear fraction was confirmed by phase contrast and fluorescence microscopy. Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS allowed the identification of 864 proteins. Among those, 272 proteins were annotated as putative uncharacterized, and 275 had not been previously reported on global T. cruzi proteome analysis. Additionally, to support our enrichment method, bioinformatics analysis in DAVID was carried out. It grouped the nuclear proteins in 65 gene clusters, wherein the clusters with the highest enrichment scores harbor members with chromatin organization and DNA binding functions.

  17. Unveiling the Trypanosoma cruzi Nuclear Proteome.

    Science.gov (United States)

    dos Santos Júnior, Agenor de Castro Moreira; Kalume, Dário Eluan; Camargo, Ricardo; Gómez-Mendoza, Diana Paola; Correa, José Raimundo; Charneau, Sébastien; de Sousa, Marcelo Valle; de Lima, Beatriz Dolabela; Ricart, Carlos André Ornelas

    2015-01-01

    Replication of Trypanosoma cruzi, the etiological agent of Chagas disease, displays peculiar features, such as absence of chromosome condensation and closed mitosis. Although previous proteome and subproteome analyses of T. cruzi have been carried out, the nuclear subproteome of this protozoan has not been described. Here, we report, for the first time to the best of our knowledge, the isolation and proteome analysis of T. cruzi nuclear fraction. For that, T. cruzi epimastigote cells were lysed and subjected to cell fractionation using two steps of sucrose density gradient centrifugation. The purity of the nuclear fraction was confirmed by phase contrast and fluorescence microscopy. Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) allowed the identification of 864 proteins. Among those, 272 proteins were annotated as putative uncharacterized, and 275 had not been previously reported on global T. cruzi proteome analysis. Additionally, to support our enrichment method, bioinformatics analysis in DAVID was carried out. It grouped the nuclear proteins in 65 gene clusters, wherein the clusters with the highest enrichment scores harbor members with chromatin organization and DNA binding functions. PMID:26383644

  18. Interaction analysis through proteomic phage display.

    Science.gov (United States)

    Sundell, Gustav N; Ivarsson, Ylva

    2014-01-01

    Phage display is a powerful technique for profiling specificities of peptide binding domains. The method is suited for the identification of high-affinity ligands with inhibitor potential when using highly diverse combinatorial peptide phage libraries. Such experiments further provide consensus motifs for genome-wide scanning of ligands of potential biological relevance. A complementary but considerably less explored approach is to display expression products of genomic DNA, cDNA, open reading frames (ORFs), or oligonucleotide libraries designed to encode defined regions of a target proteome on phage particles. One of the main applications of such proteomic libraries has been the elucidation of antibody epitopes. This review is focused on the use of proteomic phage display to uncover protein-protein interactions of potential relevance for cellular function. The method is particularly suited for the discovery of interactions between peptide binding domains and their targets. We discuss the largely unexplored potential of this method in the discovery of domain-motif interactions of potential biological relevance. PMID:25295249

  19. Membrane proteomic analysis of pancreatic cancer cells

    Directory of Open Access Journals (Sweden)

    Liu Xiaojun

    2010-09-01

    Full Text Available Abstract Background Pancreatic cancer is one of the most aggressive human tumors due to its high potential of local invasion and metastasis. The aim of this study was to characterize the membrane proteomes of pancreatic ductal adenocarcinoma (PDAC cells of primary and metastatic origins, and to identify potential target proteins related to metastasis of pancreatic cancer. Methods Membrane/membrane-associated proteins were isolated from AsPC-1 and BxPC-3 cells and identified with a proteomic approach based on SDS-PAGE, in-gel tryptic digestion and liquid chromatography with tandem mass spectrometry (LC-MS/MS. X! Tandem was used for database searching against the SwissProt human protein database. Results We identified 221 & 208 proteins from AsPC-1 and BxPC-3 cells, respectively, most of which are membrane or membrane-associated proteins. A hundred and nine proteins were found in both cell lines while the others were present in either AsPC-1 or BxPC-3 cells. Differentially expressed proteins between two cell lines include modulators of cell adhesion, cell motility or tumor invasion as well as metabolic enzymes involved in glycolysis, tricarboxylic acid cycle, or nucleotide/lipid metabolism. Conclusion Membrane proteomes of AsPC-1 (metastatic and BxPC-3 (primary cells are remarkably different. The differentially expressed membrane proteins may serve as potential targets for diagnostic and therapeutic interventions.

  20. Plant-bacterium interactions analyzed by proteomics.

    Science.gov (United States)

    Afroz, Amber; Zahur, Muzna; Zeeshan, Nadia; Komatsu, Setsuko

    2013-01-01

    The evolution of the plant immune response has resulted in a highly effective defense system that is able to resist potential attack by microbial pathogens. The primary immune response is referred to as pathogen associated molecular pattern (PAMP) triggered immunity and has evolved to recognize common features of microbial pathogens. In response to the delivery of pathogen effector proteins, plants acquired R proteins to fight against pathogen attack. R-dependent defense response is important in understanding the biochemical and cellular mechanisms and underlying these interactions will enable molecular and transgenic approaches for crops with increased biotic resistance. Proteomic analyses are particularly useful for understanding the mechanisms of host plant against the pathogen attack. Recent advances in the field of proteome analyses have initiated a new research area, i.e., the analysis of more complex microbial communities and their interaction with plant. Such areas hold great potential to elucidate, not only the interactions between bacteria and their host plants, but also of bacteria-bacteria interactions between different bacterial taxa, symbiotic, pathogenic bacteria, and commensal bacteria. During biotic stress, plant hormonal signaling pathways prioritizes defense over other cellular functions. Some plant pathogens take advantage of hormone dependent regulatory system by mimicking hormones that interfere with host immune responses to promote virulence (vir). In this review, it is discussed the cross talk that plays important role in response to pathogens attack with different infection strategies using proteomic approaches. PMID:23424014

  1. Extending mass spectrometry's reach in proteome analysis

    International Nuclear Information System (INIS)

    Full text: Mass spectrometry is an essential component of proteome analysis. The accuracy, speed and sensitivity of mass spectrometric analysis is further aided by an ability to analyse proteins and peptides directly from two-dimensional sample arrays. This is accomplished either by gel excision and recovery of proteins or their proteolysis products, or after blotting of gel-separated proteins onto membranes. The protein components are most often analysed in each case by matrix-assisted laser desorption ionisation (MALDI) mass spectrometry. Beyond automated protein identification, proteomics ultimately demands that protein function and activity be characterised. We have developed new mass spectrometry methodologies that enable protein-protein associations to be analysed by MALDI mass spectrometry. Methods to preserve protein-protein associations on 2D sample surfaces and to affect their ionisation and detection have been developed. This presentation will describe the features of protocol that are required for the successful analysis of protein-protein complexes. Data will be shown to illustrate the application of the technology to the study of important biological and immunological processes. The methods form the basis of powerful new mass spectrometric based assays for screening and affinity studies. Details of our investigations and their implications for high-throughput proteomics applications will be discussed in conjunction with directions of our future research

  2. Connecting Genomic Alterations to Cancer Biology with Proteomics: The NCI Clinical Proteomic Tumor Analysis Consortium

    Energy Technology Data Exchange (ETDEWEB)

    Ellis, Matthew; Gillette, Michael; Carr, Steven A.; Paulovich, Amanda G.; Smith, Richard D.; Rodland, Karin D.; Townsend, Reid; Kinsinger, Christopher; Mesri, Mehdi; Rodriguez, Henry; Liebler, Daniel

    2013-10-03

    The National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium is applying the latest generation of proteomic technologies to genomically annotated tumors from The Cancer Genome Atlas (TCGA) program, a joint initiative of the NCI and the National Human Genome Research Institute. By providing a fully integrated accounting of DNA, RNA, and protein abnormalities in individual tumors, these datasets will illuminate the complex relationship between genomic abnormalities and cancer phenotypes, thus producing biologic insights as well as a wave of novel candidate biomarkers and therapeutic targets amenable to verifi cation using targeted mass spectrometry methods.

  3. Knowledge Translation: Moving Proteomics Science to Innovation in Society.

    Science.gov (United States)

    Holmes, Christina; McDonald, Fiona; Jones, Mavis; Graham, Janice

    2016-06-01

    Proteomics is one of the pivotal next-generation biotechnologies in the current "postgenomics" era. Little is known about the ways in which innovative proteomics science is navigating the complex socio-political space between laboratory and society. It cannot be assumed that the trajectory between proteomics laboratory and society is linear and unidirectional. Concerned about public accountability and hopes for knowledge-based innovations, funding agencies and citizens increasingly expect that emerging science and technologies, such as proteomics, are effectively translated and disseminated as innovation in society. Here, we describe translation strategies promoted in the knowledge translation (KT) and science communication literatures and examine the use of these strategies within the field of proteomics. Drawing on data generated from qualitative interviews with proteomics scientists and ethnographic observation of international proteomics conferences over a 5-year period, we found that proteomics science incorporates a variety of KT strategies to reach knowledge users outside the field. To attain the full benefit of KT, however, proteomics scientists must challenge their own normative assumptions and approaches to innovation dissemination-beyond the current paradigm relying primarily on publication for one's scientific peers within one's field-and embrace the value of broader (interdisciplinary) KT strategies in promoting the uptake of their research. Notably, the Human Proteome Organization (HUPO) is paying increasing attention to a broader range of KT strategies, including targeted dissemination, integrated KT, and public outreach. We suggest that increasing the variety of KT strategies employed by proteomics scientists is timely and would serve well the omics system sciences community. PMID:27223900

  4. Proteomics of Trypanosoma evansi infection in rodents.

    Directory of Open Access Journals (Sweden)

    Nainita Roy

    Full Text Available BACKGROUND: Trypanosoma evansi infections, commonly called 'surra', cause significant economic losses to livestock industry. While this infection is mainly restricted to large animals such as camels, donkeys and equines, recent reports indicate their ability to infect humans. There are no World Animal Health Organization (WAHO prescribed diagnostic tests or vaccines available against this disease and the available drugs show significant toxicity. There is an urgent need to develop improved methods of diagnosis and control measures for this disease. Unlike its related human parasites T. brucei and T. cruzi whose genomes have been fully sequenced T. evansi genome sequence remains unavailable and very little efforts are being made to develop improved methods of prevention, diagnosis and treatment. With a view to identify potential diagnostic markers and drug targets we have studied the clinical proteome of T. evansi infection using mass spectrometry (MS. METHODOLOGY/PRINCIPAL FINDINGS: Using shot-gun proteomic approach involving nano-lc Quadrupole Time Of Flight (QTOF mass spectrometry we have identified over 160 proteins expressed by T. evansi in mice infected with camel isolate. Homology driven searches for protein identification from MS/MS data led to most of the matches arising from related Trypanosoma species. Proteins identified belonged to various functional categories including metabolic enzymes; DNA metabolism; transcription; translation as well as cell-cell communication and signal transduction. TCA cycle enzymes were strikingly missing, possibly suggesting their low abundances. The clinical proteome revealed the presence of known and potential drug targets such as oligopeptidases, kinases, cysteine proteases and more. CONCLUSIONS/SIGNIFICANCE: Previous proteomic studies on Trypanosomal infections, including human parasites T. brucei and T. cruzi, have been carried out from lab grown cultures. For T. evansi infection this is indeed the

  5. Human Pituitary Adenoma Proteomics: New Progresses and Perspectives.

    Science.gov (United States)

    Zhan, Xianquan; Wang, Xiaowei; Cheng, Tingting

    2016-01-01

    Pituitary adenoma (PA) is a common intracranial neoplasm that impacts on human health through interfering hypothalamus-pituitary-target organ axis systems. The development of proteomics gives great promises in the clarification of molecular mechanisms of a PA and discovery of effective biomarkers for prediction, prevention, early-stage diagnosis, and treatment for a PA. A great progress in the field of PA proteomics has been made in the past 10 years, including (i) the use of laser-capture microdissection, (ii) proteomics analyses of functional PAs (such as prolactinoma), invasive and non-invasive non-functional pituitary adenomas (NFPAs), protein post-translational modifications such as phosphorylation and tyrosine nitration, NFPA heterogeneity, and hormone isoforms, (iii) the use of protein antibody array, (iv) serum proteomics and peptidomics, (v) the integration of proteomics and other omics data, and (vi) the proposal of multi-parameter systematic strategy for a PA. This review will summarize these progresses of proteomics in PAs, point out the existing drawbacks, propose the future research directions, and address the clinical relevance of PA proteomics data, in order to achieve our long-term goal that is use of proteomics to clarify molecular mechanisms, construct molecular networks, and discover effective biomarkers. PMID:27303365

  6. Human pituitary adenoma proteomics: new progresses and perspectives

    Directory of Open Access Journals (Sweden)

    Xianquan eZhan

    2016-05-01

    Full Text Available Pituitary adenoma (PA is a commonly intracranial neoplasm that impacts on human health through interfering hypothalamus-pituitary-target organ axis systems. The development of proteomics gives great promises in clarification of molecular mechanisms of a pituitary adenoma and discovery of effective biomarkers for prediction, prevention, early-stage diagnosis and treatment of a PA. A great progress in the field of PA proteomics has been made in the past ten years, including (i the use of laser capture microdissection, (ii proteomics analyses of functional PAs (FPAs, such as prolactinoma, invasive and noninvasive nonfunctional PAs (NFPAs, protein post-translational modifications (PTMs including phosphorylation and tyrosine nitration, NFPA heterogeneity, and hormone isoforms, (iii the use of protein antibody array, (iv serum proteomics and peptidomics, (v integration of proteomics and other omics data, and (vi proposal of multi-parameter systematic strategy for a PA. This review will summarize those progresses of proteomics in PAs, point out the existing drawbacks, propose the future research directions, and address the clinical relevance of PA proteomics data, in order to achieve our long-term goal that is use of proteomics to clarify molecular mechanisms, construct molecular networks, and discover effective biomarkers.

  7. Proteomic identification of gluten proteins in relation to celiac disease

    Czech Academy of Sciences Publication Activity Database

    Šalplachta, Jiří

    Jena: ESF, 2008. s. 48. [Central and Eastern European Proteomic Conference /2./. 12.10.2008-15.10.2008, Jena] R&D Projects: GA MZe 1B53002 Institutional research plan: CEZ:AV0Z40310501 Keywords : proteomics * gluten * celiac-related proteins Subject RIV: CB - Analytical Chemistry, Separation

  8. Proteomes and Neural Stem Cells: cellular signalling during differentiation

    Czech Academy of Sciences Publication Activity Database

    Skalníková, Helena; Halada, Petr; Vodička, Petr; Motlík, Jan; Horning, O.; Jensen, O. N.; Gadher, S. J.; Pelech, S.; Kovářová, Hana

    Cambridge : -, 2007, s. 1-1. [BSPR-EBI Meeting: Integrative Proteomics: From Molecules to Systems,. Cambridge (GB), 25.07.2007-27.07.2007] Institutional research plan: CEZ:AV0Z50450515; CEZ:AV0Z50200510 Keywords : neural stem cells * differentiation * signalling * proteome Subject RIV: EB - Genetics ; Molecular Biology

  9. Computational approaches to enhance mass spectrometry-based proteomics

    OpenAIRE

    Neuhauser, Nadin

    2014-01-01

    In this thesis I present three computational approaches that improve the analysis of mass spectrometry-based proteomics data. The novel search engine Andromeda allows efficient identification of peptides and proteins. Implementation of a rule-based expert system provides more detailed information contained in the mass spectra. Furthermore I adapted our computational proteomics pipeline to high performance computers.

  10. Meiotic Division of Oocytes: Proteomic and Phosphoproteomic Study

    Czech Academy of Sciences Publication Activity Database

    Halada, Petr; Man, Petr; Šulc, Miroslav; Pelech, C.; Kovářová, Hana

    Zurich, 2005, s. 68-68. [Congress expandig proteomics /2005/. Zurich (CH), 05.12.2005-07.12.2005] R&D Projects: GA ČR GA204/04/0571; GA AV ČR 1QS500510558 Institutional research plan: CEZ:AV0Z50200510 Keywords : oocytes * proteomics Subject RIV: EE - Microbiology, Virology

  11. Tissue-based map of the human proteome

    DEFF Research Database (Denmark)

    Uhlén, Mathias; Fagerberg, Linn; Hallström, Björn M.; Lindskog, Cecilia; Oksvold, Per; Mardinoglu, Adil; Sivertsson, Åsa; Kampf, Caroline; Sjöstedt, Evelina; Asplund, Anna; Olsson, IngMarie; Edlund, Karolina; Lundberg, Emma; Navani, Sanjay; Szigyarto, Cristina Al-Khalili; Odeberg, Jacob; Djureinovic, Dijana; Takanen, Jenny Ottosson; Hober, Sophia; Alm, Tove; Edqvist, Per-Henrik; Berling, Holger; Tegel, Hanna; Mulder, Jan; Rockberg, Johan; Nilsson, Peter; Schwenk, Jochen M.; Hamsten, Marica; von Feilitzen, Kalle; Forsberg, Mattias; Persson, Lukas; Johansson, Fredric; Zwahlen, Martin; von Heijne, Gunnar; Nielsen, Jens; Pontén, Fredrik

    2015-01-01

    Resolving the molecular details of proteome variation in the different tissues and organs of the human body will greatly increase our knowledge of human biology and disease. Here, we present a map of the human tissue proteome based on an integrated omics approach that involves quantitative...

  12. Integration of proteomics into systems biology of cancer

    OpenAIRE

    Hanash, S; Schliekelman, M.; Q. Zhang; Taguchi, A

    2012-01-01

    Deciphering the complexity and heterogeneity of cancer benefits from integration of proteomic level data into systems biology efforts. The opportunities available as a result of advances in proteomic technologies, the successes to date and the challenges involved in integrating diverse datasets are addressed in this review.

  13. Mass spectrometry based proteomics, background, status and future needs

    DEFF Research Database (Denmark)

    Roepstorff, Peter

    2012-01-01

    An overview of the background for proteomics and a description of the present state of art are given with a description of the main strategies in proteomics. The advantages and limitations of the two major strategies, 2D-gel based and LC-MS based, are discussed and a combination for the two, CeLC...

  14. Skyline Reaches Agreement - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The full proteomics analysis of a small tumor sample (similar in mass to a few grains of rice) produces well over 500 megabytes of unprocessed "raw" data when analyzed on a mass spectrometer (MS). Thus, for every proteomics experiment there is a vast amount of raw data that must be analyzed and interrogated in order to extract biological information.

  15. PRIME-XS, a European infrastructure for proteomics

    DEFF Research Database (Denmark)

    Raijmakers, Reinout; Olsen, Jesper V; Aebersold, Ruedi;

    2014-01-01

    As prologue to the special issue of Molecular and Cellular Proteomics describing the research activities of the PRIME-XS consortium, a pan-European infrastructure for proteomics we, being guest editors of this issue, here provide an overview of the structure and activities of this program funded by...

  16. A platform to standardize, store, and visualize proteomics experimental data

    Institute of Scientific and Technical Information of China (English)

    Guangyong Zheng; Hong Li; Chuan Wang; Quanhu Sheng; Haiwei Fan; Shaoyou Yang; Boshu Liu; Jianliang Dai; Rong Zeng; Lu Xie

    2009-01-01

    With the development of functional genomics research,large-scale proteomics studies are now widespread, pre-senting significant challenges for data storage,exchange, and analysis. Here we present the Integrated Proteomics Exploring Database (IPED) as a platform for managing proteomics experimental data (both process and result data). IPED is based on the schema of the Proteome Experimental Data Repository (PEDRo), and complies with the General Proteomics Standard (GPS) drafted by the Proteomics Standards Committee of the Human Proteome Organization. In our work, we developed three components for the IPED platform: the IPED cfient editor, IPED server software, and IPED web interface. The client editor col-lects experimental data and generates an extensible markup language (XML) data file compliant with PEDRo and GPS; the server software parses the XML data file and loads information into a core database;and the web interface displays experimental results, to provide a convenient graphic representation of data.Given software convenience and data abundance, IPED is a powerful platform for data exchange and presents an important resource for the proteomics community.In its current release, IPED is available at http://www.biosino.org/iped2.

  17. Aspects of the barley seed proteome during development and germination

    DEFF Research Database (Denmark)

    Finnie, Christine; Maeda, K.; Østergaard, O.;

    2004-01-01

    Analysis of the water-soluble barley seed proteome has led to the identification of proteins by MS in the major spots on two-dimensional gels covering the pi ranges 4-7 and 6-11. This provides the basis for in-depth studies of proteome changes during seed development and germination, tissue...

  18. Liquid Chromatography-Mass Spectrometry-based Quantitative Proteomics*

    OpenAIRE

    Xie, Fang; Liu, Tao; Qian, Wei-Jun; Petyuk, Vladislav A.; Smith, Richard D.

    2011-01-01

    LC-MS-based quantitative proteomics has become increasingly applied to a wide range of biological applications due to growing capabilities for broad proteome coverage and good accuracy and precision in quantification. Herein, we review the current LC-MS-based quantification methods with respect to their advantages and limitations and highlight their potential applications.

  19. Liquid Chromatography-Mass Spectrometry-based Quantitative Proteomics

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Fang; Liu, Tao; Qian, Weijun; Petyuk, Vladislav A.; Smith, Richard D.

    2011-07-22

    Liquid chromatography-mass spectrometry (LC-MS)-based quantitative proteomics has become increasingly applied for a broad range of biological applications due to growing capabilities for broad proteome coverage and good accuracy in quantification. Herein, we review the current LC-MS-based quantification methods with respect to their advantages and limitations, and highlight their potential applications.

  20. Exploring the Arabidopsis Proteome: Influence of Protein Solubilization Buffers on Proteome Coverage

    Directory of Open Access Journals (Sweden)

    Claudius Marondedze

    2014-12-01

    Full Text Available The study of proteomes provides new insights into stimulus-specific responses of protein synthesis and turnover, and the role of post-translational modifications at the systems level. Due to the diverse chemical nature of proteins and shortcomings in the analytical techniques used in their study, only a partial display of the proteome is achieved in any study, and this holds particularly true for plant proteomes. Here we show that different solubilization and separation methods have profound effects on the resulting proteome. In particular, we observed that the type of detergents employed in the solubilization buffer preferentially enriches proteins in different functional categories. These include proteins with a role in signaling, transport, response to temperature stimuli and metabolism. This data may offer a functional bias on comparative analysis studies. In order to obtain a broader coverage, we propose a two-step solubilization protocol with first a detergent-free buffer and then a second step utilizing a combination of two detergents to solubilize proteins.

  1. Proteomic analysis of the human skin proteome after in vivo treatment with sodium dodecyl sulphate.

    Directory of Open Access Journals (Sweden)

    Erika Parkinson

    Full Text Available BACKGROUND: Skin has a variety of functions that are incompletely understood at the molecular level. As the most accessible tissue in the body it often reveals the first signs of inflammation or infection and also represents a potentially valuable source of biomarkers for several diseases. In this study we surveyed the skin proteome qualitatively using gel electrophoresis, liquid chromatography tandem mass spectrometry (GeLC-MS/MS and quantitatively using an isobaric tagging strategy (iTRAQ to characterise the response of human skin following exposure to sodium dodecyl sulphate (SDS. RESULTS: A total of 653 skin proteins were assigned, 159 of which were identified using GeLC-MS/MS and 616 using iTRAQ, representing the most comprehensive proteomic study in human skin tissue. Statistical analysis of the available iTRAQ data did not reveal any significant differences in the measured skin proteome after 4 hours exposure to the model irritant SDS. CONCLUSIONS: This study represents the first step in defining the critical response to an irritant at the level of the proteome and provides a valuable resource for further studies at the later stages of irritant exposure.

  2. Directed Shotgun Proteomics Guided by Saturated RNA-seq Identifies a Complete Expressed Prokaryotic Proteome

    Energy Technology Data Exchange (ETDEWEB)

    Omasits, U.; Quebatte, Maxime; Stekhoven, Daniel J.; Fortes, Claudia; Roschitzki, Bernd; Robinson, Mark D.; Dehio, Christoph; Ahrens, Christian H.

    2013-11-01

    Prokaryotes, due to their moderate complexity, are particularly amenable to the comprehensive identification of the protein repertoire expressed under different conditions. We applied a generic strategy to identify a complete expressed prokaryotic proteome, which is based on the analysis of RNA and proteins extracted from matched samples. Saturated transcriptome profiling by RNA-seq provided an endpoint estimate of the protein-coding genes expressed under two conditions which mimic the interaction of Bartonella henselae with its mammalian host. Directed shotgun proteomics experiments were carried out on four subcellular fractions. By specifically targeting proteins which are short, basic, low abundant, and membrane localized, we could eliminate their initial underrepresentation compared to the estimated endpoint. A total of 1250 proteins were identified with an estimated false discovery rate below 1%. This represents 85% of all distinct annotated proteins and ~90% of the expressed protein-coding genes. Genes that were detected at the transcript but not protein level, were found to be highly enriched in several genomic islands. Furthermore, genes that lacked an ortholog and a functional annotation were not detected at the protein level; these may represent examples of overprediction in genome annotations. A dramatic membrane proteome reorganization was observed, including differential regulation of autotransporters, adhesins, and hemin binding proteins. Particularly noteworthy was the complete membrane proteome coverage, which included expression of all members of the VirB/D4 type IV secretion system, a key virulence factor.

  3. Human post-mortem synapse proteome integrity screening for proteomic studies of postsynaptic complexes

    OpenAIRE

    Bayés, Alex; Collins, Mark O; Galtrey, Clare M; Simonnet, Clémence; Roy, Marcia; Croning, Mike; Gou, Gemma; van de Lagemaat, Louie N.; Milward, David; Whittle, Ian R.; Smith, Colin; Choudhary, Jyoti S.; Grant, Seth

    2014-01-01

    BackgroundSynapses are fundamental components of brain circuits and are disrupted in over 100 neurological and psychiatric diseases. The synapse proteome is physically organized into multiprotein complexes and polygenic mutations converge on postsynaptic complexes in schizophrenia, autism and intellectual disability. Directly characterising human synapses and their multiprotein complexes from post-mortem tissue is essential to understanding disease mechanisms. However, multiprotein complexes ...

  4. Human post-mortem synapse proteome integrity screening for proteomic studies of postsynaptic complexes

    OpenAIRE

    Bayés, Àlex; Collins, Mark O; Galtrey, Clare M; Simonnet, Clémence; Roy, Marcia; Croning, Mike DR; Gou, Gemma; van de Lagemaat, Louie N.; Milward, David; Whittle, Ian R.; Smith, Colin; Choudhary, Jyoti S.; Grant, Seth GN

    2014-01-01

    Background Synapses are fundamental components of brain circuits and are disrupted in over 100 neurological and psychiatric diseases. The synapse proteome is physically organized into multiprotein complexes and polygenic mutations converge on postsynaptic complexes in schizophrenia, autism and intellectual disability. Directly characterising human synapses and their multiprotein complexes from post-mortem tissue is essential to understanding disease mechanisms. However, multiprotein complexes...

  5. The proteome of Hypobaric Induced Hypoxic Lung: Insights from Temporal Proteomic Profiling for Biomarker Discovery

    Science.gov (United States)

    Ahmad, Yasmin; Sharma, Narendra K.; Ahmad, Mohammad Faiz; Sharma, Manish; Garg, Iti; Srivastava, Mousami; Bhargava, Kalpana

    2015-01-01

    Exposure to high altitude induces physiological responses due to hypoxia. Lungs being at the first level to face the alterations in oxygen levels are critical to counter and balance these changes. Studies have been done analysing pulmonary proteome alterations in response to exposure to hypobaric hypoxia. However, such studies have reported the alterations at specific time points and do not reflect the gradual proteomic changes. These studies also identify the various biochemical pathways and responses induced after immediate exposure and the resolution of these effects in challenge to hypobaric hypoxia. In the present study, using 2-DE/MS approach, we attempt to resolve these shortcomings by analysing the proteome alterations in lungs in response to different durations of exposure to hypobaric hypoxia. Our study thus highlights the gradual and dynamic changes in pulmonary proteome following hypobaric hypoxia. For the first time, we also report the possible consideration of SULT1A1, as a biomarker for the diagnosis of high altitude pulmonary edema (HAPE). Higher SULT1A1 levels were observed in rats as well as in humans exposed to high altitude, when compared to sea-level controls. This study can thus form the basis for identifying biomarkers for diagnostic and prognostic purposes in responses to hypobaric hypoxia. PMID:26022216

  6. Exploring the Arabidopsis Proteome: Influence of Protein Solubilization Buffers on Proteome Coverage

    KAUST Repository

    Marondedze, Claudius

    2014-12-31

    The study of proteomes provides new insights into stimulus-specific responses of protein synthesis and turnover, and the role of post-translational modifications at the systems level. Due to the diverse chemical nature of proteins and shortcomings in the analytical techniques used in their study, only a partial display of the proteome is achieved in any study, and this holds particularly true for plant proteomes. Here we show that different solubilization and separation methods have profound effects on the resulting proteome. In particular, we observed that the type of detergents employed in the solubilization buffer preferentially enriches proteins in different functional categories. These include proteins with a role in signaling, transport, response to temperature stimuli and metabolism. This data may offer a functional bias on comparative analysis studies. In order to obtain a broader coverage, we propose a two-step solubilization protocol with first a detergent-free buffer and then a second step utilizing a combination of two detergents to solubilize proteins.

  7. Dicty_cDB: Contig-U15957-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ne) Carboxydothermus hydrogenoforma... 75 6e-14 AL646052_1055( AL646052 |pid:none) Ralsto...m leaves, 1... 48 0.66 1 ( EE258429 ) RFABC66TH Castor bean cDNA library from flowers,8... 48 0.66 1 ( DC001823 ) Xenop...ne) Photobacterium profundum acyl carr... 88 4e-16 AE004091_2966( AE004091 |pid:none) Pseudomonas aerugino...ne) Arthrobacter chlorophenolicus A6 ... 80 9e-14 CP001279_275( CP001279 |pid:none) Nautilia prof...bacterium radiobacter K84 c... 72 3e-11 CP000738_1713( CP000738 |pid:none) Sinor

  8. Environmental Microbial Community Proteomics: Status, Challenges and Perspectives.

    Science.gov (United States)

    Wang, Da-Zhi; Kong, Ling-Fen; Li, Yuan-Yuan; Xie, Zhang-Xian

    2016-01-01

    Microbial community proteomics, also termed metaproteomics, is an emerging field within the area of microbiology, which studies the entire protein complement recovered directly from a complex environmental microbial community at a given point in time. Although it is still in its infancy, microbial community proteomics has shown its powerful potential in exploring microbial diversity, metabolic potential, ecological function and microbe-environment interactions. In this paper, we review recent advances achieved in microbial community proteomics conducted in diverse environments, such as marine and freshwater, sediment and soil, activated sludge, acid mine drainage biofilms and symbiotic communities. The challenges facing microbial community proteomics are also discussed, and we believe that microbial community proteomics will greatly enhance our understanding of the microbial world and its interactions with the environment. PMID:27527164

  9. Current application of proteomics in biomarker discoveryfor inflammatory bowel disease

    Institute of Scientific and Technical Information of China (English)

    2016-01-01

    Recently, the field of proteomics has rapidly expanded inits application towards clinical research with objectivesranging from elucidating disease pathogenesis todiscovering clinical biomarkers. As proteins governand/or reflect underlying cellular processes, the studyof proteomics provides an attractive avenue for researchas it allows for the rapid identification of proteinprofiles in a biological sample. Inflammatory boweldisease (IBD) encompasses several heterogeneousand chronic conditions of the gastrointestinal tract.Proteomic technology provides a powerful means ofaddressing major challenges in IBD today, especiallyfor identifying biomarkers to improve its diagnosis andmanagement. This review will examine the current stateof IBD proteomics research and its use in biomarkerresearch. Furthermore, we also discuss the challengesof translating proteomic research into clinically relevanttools. The potential application of this growing field isenormous and is likely to provide significant insightstowards improving our future understanding and managementof IBD.

  10. Application for proteomic techniques in studying osteoarthritis: a review

    Directory of Open Access Journals (Sweden)

    YvesHenrotin

    2011-12-01

    Full Text Available After the genomic era, proteomic corresponds to a wide variety of techniques to study the protein content of cells, tissue or organism and to isolate protein of interest. It offers the choice between gel-based and gel-free methods or shotgun proteomics. Applications of proteomic technology may concern three principal objectives in several biomedical or clinical domains of research as in osteoarthritis: (i to understand the physiopathology and underlying mechanisms leading to a disease or associated to a particular model, (ii, to find disease-specific biomarker and (iii to identify new therapeutic targets. This review aimed at gathering most of the data regarding the proteomic techniques and their applications to arthritis research. It also reported technical limitations and solutions, as for example for sample preparation. Proteomics open wide perspectives in biochemical research but many technical matters still remain to be solved.

  11. Environmental Microbial Community Proteomics: Status, Challenges and Perspectives

    Science.gov (United States)

    Wang, Da-Zhi; Kong, Ling-Fen; Li, Yuan-Yuan; Xie, Zhang-Xian

    2016-01-01

    Microbial community proteomics, also termed metaproteomics, is an emerging field within the area of microbiology, which studies the entire protein complement recovered directly from a complex environmental microbial community at a given point in time. Although it is still in its infancy, microbial community proteomics has shown its powerful potential in exploring microbial diversity, metabolic potential, ecological function and microbe-environment interactions. In this paper, we review recent advances achieved in microbial community proteomics conducted in diverse environments, such as marine and freshwater, sediment and soil, activated sludge, acid mine drainage biofilms and symbiotic communities. The challenges facing microbial community proteomics are also discussed, and we believe that microbial community proteomics will greatly enhance our understanding of the microbial world and its interactions with the environment. PMID:27527164

  12. Using R and Bioconductor for proteomics data analysis.

    Science.gov (United States)

    Gatto, Laurent; Christoforou, Andy

    2014-01-01

    This review presents how R, the popular statistical environment and programming language, can be used in the frame of proteomics data analysis. A short introduction to R is given, with special emphasis on some of the features that make R and its add-on packages premium software for sound and reproducible data analysis. The reader is also advised on how to find relevant R software for proteomics. Several use cases are then presented, illustrating data input/output, quality control, quantitative proteomics and data analysis. Detailed code and additional links to extensive documentation are available in the freely available companion package RforProteomics. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. PMID:23692960

  13. Biomarker discovery in mass spectrometry-based urinary proteomics.

    Science.gov (United States)

    Thomas, Samuel; Hao, Ling; Ricke, William A; Li, Lingjun

    2016-04-01

    Urinary proteomics has become one of the most attractive topics in disease biomarker discovery. MS-based proteomic analysis has advanced continuously and emerged as a prominent tool in the field of clinical bioanalysis. However, only few protein biomarkers have made their way to validation and clinical practice. Biomarker discovery is challenged by many clinical and analytical factors including, but not limited to, the complexity of urine and the wide dynamic range of endogenous proteins in the sample. This article highlights promising technologies and strategies in the MS-based biomarker discovery process, including study design, sample preparation, protein quantification, instrumental platforms, and bioinformatics. Different proteomics approaches are discussed, and progresses in maximizing urinary proteome coverage and standardization are emphasized in this review. MS-based urinary proteomics has great potential in the development of noninvasive diagnostic assays in the future, which will require collaborative efforts between analytical scientists, systems biologists, and clinicians. PMID:26703953

  14. Micro-proteomics with iterative data analysis: Proteome analysis in C. elegans at the single worm level.

    Science.gov (United States)

    Bensaddek, Dalila; Narayan, Vikram; Nicolas, Armel; Murillo, Alejandro Brenes; Gartner, Anton; Kenyon, Cynthia J; Lamond, Angus I

    2016-02-01

    Proteomics studies typically analyze proteins at a population level, using extracts prepared from tens of thousands to millions of cells. The resulting measurements correspond to average values across the cell population and can mask considerable variation in protein expression and function between individual cells or organisms. Here, we report the development of micro-proteomics for the analysis of Caenorhabditis elegans, a eukaryote composed of 959 somatic cells and ∼1500 germ cells, measuring the worm proteome at a single organism level to a depth of ∼3000 proteins. This includes detection of proteins across a wide dynamic range of expression levels (>6 orders of magnitude), including many chromatin-associated factors involved in chromosome structure and gene regulation. We apply the micro-proteomics workflow to measure the global proteome response to heat-shock in individual nematodes. This shows variation between individual animals in the magnitude of proteome response following heat-shock, including variable induction of heat-shock proteins. The micro-proteomics pipeline thus facilitates the investigation of stochastic variation in protein expression between individuals within an isogenic population of C. elegans. All data described in this study are available online via the Encyclopedia of Proteome Dynamics (http://www.peptracker.com/epd), an open access, searchable database resource. PMID:26552604

  15. Improving HIV proteome annotation: new features of BioAfrica HIV Proteomics Resource.

    Science.gov (United States)

    Druce, Megan; Hulo, Chantal; Masson, Patrick; Sommer, Paula; Xenarios, Ioannis; Le Mercier, Philippe; De Oliveira, Tulio

    2016-01-01

    The Human Immunodeficiency Virus (HIV) is one of the pathogens that cause the greatest global concern, with approximately 35 million people currently infected with HIV. Extensive HIV research has been performed, generating a large amount of HIV and host genomic data. However, no effective vaccine that protects the host from HIV infection is available and HIV is still spreading at an alarming rate, despite effective antiretroviral (ARV) treatment. In order to develop effective therapies, we need to expand our knowledge of the interaction between HIV and host proteins. In contrast to virus proteins, which often rapidly evolve drug resistance mutations, the host proteins are essentially invariant within all humans. Thus, if we can identify the host proteins needed for virus replication, such as those involved in transporting viral proteins to the cell surface, we have a chance of interrupting viral replication. There is no proteome resource that summarizes this interaction, making research on this subject a difficult enterprise. In order to fill this gap in knowledge, we curated a resource presents detailed annotation on the interaction between the HIV proteome and host proteins. Our resource was produced in collaboration with ViralZone and used manual curation techniques developed by UniProtKB/Swiss-Prot. Our new website also used previous annotations of the BioAfrica HIV-1 Proteome Resource, which has been accessed by approximately 10 000 unique users a year since its inception in 2005. The novel features include a dedicated new page for each HIV protein, a graphic display of its function and a section on its interaction with host proteins. Our new webpages also add information on the genomic location of each HIV protein and the position of ARV drug resistance mutations. Our improved BioAfrica HIV-1 Proteome Resource fills a gap in the current knowledge of biocuration.Database URL:http://www.bioafrica.net/proteomics/HIVproteome.html. PMID:27087306

  16. The proteome landscape of Giardia lamblia encystation.

    Directory of Open Access Journals (Sweden)

    Carmen Faso

    Full Text Available Giardia lamblia is an intestinal protozoan parasite required to survive in the environment in order to be transmitted to a new host. To ensure parasite survival, flagellated trophozoites colonizing the small intestine differentiate into non-motile environmentally-resistant cysts which are then shed in the environment. This cell differentiation process called encystation is characterized by significant morphological remodeling which includes secretion of large amounts of cyst wall material. Although much is known about the transcriptional regulation of encystation and the synthesis and trafficking of cyst wall material, the investigation of global changes in protein content and abundance during G. lamblia encystation is still unaddressed. In this study, we report on the quantitative analysis of the G. lamblia proteome during encystation using tandem mass spectrometry. Quantification of more than 1000 proteins revealed major changes in protein abundance in early, mid and late encystation, notably in constitutive secretory protein trafficking. Early stages of encystation were marked by a striking decrease of endoplasmic reticulum-targeted variant-specific surface proteins and significant increases in cytoskeleton regulatory components, NEK protein kinases and proteins involved in protein folding and glycolysis. This was in stark contrast to cells in the later stages of encystation which presented a surprisingly similar proteome composition to non-encysting trophozoites. Altogether these data constitute the first quantitative atlas of the Giardia proteome covering the whole process of encystation and point towards an important role for post-transcriptional control of gene expression in Giardia differentiation. Furthermore, our data provide a valuable resource for the community-based annotation effort of the G. lamblia genome, where almost 70% of all predicted gene models remains "hypothetical".

  17. The proteome landscape of Giardia lamblia encystation.

    Science.gov (United States)

    Faso, Carmen; Bischof, Sylvain; Hehl, Adrian B

    2013-01-01

    Giardia lamblia is an intestinal protozoan parasite required to survive in the environment in order to be transmitted to a new host. To ensure parasite survival, flagellated trophozoites colonizing the small intestine differentiate into non-motile environmentally-resistant cysts which are then shed in the environment. This cell differentiation process called encystation is characterized by significant morphological remodeling which includes secretion of large amounts of cyst wall material. Although much is known about the transcriptional regulation of encystation and the synthesis and trafficking of cyst wall material, the investigation of global changes in protein content and abundance during G. lamblia encystation is still unaddressed. In this study, we report on the quantitative analysis of the G. lamblia proteome during encystation using tandem mass spectrometry. Quantification of more than 1000 proteins revealed major changes in protein abundance in early, mid and late encystation, notably in constitutive secretory protein trafficking. Early stages of encystation were marked by a striking decrease of endoplasmic reticulum-targeted variant-specific surface proteins and significant increases in cytoskeleton regulatory components, NEK protein kinases and proteins involved in protein folding and glycolysis. This was in stark contrast to cells in the later stages of encystation which presented a surprisingly similar proteome composition to non-encysting trophozoites. Altogether these data constitute the first quantitative atlas of the Giardia proteome covering the whole process of encystation and point towards an important role for post-transcriptional control of gene expression in Giardia differentiation. Furthermore, our data provide a valuable resource for the community-based annotation effort of the G. lamblia genome, where almost 70% of all predicted gene models remains "hypothetical". PMID:24391747

  18. Methods for Pseudopodia Purification and Proteomic Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yingchun; Ding, Shi-Jian; Wang, Wei; Yang, Feng; Jacobs, Jon M.; Camp, David G.; Smith, Richard D.; Klemke, Richard L.

    2007-08-21

    Directional cell migration (chemotaxis) plays a central role in a wide spectrum of physiological and pathological processes, including embryo development, wounding healing, immunity, and cancer metastasis (1, 2). The process of chemotaxis is characterized by the sustained migration of cells in the direction of an increasing concentration of chemoattractant and/or ECM protein. Upon sensing the chemoattractant cells response with localized amplification of signals on the side facing the gradient (3-7). The spatial signal propagation facilitates reorganization of the actin-myosin cytoskeleton leading to extension of a dominant pseudopodium (PD) only in the direction of chemoattractant (7-10). While it is clear that localized signaling is critical for pseudopodium formation and chemotaxis, the molecular mechanisms that mediate this response remain poorly defined. To investigate mechanisms of pseudopodia formation, we recently described a novel approach to separate the PD and cell body (CB) compartments for large scale proteomic and phosphoproteomic analyses using chambers equipped with microporous filters (Fig. 1) (3, 7, 11). This in vitro system recapitulates physiological events associates with pseudopodial protrusion through small openings in the ECM and the vessel wall during immune cell intravasation and cancer cell metastasis (12, 13). The model system has been used to reveal important signaling pathways and novel proteins that mediate cell migration. This model, combined with the state-of-the-art proteomics and phosphoproteomics technology, will provide an effective approach to systematically analyze the proteins that differentially localized or phosphorylated in the front and the back of polarized migrating cells. In the following sections, we will describe in detail the protocols used to purify the PD and CB compartments for large-scale proteomic and phosphoproteomic analyses using mass spectrometry.

  19. Valvular Aortic Stenosis: A Proteomic Insight

    Directory of Open Access Journals (Sweden)

    Fernando Vivanco

    2010-02-01

    Full Text Available Calcified aortic valve disease is a slowly progressive disorder that ranges from mild valve thickening with no obstruction of blood flow, known as aortic sclerosis, to severe calcification with impaired leaflet motion or aortic stenosis. In the present work we describe a rapid, reproducible and effective method to carry out proteomic analysis of stenotic human valves by conventional 2-DE and 2D-DIGE, minimizing the interference due to high calcium concentrations. Furthermore, the protocol permits the aortic stenosis proteome to be analysed, advancing our knowledge in this area. Summary: Until recently, aortic stenosis (AS was considered a passive process secondary to calcium deposition in the aortic valves. However, it has recently been highlighted that the risk factors associated with the development of calcified AS in the elderly are similar to those of coronary artery disease. Furthermore, degenerative AS shares histological characteristics with atherosclerotic plaques, leading to the suggestion that calcified aortic valve disease is a chronic inflammatory process similar to atherosclerosis. Nevertheless, certain data does not fit with this theory making it necessary to further study this pathology. The aim of this study is to develop an effective protein extraction protocol for aortic stenosis valves such that proteomic analyses can be performed on these structures. In the present work we have defined a rapid, reproducible and effective method to extract proteins and that is compatible with 2-DE, 2D-DIGE and MS techniques. Defining the protein profile of this tissue is an important and challenging task that will help to understand the mechanisms of physiological/pathological processes in aortic stenosis valves.

  20. Proteomics-grade de novo sequencing approach.

    Science.gov (United States)

    Savitski, Mikhail M; Nielsen, Michael L; Kjeldsen, Frank; Zubarev, Roman A

    2005-01-01

    The conventional approach in modern proteomics to identify proteins from limited information provided by molecular and fragment masses of their enzymatic degradation products carries an inherent risk of both false positive and false negative identifications. For reliable identification of even known proteins, complete de novo sequencing of their peptides is desired. The main problems of conventional sequencing based on tandem mass spectrometry are incomplete backbone fragmentation and the frequent overlap of fragment masses. In this work, the first proteomics-grade de novo approach is presented, where the above problems are alleviated by the use of complementary fragmentation techniques CAD and ECD. Implementation of a high-current, large-area dispenser cathode as a source of low-energy electrons provided efficient ECD of doubly charged peptides, the most abundant species (65-80%), in a typical trypsin-based proteomics experiment. A new linear de novo algorithm is developed combining efficiency and speed, processing on a conventional 3 GHz PC, 1000 MS/MS data sets in 60 s. More than 6% of all MS/MS data for doubly charged peptides yielded complete sequences, and another 13% gave nearly complete sequences with a maximum gap of two amino acid residues. These figures are comparable with the typical success rates (5-15%) of database identification. For peptides reliably found in the database (Mowse score > or = 34), the agreement with de novo-derived full sequences was >95%. Full sequences were derived in 67% of the cases when full sequence information was present in MS/MS spectra. Thus the new de novo sequencing approach reached the same level of efficiency and reliability as conventional database-identification strategies. PMID:16335984

  1. Environmental Proteomics: Changes in the Proteome of Marine Organisms in Response to Environmental Stress, Pollutants, Infection, Symbiosis, and Development

    Science.gov (United States)

    Tomanek, Lars

    2011-01-01

    Environmental proteomics, the study of changes in the abundance of proteins and their post-translational modifications, has become a powerful tool for generating hypotheses regarding how the environment affects the biology of marine organisms. Proteomics discovers hitherto unknown cellular effects of environmental stressors such as changes in thermal, osmotic, and anaerobic conditions. Proteomic analyses have advanced the characterization of the biological effects of pollutants and identified comprehensive and pollutant-specific sets of biomarkers, especially those highlighting post-translational modifications. Proteomic analyses of infected organisms have highlighted the broader changes occurring during immune responses and how the same pathways are attenuated during the maintenance of symbiotic relationships. Finally, proteomic changes occurring during the early life stages of marine organisms emphasize the importance of signaling events during development in a rapidly changing environment. Changes in proteins functioning in energy metabolism, cytoskeleton, protein stabilization and turnover, oxidative stress, and signaling are common responses to environmental change.

  2. Pan-proteomics, a concept for unifying quantitative proteome measurements when comparing closely-related bacterial strains.

    Science.gov (United States)

    Broadbent, James A; Broszczak, Daniel A; Tennakoon, Imalka U K; Huygens, Flavia

    2016-04-01

    The comparison of proteomes between genetically heterogeneous bacterial strains may offer valuable insights into physiological diversity and function, particularly where such variation aids in the survival and virulence of clinically-relevant strains. However, reports of such comparisons frequently fail to account for underlying genetic variance. As a consequence, the current knowledge regarding bacterial physiological diversity at the protein level may be incomplete or inaccurate. To address this, greater consideration must be given to the impact of genetic heterogeneity on proteome comparisons. This may be possible through the use of pan-proteomics, an analytical concept that permits the ability to qualitatively and quantitatively compare the proteomes of genetically heterogeneous organisms. Limited examples of this emerging technology highlight currently unmet analytical challenges. In this article we define pan-proteomics, where its value lies in microbiology, and discuss the technical considerations critical to its successful execution and potential future application. PMID:26889693

  3. Quantitative Proteomics Analysis of Leukemia Cells.

    Science.gov (United States)

    Halbach, Sebastian; Dengjel, Jörn; Brummer, Tilman

    2016-01-01

    Chronic myeloid leukemia (CML) is driven by the oncogenic fusion kinase Bcr-Abl, which organizes its own signaling network with various proteins. These proteins, their interactions, and their role in relevant signaling pathways can be analyzed by quantitative mass spectrometry (MS) approaches in various models systems, e.g., in cell culture models. In this chapter, we describe in detail immunoprecipitations and quantitative proteomics analysis using stable isotope labeling by amino acids in cell culture (SILAC) of components of the Bcr-Abl signaling pathway in the human CML cell line K562. PMID:27581145

  4. The Proteome of Primary Prostate Cancer

    DEFF Research Database (Denmark)

    Iglesias-Gato, Diego; Wikström, Pernilla; Tyanova, Stefka;

    2016-01-01

    for disease aggressiveness. DESIGN, SETTING, AND PARTICIPANTS: Mass spectrometry was used for genome-scale quantitative proteomic profiling of 28 prostate tumors (Gleason score 6-9) and neighboring nonmalignant tissue in eight cases, obtained from formalin-fixed paraffin-embedded prostatectomy samples....... Two independent cohorts of PCa patients (summing 752 cases) managed by expectancy were used for immunohistochemical evaluation of proneuropeptide-Y (pro-NPY) as a prognostic biomarker. RESULTS AND LIMITATIONS: Over 9000 proteins were identified as expressed in the human prostate. Tumor tissue...

  5. BFluenza: A Proteomic Database on Bird Flu

    OpenAIRE

    Salahuddin, Parveen; Khan, Asad U.

    2011-01-01

    Influenza A virus subtype H5N1, also known as “bird flu” has been documented to cause an outbreak of respiratory diseases in humans. The unprecedented spread of highly pathogenic avian influenza type A is a threat to veterinary and human health. The BFluenza is a relational database which is solely devoted to proteomic information of H5N1 subtype. Bfluenza has novel features including computed physico-chemical properties data of H5N1 viral proteins, modeled structures of viral proteins, data ...

  6. The Multinational Arabidopsis Steering Subcommittee for Proteomics Assembles the Largest Proteome Database Resource for Plant Systems Biology

    Energy Technology Data Exchange (ETDEWEB)

    Weckwerth, Wolfram; Baginsky, Sacha; Van Wijk, Klass; Heazlewood, Joshua; Millar, Harvey

    2009-12-01

    In the past 10 years, we have witnessed remarkable advances in the field of plant molecular biology. The rapid development of proteomic technologies and the speed with which these techniques have been applied to the field have altered our perception of how we can analyze proteins in complex systems. At nearly the same time, the availability of the complete genome for the model plant Arabidopsis thaliana was released; this effort provides an unsurpassed resource for the identification of proteins when researchers use MS to analyze plant samples. Recognizing the growth in this area, the Multinational Arabidopsis Steering Committee (MASC) established a subcommittee for A. thaliana proteomics in 2006 with the objective of consolidating databases, technique standards, and experimentally validated candidate genes and functions. Since the establishment of the Multinational Arabidopsis Steering Subcommittee for Proteomics (MASCP), many new approaches and resources have become available. Recently, the subcommittee established a webpage to consolidate this information (www.masc-proteomics.org). It includes links to plant proteomic databases, general information about proteomic techniques, meeting information, a summary of proteomic standards, and other relevant resources. Altogether, this website provides a useful resource for the Arabidopsis proteomics community. In the future, the website will host discussions and investigate the cross-linking of databases. The subcommittee members have extensive experience in arabidopsis proteomics and collectively have produced some of the most extensive proteomics data sets for this model plant (Table S1 in the Supporting Information has a list of resources). The largest collection of proteomics data from a single study in A. thaliana was assembled into an accessible database (AtProteome; http://fgcz-atproteome.unizh.ch/index.php) and was recently published by the Baginsky lab.1 The database provides links to major Arabidopsis online

  7. Comparative and Quantitative Global Proteomics Approaches: An Overview

    Directory of Open Access Journals (Sweden)

    Barbara Deracinois

    2013-10-01

    Full Text Available Proteomics became a key tool for the study of biological systems. The comparison between two different physiological states allows unravelling the cellular and molecular mechanisms involved in a biological process. Proteomics can confirm the presence of proteins suggested by their mRNA content and provides a direct measure of the quantity present in a cell. Global and targeted proteomics strategies can be applied. Targeted proteomics strategies limit the number of features that will be monitored and then optimise the methods to obtain the highest sensitivity and throughput for a huge amount of samples. The advantage of global proteomics strategies is that no hypothesis is required, other than a measurable difference in one or more protein species between the samples. Global proteomics methods attempt to separate quantify and identify all the proteins from a given sample. This review highlights only the different techniques of separation and quantification of proteins and peptides, in view of a comparative and quantitative global proteomics analysis. The in-gel and off-gel quantification of proteins will be discussed as well as the corresponding mass spectrometry technology. The overview is focused on the widespread techniques while keeping in mind that each approach is modular and often recovers the other.

  8. Proteomics of cell-cell interactions in health and disease.

    Science.gov (United States)

    Lindoso, Rafael S; Sandim, Vanessa; Collino, Federica; Carvalho, Adriana B; Dias, Juliana; da Costa, Milene R; Zingali, Russolina B; Vieyra, Adalberto

    2016-01-01

    The mechanisms of cell-cell communications are now under intense study by proteomic approaches. Proteomics has unraveled changes in protein profiling as the result of cell interactions mediated by ligand/receptor, hormones, soluble factors, and the content of extracellular vesicles. Besides being a brief overview of the main and profitable methodologies now available (evaluating theory behind the methods, their usefulness, and pitfalls), this review focuses on-from a proteome perspective-some signaling pathways and post-translational modifications (PTMs), which are essential for understanding ischemic lesions and their recovery in two vital organs in mammals, the heart, and the kidney. Knowledge of misdirection of the proteome during tissue recovery, such as represented by the convergence between fibrosis and cancer, emerges as an important tool in prognosis. Proteomics of cell-cell interaction is also especially useful for understanding how stem cells interact in injured tissues, anticipating clues for rational therapeutic interventions. In the effervescent field of induced pluripotency and cell reprogramming, proteomic studies have shown what proteins from specialized cells contribute to the recovery of infarcted tissues. Overall, we conclude that proteomics is at the forefront in helping us to understand the mechanisms that underpin prevalent pathological processes. PMID:26552723

  9. Mass-spectrometry-based draft of the human proteome.

    Science.gov (United States)

    Wilhelm, Mathias; Schlegl, Judith; Hahne, Hannes; Moghaddas Gholami, Amin; Lieberenz, Marcus; Savitski, Mikhail M; Ziegler, Emanuel; Butzmann, Lars; Gessulat, Siegfried; Marx, Harald; Mathieson, Toby; Lemeer, Simone; Schnatbaum, Karsten; Reimer, Ulf; Wenschuh, Holger; Mollenhauer, Martin; Slotta-Huspenina, Julia; Boese, Joos-Hendrik; Bantscheff, Marcus; Gerstmair, Anja; Faerber, Franz; Kuster, Bernhard

    2014-05-29

    Proteomes are characterized by large protein-abundance differences, cell-type- and time-dependent expression patterns and post-translational modifications, all of which carry biological information that is not accessible by genomics or transcriptomics. Here we present a mass-spectrometry-based draft of the human proteome and a public, high-performance, in-memory database for real-time analysis of terabytes of big data, called ProteomicsDB. The information assembled from human tissues, cell lines and body fluids enabled estimation of the size of the protein-coding genome, and identified organ-specific proteins and a large number of translated lincRNAs (long intergenic non-coding RNAs). Analysis of messenger RNA and protein-expression profiles of human tissues revealed conserved control of protein abundance, and integration of drug-sensitivity data enabled the identification of proteins predicting resistance or sensitivity. The proteome profiles also hold considerable promise for analysing the composition and stoichiometry of protein complexes. ProteomicsDB thus enables navigation of proteomes, provides biological insight and fosters the development of proteomic technology. PMID:24870543

  10. Effects of Hypertension and Exercise on Cardiac Proteome Remodelling

    Directory of Open Access Journals (Sweden)

    Bernardo A. Petriz

    2014-01-01

    Full Text Available Left ventricle hypertrophy is a common outcome of pressure overload stimulus closely associated with hypertension. This process is triggered by adverse molecular signalling, gene expression, and proteome alteration. Proteomic research has revealed that several molecular targets are associated with pathologic cardiac hypertrophy, including angiotensin II, endothelin-1 and isoproterenol. Several metabolic, contractile, and stress-related proteins are shown to be altered in cardiac hypertrophy derived by hypertension. On the other hand, exercise is a nonpharmacologic agent used for hypertension treatment, where cardiac hypertrophy induced by exercise training is characterized by improvement in cardiac function and resistance against ischemic insult. Despite the scarcity of proteomic research performed with exercise, healthy and pathologic heart proteomes are shown to be modulated in a completely different way. Hence, the altered proteome induced by exercise is mostly associated with cardioprotective aspects such as contractile and metabolic improvement and physiologic cardiac hypertrophy. The present review, therefore, describes relevant studies involving the molecular characteristics and alterations from hypertensive-induced and exercise-induced hypertrophy, as well as the main proteomic research performed in this field. Furthermore, proteomic research into the effect of hypertension on other target-demerged organs is examined.

  11. Implementation of proteomics for cancer research: past, present, and future.

    Science.gov (United States)

    Karimi, Parisa; Shahrokni, Armin; Ranjbar, Mohammad R Nezami

    2014-01-01

    Cancer is the leading cause of the death, accounts for about 13% of all annual deaths worldwide. Many different fields of science are collaborating together studying cancer to improve our knowledge of this lethal disease, and find better solutions for diagnosis and treatment. Proteomics is one of the most recent and rapidly growing areas in molecular biology that helps understanding cancer from an omics data analysis point of view. The human proteome project was officially initiated in 2008. Proteomics enables the scientists to interrogate a variety of biospecimens for their protein contents and measure the concentrations of these proteins. Current necessary equipment and technologies for cancer proteomics are mass spectrometry, protein microarrays, nanotechnology and bioinformatics. In this paper, we provide a brief review on proteomics and its application in cancer research. After a brief introduction including its definition, we summarize the history of major previous work conducted by researchers, followed by an overview on the role of proteomics in cancer studies. We also provide a list of different utilities in cancer proteomics and investigate their advantages and shortcomings from theoretical and practical angles. Finally, we explore some of the main challenges and conclude the paper with future directions in this field. PMID:24761843

  12. Microfluidic integration for automated targeted proteomic assays.

    Science.gov (United States)

    Hughes, Alex J; Lin, Robert K C; Peehl, Donna M; Herr, Amy E

    2012-04-17

    A dearth of protein isoform-based clinical diagnostics currently hinders advances in personalized medicine. A well-organized protein biomarker validation process that includes facile measurement of protein isoforms would accelerate development of effective protein-based diagnostics. Toward scalable protein isoform analysis, we introduce a microfluidic "single-channel, multistage" immunoblotting strategy. The multistep assay performs all immunoblotting steps: separation, immobilization of resolved proteins, antibody probing of immobilized proteins, and all interim wash steps. Programmable, low-dispersion electrophoretic transport obviates the need for pumps and valves. A three-dimensional bulk photoreactive hydrogel eliminates manual blotting. In addition to simplified operation and interfacing, directed electrophoretic transport through our 3D nanoporous reactive hydrogel yields superior performance over the state-of-the-art in enhanced capture efficiency (on par with membrane electroblotting) and sparing consumption of reagents (ca. 1 ng antibody), as supported by empirical and by scaling analyses. We apply our fully integrated microfluidic assay to protein measurements of endogenous prostate specific antigen isoforms in (i) minimally processed human prostate cancer cell lysate (1.1 pg limit of detection) and (ii) crude sera from metastatic prostate cancer patients. The single-instrument functionality establishes a scalable microfluidic framework for high-throughput targeted proteomics, as is relevant to personalized medicine through robust protein biomarker verification, systematic characterization of new antibody probes for functional proteomics, and, more broadly, to characterization of human biospecimen repositories. PMID:22474344

  13. Isotope dilution strategies for absolute quantitative proteomics

    International Nuclear Information System (INIS)

    The development of mass spectrometry (MS)-based methodologies for high-throughput protein identification has generated a concomitant need for protein quantification. Numerous MS-based relative quantification methodologies have been dedicated to the extensive comparison of multiple proteomes. On the other hand, absolute quantification methodologies, which allow the determination of protein concentrations in biological samples, are generally restricted to defined sets of proteins. Depending on the selected analytical procedure, absolute quantification approaches can provide accurate and precise estimations. These analytical performances are crucial for specific applications such as the evaluation of clinical bio-marker candidates. According to bioanalytical guidelines, accurate analytical processes require internal standards and quality controls. Regarding MS-based analysis of small molecules, isotope dilution has been recognized as the reference method for internal standardization. However, protein quantification methodologies which rely on the isotope dilution principle have been implemented in the proteomic field only recently. In these approaches, the sample is spiked with defined amounts of isotope-labeled analogue(s) of specific proteolytic peptide(s) (AQUA and QconCAT strategies) or protein(s) (PSAQ strategy). In this review, we present a critical overview of these isotope dilution methodologies. (authors)

  14. Proteomic maps of breast cancer subtypes.

    Science.gov (United States)

    Tyanova, Stefka; Albrechtsen, Reidar; Kronqvist, Pauliina; Cox, Juergen; Mann, Matthias; Geiger, Tamar

    2016-01-01

    Systems-wide profiling of breast cancer has almost always entailed RNA and DNA analysis by microarray and sequencing techniques. Marked developments in proteomic technologies now enable very deep profiling of clinical samples, with high identification and quantification accuracy. We analysed 40 oestrogen receptor positive (luminal), Her2 positive and triple negative breast tumours and reached a quantitative depth of >10,000 proteins. These proteomic profiles identified functional differences between breast cancer subtypes, related to energy metabolism, cell growth, mRNA translation and cell-cell communication. Furthermore, we derived a signature of 19 proteins, which differ between the breast cancer subtypes, through support vector machine (SVM)-based classification and feature selection. Remarkably, only three proteins of the signature were associated with gene copy number variations and eleven were also reflected on the mRNA level. These breast cancer features revealed by our work provide novel insights that may ultimately translate to development of subtype-specific therapeutics. PMID:26725330

  15. Urinary proteomics to support diagnosis of stroke.

    Directory of Open Access Journals (Sweden)

    Jesse Dawson

    Full Text Available Accurate diagnosis in suspected ischaemic stroke can be difficult. We explored the urinary proteome in patients with stroke (n = 69, compared to controls (n = 33, and developed a biomarker model for the diagnosis of stroke. We performed capillary electrophoresis online coupled to micro-time-of-flight mass spectrometry. Potentially disease-specific peptides were identified and a classifier based on these was generated using support vector machine-based software. Candidate biomarkers were sequenced by liquid chromatography-tandem mass spectrometry. We developed two biomarker-based classifiers, employing 14 biomarkers (nominal p-value <0.004 or 35 biomarkers (nominal p-value <0.01. When tested on a blinded test set of 47 independent samples, the classification factor was significantly different between groups; for the 35 biomarker model, median value of the classifier was 0.49 (-0.30 to 1.25 in cases compared to -1.04 (IQR -1.86 to -0.09 in controls, p<0.001. The 35 biomarker classifier gave sensitivity of 56%, specificity was 93% and the AUC on ROC analysis was 0.86. This study supports the potential for urinary proteomic biomarker models to assist with the diagnosis of acute stroke in those with mild symptoms. We now plan to refine further and explore the clinical utility of such a test in large prospective clinical trials.

  16. Proteomic profiling of Tectona grandis L. leaf.

    Science.gov (United States)

    Quiala, Elisa; Cañal, María Jesús; Rodríguez, Roberto; Yagüe, Norma; Chávez, Maité; Barbón, Raúl; Valledor, Luis

    2012-04-01

    Tectona grandis L. (teak) is one of the premier hardwood timbers in the world, ranking at present in the top five tropical hardwood species in terms of worldwide plantation area. Characterization of the proteins present in teak leaves will provide a basis for the development of new tools aimed at assisting tree selection, the monitoring of plant propagation, and the certification of clonal and phenotypic identities. In this paper, we describe the extraction, separation, and identification of leaf proteins from T. grandis using a TCA/acetone protocol, 2DE, and MALDI-TOF. After TCA/acetone protein extraction of leaves, 998 well-resolved spots were detected in Coomassie-stained gels within the 10-114 kDa relative molecular mass (Mr) range at a pH ranging from 3 to 11. A total of 120 spots were digested and subjected to MS. Of these, 100 nonredundant protein species were successfully identified. Functional classification of the identified proteins revealed that proteins involved in photosynthesis, protein translation, and energy production were the most abundant. This work is the first high-throughput attempt to study the T. grandis leaf proteome and represents a stepping stone for further differential expression proteomic studies related to growth, development, biomass production, and culture-associated physiological responses. PMID:22522810

  17. The PROTICdb database for 2-DE proteomics.

    Science.gov (United States)

    Langella, Olivier; Zivy, Michel; Joets, Johann

    2007-01-01

    PROTICdb is a web-based database mainly designed to store and analyze plant proteome data obtained by 2D polyacrylamide gel electrophoresis (2D PAGE) and mass spectrometry (MS). The goals of PROTICdb are (1) to store, track, and query information related to proteomic experiments, i.e., from tissue sampling to protein identification and quantitative measurements; and (2) to integrate information from the user's own expertise and other sources into a knowledge base, used to support data interpretation (e.g., for the determination of allelic variants or products of posttranslational modifications). Data insertion into the relational database of PROTICdb is achieved either by uploading outputs from Mélanie, PDQuest, IM2d, ImageMaster(tm) 2D Platinum v5.0, Progenesis, Sequest, MS-Fit, and Mascot software, or by filling in web forms (experimental design and methods). 2D PAGE-annotated maps can be displayed, queried, and compared through the GelBrowser. Quantitative data can be easily exported in a tabulated format for statistical analyses with any third-party software. PROTICdb is based on the Oracle or the PostgreSQLDataBase Management System (DBMS) and is freely available upon request at http://cms.moulon.inra.fr/content/view/14/44/. PMID:17093318

  18. The proteome of human brain microdialysate

    Directory of Open Access Journals (Sweden)

    Feldmann Robert E

    2003-12-01

    Full Text Available Abstract Background Cerebral microdialysis has been established as a monitoring tool in neurocritically ill patients suffering from severe stroke. The technique allows to sample small molecules in the brain tissue for subsequent biochemical analysis. In this study, we investigated the proteomic profile of human cerebral microdialysate and if the identified proteins might be useful predictors for disease characteristics in stroke for tissue at risk in the contralateral hemisphere. We analysed cerebral protein expression in microdialysate from three stroke patients sampled from the hemisphere contralateral to the lesion. Using a proteomic approach based on two-dimensional gel electrophoresis and subsequent mass spectrometry, we created a protein map for the global protein expression pattern of human microdialyste. Results We found an average of 158 ± 24 (N = 18 protein spots in the human cerebral microdialysate and could identify 95 spots, representing 27 individual proteins. Most of these have been detected in human cerebrospinal fluid before, but 10 additional proteins mainly of cerebral intracellular origin were identified exclusively in the microdialysate. Conclusions The 10 proteins found exclusively in human cerebral microdialysate, but not in cerebrospinal fluid, indicate the possibility to monitor the progression of the disease towards deterioration. The correlation of protein composition in the human cerebral microdialysate with the patients' clinical condition and results of cerebral imaging may be a useful approach to future applications for neurological stroke diagnosis, prognosis, and treatment.

  19. Proteome analysis of chick embryonic cerebrospinal fluid.

    Science.gov (United States)

    Parada, Carolina; Gato, Angel; Aparicio, Mariano; Bueno, David

    2006-01-01

    During early stages of embryo development, the brain cavity is filled with embryonic cerebrospinal fluid (E-CSF), a complex fluid containing different protein fractions that contributes to the regulation of the survival, proliferation and neurogenesis of the neuroectodermal stem cells. Using 2-DE, protein sequencing and database searches, we identified and analyzed the proteome of the E-CSF from chick embryos (Gallus gallus). We identified 26 different gene products, including proteins related to the extracellular matrix, proteins associated with the regulation of osmotic pressure and metal transport, proteins related to cell survival, MAP kinase activators, proteins involved in the transport of retinol and vitamin D, antioxidant and antimicrobial proteins, intracellular proteins and some unknown proteins. Most of these gene products are involved in the regulation of developmental processes during embryogenesis in systems other than E-CSF. Interestingly, 14 of them are also present in adult human CSF proteome, and it has been reported that they are altered in the CSF of patients suffering neurodegenerative diseases and/or neurological disorders. Understanding these molecules and the mechanisms they control during embryonic neurogenesis is a key contribution to the general understanding of CNS development, and may also contribute to greater knowledge of these human diseases. PMID:16287170

  20. Biochemical and proteomic characterization of alkaptonuric chondrocytes.

    Science.gov (United States)

    Braconi, Daniela; Bernardini, Giulia; Bianchini, Claretta; Laschi, Marcella; Millucci, Lia; Amato, Loredana; Tinti, Laura; Serchi, Tommaso; Chellini, Federico; Spreafico, Adriano; Santucci, Annalisa

    2012-09-01

    Alkaptonuria (AKU) is a rare genetic disease associated with the accumulation of homogentisic acid (HGA) and its oxidized/polymerized products which leads to the deposition of melanin-like pigments (ochronosis) in connective tissues. Although numerous case reports have described ochronosis in joints, little is known on the molecular mechanisms leading to such a phenomenon. For this reason, we characterized biochemically chondrocytes isolated from the ochronotic cartilage of AKU patients. Based on the macroscopic appearance of the ochronotic cartilage, two sub-populations were identified: cells coming from the black portion of the cartilage were referred to as "black" AKU chondrocytes, while those coming from the white portion were referred to as "white" AKU chondrocytes. Notably, both AKU chondrocytic types were characterized by increased apoptosis, NO release, and levels of pro-inflammatory cytokines. Transmission electron microscopy also revealed that intracellular ochronotic pigment deposition was common to both "white" and "black" AKU cells. We then undertook a proteomic and redox-proteomic analysis of AKU chondrocytes which revealed profound alterations in the levels of proteins involved in cell defence, protein folding, and cell organization. An increased post-translational oxidation of proteins, which also involved high molecular weight protein aggregates, was found to be particularly relevant in "black" AKU chondrocytes. PMID:22213341

  1. Combining Search Engines for Comparative Proteomics

    Science.gov (United States)

    Tabb, David

    2012-01-01

    Many proteomics laboratories have found spectral counting to be an ideal way to recognize biomarkers that differentiate cohorts of samples. This approach assumes that proteins that differ in quantity between samples will generate different numbers of identifiable tandem mass spectra. Increasingly, researchers are employing multiple search engines to maximize the identifications generated from data collections. This talk evaluates four strategies to combine information from multiple search engines in comparative proteomics. The “Count Sum” model pools the spectra across search engines. The “Vote Counting” model combines the judgments from each search engine by protein. Two other models employ parametric and non-parametric analyses of protein-specific p-values from different search engines. We evaluated the four strategies in two different data sets. The ABRF iPRG 2009 study generated five LC-MS/MS analyses of “red” E. coli and five analyses of “yellow” E. coli. NCI CPTAC Study 6 generated five concentrations of Sigma UPS1 spiked into a yeast background. All data were identified with X!Tandem, Sequest, MyriMatch, and TagRecon. For both sample types, “Vote Counting” appeared to manage the diverse identification sets most effectively, yielding heightened discrimination as more search engines were added.

  2. SILK FIBRE DEGRADATION AND ANALYSIS BY PROTEOMICS

    Directory of Open Access Journals (Sweden)

    YUKSELOGLU S.Muge

    2016-05-01

    Full Text Available Silk is one of the promising natural fibres and has a long established history in textile production throughout the centuries. Silk is produced by cultured silk worms, spiders, scorpions, mites and flies. It is extracellular proteinaceous fibres which consist of highly crystalline and insoluble proteins, the fibroins glued with sericin and an amourphous protein. On the other hand, understanding and controlling the degradation of protein materials are important for determining quality and the value of appearance retention in textiles. Hence, for silk textiles, appearance retention is critical value for the quality. And this is one of the key properties directly related to the degree and nature of protein degradation. It is therefore necessary to understand the silk composition and damage to obtain good conservation treatments and long-term preservation especially for the historical silk fabrics. In this study, silk fibre and its properties are briefly introduced along with images on their fibre damages. Additionally, proteomics method which helps to understand the degradation at the molecular level in textiles is introduced. Finally, proteomic evaluation of silk is summarized according to the researchers carried out in the literature.

  3. Proteomic analysis of hippocampus in the rat

    Institute of Scientific and Technical Information of China (English)

    ZHANG Bo; WANG Ren-zhi; LIAN Zhi-gang; YAO Yong

    2004-01-01

    Objective To analyze the protein expression in the rat hippocampus by the proteomic approach.Methods Proteins from hippocampal tissue homogenates of the rat were separated by two-dimensional gel electrophoresis(2-DE),and stained with colloidal Coomassie blue to produce a high-resolution map of the rat hippocampus proteome.Selected proteins from this map were digested with trypsin,and the resulting tryptic peptides were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry(MALDI-TOF-MS).The mass spectrometric data were used to identify the proteins through searches of the NCBI protein sequence database.Results 37 prominent proteins with various functional characteristics were identified.The identified brain protein classes covered metabolism enzymes,cytoskeleton proteins,heat shock proteins,antioxidant proteins,signalling proteins,proteasome-related proteins,neuron-specific proteins and glial-associated proteins.Furthermore,3 hypothetical proteins,unknown proteins so far only proposed from their nucleic acid structure,were identified.Conclusion This study provides the first unbiased characterization of proteins of the rat hippocampus and will be used for future studies of differential protein expression in rat models of neurological disorders.

  4. Oxidative proteome alterations during skeletal muscle ageing

    Directory of Open Access Journals (Sweden)

    Sofia Lourenço dos Santos

    2015-08-01

    Full Text Available Sarcopenia corresponds to the degenerative loss of skeletal muscle mass, quality, and strength associated with ageing and leads to a progressive impairment of mobility and quality of life. However, the cellular and molecular mechanisms involved in this process are not completely understood. A hallmark of cellular and tissular ageing is the accumulation of oxidatively modified (carbonylated proteins, leading to a decreased quality of the cellular proteome that could directly impact on normal cellular functions. Although increased oxidative stress has been reported during skeletal muscle ageing, the oxidized protein targets, also referred as to the ‘oxi-proteome’ or ‘carbonylome’, have not been characterized yet. To better understand the mechanisms by which these damaged proteins build up and potentially affect muscle function, proteins targeted by these modifications have been identified in human rectus abdominis muscle obtained from young and old healthy donors using a bi-dimensional gel electrophoresis-based proteomic approach coupled with immunodetection of carbonylated proteins. Among evidenced protein spots, 17 were found as increased carbonylated in biopsies from old donors comparing to young counterparts. These proteins are involved in key cellular functions such as cellular morphology and transport, muscle contraction and energy metabolism. Importantly, impairment of these pathways has been described in skeletal muscle during ageing. Functional decline of these proteins due to irreversible oxidation may therefore impact directly on the above-mentioned pathways, hence contributing to the generation of the sarcopenic phenotype.

  5. The initiative on Model Organism Proteomes (iMOP) Session

    DEFF Research Database (Denmark)

    Schrimpf, Sabine P; Mering, Christian von; Bendixen, Emøke;

    2012-01-01

    iMOP – the Initiative on Model Organism Proteomes – was accepted as a new HUPO initiative at the Ninth HUPO meeting in Sydney in 2010. A goal of iMOP is to integrate research groups working on a great diversity of species into a model organism community. At the Tenth HUPO meeting in Geneva this...... variety was reflected in the iMOP session on Tuesday September 6, 2011. The presentations covered the quantitative proteome database PaxDb, proteomics projects studying farm animals, Arabidopsis thaliana, as well as host–pathogen interactions....

  6. Quantitative proteome profiling of normal human circulating microparticles

    DEFF Research Database (Denmark)

    Østergaard, Ole; Nielsen, Christoffer T; Iversen, Line V;

    2012-01-01

    Circulating microparticles (MPs) are produced as part of normal physiology. Their numbers, origin, and composition change in pathology. Despite this, the normal MP proteome has not yet been characterized with standardized high-resolution methods. We here quantitatively profile the normal MP...... proteome using nano-LC-MS/MS on an LTQ-Orbitrap with optimized sample collection, preparation, and analysis of 12 different normal samples. Analytical and procedural variation were estimated in triply processed samples analyzed in triplicate from two different donors. Label-free quantitation was validated...... quantitated. Of these, 334 (63%) were present in all samples and represent an MP core proteome. Technical triplicates showed...

  7. Web Resources for Mass Spectrometry-based Proteomics

    Institute of Scientific and Technical Information of China (English)

    Tao Chen; Jie Zhao; Jie Ma; Yunping Zhu

    2015-01-01

    With the development of high-resolution and high-throughput mass spectrometry (MS) technology, a large quantum of proteomic data is continually being generated. Collecting and shar-ing these data are a challenge that requires immense and sustained human effort. In this report, we provide a classification of important web resources for MS-based proteomics and present rating of these web resources, based on whether raw data are stored, whether data submission is supported, and whether data analysis pipelines are provided. These web resources are important for biologists involved in proteomics research.

  8. Proteomics in China:Ready for prime time

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Proteomics is a newborn science focusing on the comprehensive systematic analysis of all proteins in molecule machineries,organelles,cells,tissues,organs or intact organisms.It has been becoming one of the focuses in life sciences and cutting-edge techniques in biotechnologies in the 21st century.During the last decade,proteomics in China has developed much faster than other developing fields in the life sciences.This review article briefly retrospects the origin and development of proteomics in China,and provides an overview of representative scientific progress and perspectives.

  9. Application of pressurized solvents for ultra fast trypsin hydrolysis in proteomics: Proteomics on the fly

    OpenAIRE

    López-Ferrer, Daniel; Petritis, Konstantinos; Hixson, Kim K.; Heibeck, Tyler H.; Moore, Ronald J.; Belov, Mikhail E.; Camp, David G; Smith, Richard D.

    2008-01-01

    A new method for rapid proteolytic digestion of proteins under high pressure that uses pressure cycling technology in the range of 5 to 35 kpsi was demonstrated for proteomic analysis. Successful in-solution digestions of single proteins and complex protein mixtures were achieved in 60 s and then analyzed by reversed phase liquid chromatography-electrospray ionization ion trap-mass spectrometry. Method performance in terms of the number of Shewanella oneidensis peptides and proteins identifie...

  10. Mammalian embryonic cerebrospinal fluid proteome has greater apolipoprotein and enzyme pattern complexity than the avian proteome.

    Science.gov (United States)

    Parada, Carolina; Gato, Angel; Bueno, David

    2005-01-01

    During early stages of embryo development, the brain cavity is filled with Embryonic Cerebro-Spinal Fluid, which has an essential role in the survival, proliferation and neurogenesis of the neuroectodermal stem cells. We identified and analyzed the proteome of Embryonic Cerebro-Spinal Fluid from rat embryos (Rattus norvegicus), which includes proteins involved in the regulation of Central Nervous System development. The comparison between mammalian and avian Embryonic Cerebro-Spinal Fluid proteomes reveals great similarity, but also greater complexity in some protein groups. The pattern of apolipoproteins and enzymes in CSF is more complex in the mammals than in birds. This difference may underlie the greater neural complexity and synaptic plasticity found in mammals. Fourteen Embryonic Cerebro-Spinal Fluid gene products were previously identified in adult human Cerebro-Spinal Fluid proteome, and interestingly they are altered in patients with neurodegenerative diseases and/or neurological disorders. Understanding these molecules and the mechanisms they control during embryonic neurogenesis may contribute to our understanding of Central Nervous System development and evolution, and these human diseases. PMID:16335996

  11. Partial Proteome Map of Campylobacter Jejuni Strain Nctc11168 by Gel-Free Proteomics Analysis

    Directory of Open Access Journals (Sweden)

    Zilun Shi

    2014-12-01

    Full Text Available A proteome map of the foodborne pathogen Campylobacter jejuni NCTC11168 was analyzed using a state-of-the-art gel-free proteomic approach for the first time. A whole cell protein extract was prepared from the C. jejuni strain NCTC11168 grown in brain heart infusion (BHI broth at 42°C under microaerobic conditions. A gel-free technique using isobaric tags for relative and absolute quantitation (iTRAQ was employed to create a protein expression profile of the strain. Liquid chromatography-mass spectrometry (LC-MS/MS was used to identify the proteins. Protein functionalities were searched to classify them. A total of 235 proteins were identified in the whole cell protein fraction of C. jejuni NCTC11168 cells using iTRAQ analysis. Functional grouping of the identified proteins showed that forty percent of these proteins were associated with energy metabolism, protein synthesis and genetic information processing. iTRAQ was faster, easier and proved more sensitive than two-dimensional gel-based proteomics approaches previously applied to C. jejuni, making it an attractive tool for further studies of cellular physiological response.

  12. MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes

    DEFF Research Database (Denmark)

    Zhang, Yanling; Zhang, Yong; Adachi, Jun;

    2007-01-01

    Mass spectrometry (MS)-based proteomics has become a powerful technology to map the protein composition of organelles, cell types and tissues. In our department, a large-scale effort to map these proteomes is complemented by the Max-Planck Unified (MAPU) proteome database. MAPU contains several...... body fluid proteomes; including plasma, urine, and cerebrospinal fluid. Cell lines have been mapped to a depth of several thousand proteins and the red blood cell proteome has also been analyzed in depth. The liver proteome is represented with 3200 proteins. By employing high resolution MS and......://www.mapuproteome.com using a clickable interface of cell or body parts. Proteome data can be queried across proteomes by protein name, accession number, sequence similarity, peptide sequence and annotation information. More than 4500 mouse and 2500 human proteins have already been identified in at least one proteome. Basic...

  13. Liver proteomics in progressive alcoholic steatosis

    International Nuclear Information System (INIS)

    Fatty liver is an early stage of alcoholic and nonalcoholic liver disease (ALD and NALD) that progresses to steatohepatitis and other irreversible conditions. In this study, we identified proteins that were differentially expressed in the livers of rats fed 5% ethanol in a Lieber–DeCarli diet daily for 1 and 3 months by discovery proteomics (two-dimensional gel electrophoresis and mass spectrometry) and non-parametric modeling (Multivariate Adaptive Regression Splines). Hepatic fatty infiltration was significantly higher in ethanol-fed animals as compared to controls, and more pronounced at 3 months of ethanol feeding. Discovery proteomics identified changes in the expression of proteins involved in alcohol, lipid, and amino acid metabolism after ethanol feeding. At 1 and 3 months, 12 and 15 different proteins were differentially expressed. Of the identified proteins, down regulation of alcohol dehydrogenase (− 1.6) at 1 month and up regulation of aldehyde dehydrogenase (2.1) at 3 months could be a protective/adaptive mechanism against ethanol toxicity. In addition, betaine-homocysteine S-methyltransferase 2 a protein responsible for methionine metabolism and previously implicated in fatty liver development was significantly up regulated (1.4) at ethanol-induced fatty liver stage (1 month) while peroxiredoxin-1 was down regulated (− 1.5) at late fatty liver stage (3 months). Nonparametric analysis of the protein spots yielded fewer proteins and narrowed the list of possible markers and identified D-dopachrome tautomerase (− 1.7, at 3 months) as a possible marker for ethanol-induced early steatohepatitis. The observed differential regulation of proteins have potential to serve as biomarker signature for the detection of steatosis and its progression to steatohepatitis once validated in plasma/serum. -- Graphical abstract: The figure shows the Hierarchial cluster analysis of differentially expressed protein spots obtained after ethanol feeding for 1 (1–3

  14. Liver proteomics in progressive alcoholic steatosis

    Energy Technology Data Exchange (ETDEWEB)

    Fernando, Harshica [Department of Pathology, The University of Texas Medical Branch, Galveston, TX 77555 (United States); Wiktorowicz, John E.; Soman, Kizhake V. [Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77555 (United States); Kaphalia, Bhupendra S.; Khan, M. Firoze [Department of Pathology, The University of Texas Medical Branch, Galveston, TX 77555 (United States); Shakeel Ansari, G.A., E-mail: sansari@utmb.edu [Department of Pathology, The University of Texas Medical Branch, Galveston, TX 77555 (United States)

    2013-02-01

    Fatty liver is an early stage of alcoholic and nonalcoholic liver disease (ALD and NALD) that progresses to steatohepatitis and other irreversible conditions. In this study, we identified proteins that were differentially expressed in the livers of rats fed 5% ethanol in a Lieber–DeCarli diet daily for 1 and 3 months by discovery proteomics (two-dimensional gel electrophoresis and mass spectrometry) and non-parametric modeling (Multivariate Adaptive Regression Splines). Hepatic fatty infiltration was significantly higher in ethanol-fed animals as compared to controls, and more pronounced at 3 months of ethanol feeding. Discovery proteomics identified changes in the expression of proteins involved in alcohol, lipid, and amino acid metabolism after ethanol feeding. At 1 and 3 months, 12 and 15 different proteins were differentially expressed. Of the identified proteins, down regulation of alcohol dehydrogenase (− 1.6) at 1 month and up regulation of aldehyde dehydrogenase (2.1) at 3 months could be a protective/adaptive mechanism against ethanol toxicity. In addition, betaine-homocysteine S-methyltransferase 2 a protein responsible for methionine metabolism and previously implicated in fatty liver development was significantly up regulated (1.4) at ethanol-induced fatty liver stage (1 month) while peroxiredoxin-1 was down regulated (− 1.5) at late fatty liver stage (3 months). Nonparametric analysis of the protein spots yielded fewer proteins and narrowed the list of possible markers and identified D-dopachrome tautomerase (− 1.7, at 3 months) as a possible marker for ethanol-induced early steatohepatitis. The observed differential regulation of proteins have potential to serve as biomarker signature for the detection of steatosis and its progression to steatohepatitis once validated in plasma/serum. -- Graphical abstract: The figure shows the Hierarchial cluster analysis of differentially expressed protein spots obtained after ethanol feeding for 1 (1–3

  15. Simple sequence proteins in prokaryotic proteomes

    Directory of Open Access Journals (Sweden)

    Ramachandran Srinivasan

    2006-06-01

    Full Text Available Abstract Background The structural and functional features associated with Simple Sequence Proteins (SSPs are non-globularity, disease states, signaling and post-translational modification. SSPs are also an important source of genetic and possibly phenotypic variation. Analysis of 249 prokaryotic proteomes offers a new opportunity to examine the genomic properties of SSPs. Results SSPs are a minority but they grow with proteome size. This relationship is exhibited across species varying in genomic GC, mutational bias, life style, and pathogenicity. Their proportion in each proteome is strongly influenced by genomic base compositional bias. In most species simple duplications is favoured, but in a few cases such as Mycobacteria, large families of duplications occur. Amino acid preference in SSPs exhibits a trend towards low cost of biosynthesis. In SSPs and in non-SSPs, Alanine, Glycine, Leucine, and Valine are abundant in species widely varying in genomic GC whereas Isoleucine and Lysine are rich only in organisms with low genomic GC. Arginine is abundant in SSPs of two species and in the non-SSPs of Xanthomonas oryzae. Asparagine is abundant only in SSPs of low GC species. Aspartic acid is abundant only in the non-SSPs of Halobacterium sp NRC1. The abundance of Serine in SSPs of 62 species extends over a broader range compared to that of non-SSPs. Threonine(T is abundant only in SSPs of a couple of species. SSPs exhibit preferential association with Cell surface, Cell membrane and Transport functions and a negative association with Metabolism. Mesophiles and Thermophiles display similar ranges in the content of SSPs. Conclusion Although SSPs are a minority, the genomic forces of base compositional bias and duplications influence their growth and pattern in each species. The preferences and abundance of amino acids are governed by low biosynthetic cost, evolutionary age and base composition of codons. Abundance of charged amino acids Arginine

  16. Expanding the bovine milk proteome through extensive fractionation

    DEFF Research Database (Denmark)

    Nissen, Asger; Bendixen, Emøke; Ingvartsen, Klaus Lønne;

    2013-01-01

    of low abundant proteins. Further, the general health and udder health of the dairy cows delivering the milk may influence the composition of the milk proteome. To gain a more exhaustive and true picture of the milk proteome, we performed an extensive preanalysis fractionation of raw composite milk......, whose content of proteins were compared with the proteins of nonfractionated milk using 2-dimensional liquid chromatography tandem mass spectrometry analysis. To validate the proteome analysis, spectral counts and ELISA were performed on 7 proteins using the ELISA for estimation of the detection...... sensitivity limit of the 2-dimensional liquid chromatography tandem mass spectrometry analysis. Each fractionation technique resulted in identification of a unique subset of proteins. However, high-speed centrifugation of milk to whey was by far the best method to achieve high and repeatable proteome coverage...

  17. A Biologist's Field Guide to Multiplexed Quantitative Proteomics.

    Science.gov (United States)

    Bakalarski, Corey E; Kirkpatrick, Donald S

    2016-05-01

    High-throughput genomic and proteomic studies have generated near-comprehensive catalogs of biological constituents within many model systems. Nevertheless, static catalogs are often insufficient to fully describe the dynamic processes that drive biology. Quantitative proteomic techniques address this need by providing insight into closely related biological states such as the stages of a therapeutic response or cellular differentiation. The maturation of quantitative proteomics in recent years has brought about a variety of technologies, each with their own strengths and weaknesses. It can be difficult for those unfamiliar with this evolving landscape to match the experiment at hand with the best tool for the job. Here, we outline quantitative methods for proteomic mass spectrometry and discuss their benefits and weaknesses from the perspective of the biologist aiming to generate meaningful data and address mechanistic questions. PMID:26873251

  18. Mass Spectrometry-Based Label-Free Quantitative Proteomics

    Directory of Open Access Journals (Sweden)

    Wenhong Zhu

    2010-01-01

    Full Text Available In order to study the differential protein expression in complex biological samples, strategies for rapid, highly reproducible and accurate quantification are necessary. Isotope labeling and fluorescent labeling techniques have been widely used in quantitative proteomics research. However, researchers are increasingly turning to label-free shotgun proteomics techniques for faster, cleaner, and simpler results. Mass spectrometry-based label-free quantitative proteomics falls into two general categories. In the first are the measurements of changes in chromatographic ion intensity such as peptide peak areas or peak heights. The second is based on the spectral counting of identified proteins. In this paper, we will discuss the technologies of these label-free quantitative methods, statistics, available computational software, and their applications in complex proteomics studies.

  19. Challenges of protein extraction from recalcitrant plant tissues for proteomics

    Science.gov (United States)

    Proteins play an important role in several biological processes. Proteomics encompasses basically four principal applications, namely protein mining, protein expression profiling, protein-network mapping and mapping of protein modifications. The results in these applications depend mostly on the c...

  20. ProteoWizard - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    ProteoWizard highlight - 2007, Dr. Parag Mallick and Darren Kessner had one idea in mind – how could they develop robust proteomics software that is relatively “easy” to use and transferable between labs.

  1. Application of Proteomics in the Study of Tumor Metastasis

    Institute of Scientific and Technical Information of China (English)

    Zhen Cai; Jen-Fu Chiu; Qing-Yu He

    2004-01-01

    Tumor metastasis is the dominant cause of death in cancer patients. However, the molecular and cellular mechanisms underlying tumor metastasis are still elusive.The identification of protein molecules with their expressions correlated to the metastatic process would help to understand the metastatic mechanisms and thus facilitate the development of strategies for the therapeutic interventions and clinical management of cancer. Proteomics is a systematic research approach aiming to provide the global characterization of protein expression and function under given conditions. Proteomic technology has been widely used in biomarker discovery and pathogenetic studies including tumor metastasis. This article provides a brief review of the application of proteomics in identifying molecular factors in tumor metastasis process. The combination of proteomics with other experimental approaches in biochemistry, cell biology, molecular genetics and chemistry, together with the development of new technologies and improvements in existing method ologies will continue to extend its application in studying cancer metastasis.

  2. Toxicogenomics of bromobenzene hepatotoxicity: A combined transcriptomics and proteomics approach

    NARCIS (Netherlands)

    Heijne, W.H.M.; Stierum, R.H.; Slijper, M.; Bladeren, P.J. van; Ommen, B. van

    2003-01-01

    Toxicogenomics is a novel approach integrating the expression analysis of thousands of genes (transcriptomics) or proteins (proteomics) with classical methods in toxicology. Effects at the molecular level are related to pathophysiological changes of the organisms, enabling detailed comparison of mec

  3. Toxicogenomics of bromobenzene hepatotoxicity: a combined transcriptomics and proteomics approach

    NARCIS (Netherlands)

    Heijne, W.H.M.; Stierum, R.H.; Slijper, M.; Bladeren, van P.J.; Ommen, van B.

    2003-01-01

    Toxicogenomics is a novel approach integrating the expression analysis of thousands of genes (transcriptomics) or proteins (proteomics) with classical methods in toxicology. Effects at the molecular level are related to pathophysiological changes of the organisms, enabling detailed comparison of mec

  4. Contribution of proteomics to the management of vascular disorders

    Directory of Open Access Journals (Sweden)

    Fernando de la Cuesta

    2015-06-01

    Full Text Available Vascular disorders, and in particular atherothrombosis, are currently a leading cause of morbidity and mortality in Western societies. Proteomics research into these disorders has helped improving our knowledge of the underlying mechanisms involved in the development of atherothrombosis, as well as providing novel biomarkers to diagnose and for the prognosis of this disease. However, the application of these advances into clinical use has not followed this trend. In this review we explore the potential of Proteomics and Metabolomics for the management of vascular disorders, paying special attention to atherothrombosis and aiming to guide the reader from the experimental design of proteomic analysis through the initial discovery phase to the clinical implementation of biomarkers or therapeutic targets (Fig. 1, providing state-of-the-art proteomic studies to exemplify the concepts addressed.

  5. Shotgun proteomics of bacterial pathogens: advances, challenges and clinical implications.

    Science.gov (United States)

    Semanjski, Maja; Macek, Boris

    2016-02-01

    Mass spectrometry-based proteomics is increasingly used in analysis of bacterial pathogens. Simple experimental set-ups based on high accuracy mass spectrometry and powerful biochemical and bioinformatics tools are capable of reliably quantifying levels of several thousand bacterial proteins in a single experiment, reaching the analytical capacity to completely map whole proteomes. Here the authors present the state-of-the-art in bacterial pathogen proteomics and discuss challenges that the field is facing, especially in analysis of low abundant, modified proteins from organisms that are difficult to culture. Constant improvements in speed and sensitivity of mass spectrometers, as well as in bioinformatic and biochemical workflows will soon allow for comprehensive analysis of regulatory mechanisms of pathogenicity and enable routine application of proteomics in the clinical setting. PMID:26653908

  6. Towards a functional definition of the mitochondrial human proteome

    Directory of Open Access Journals (Sweden)

    Mauro Fasano

    2016-03-01

    Full Text Available The mitochondrial human proteome project (mt-HPP was initiated by the Italian HPP group as a part of both the chromosome-centric initiative (C-HPP and the “biology and disease driven” initiative (B/D-HPP. In recent years several reports highlighted how mitochondrial biology and disease are regulated by specific interactions with non-mitochondrial proteins. Thus, it is of great relevance to extend our present view of the mitochondrial proteome not only to those proteins that are encoded by or transported to mitochondria, but also to their interactors that take part in mitochondria functionality. Here, we propose a graphical representation of the functional mitochondrial proteome by retrieving mitochondrial proteins from the NeXtProt database and adding to the network their interactors as annotated in the IntAct database. Notably, the network may represent a reference to map all the proteins that are currently being identified in mitochondrial proteomics studies.

  7. The Clinical Proteomic Technologies for Cancer | Antibody Portal

    Science.gov (United States)

    An objective of the Reagents and Resources component of NCI's Clinical Proteomic Technologies for Cancer Initiative is to generate highly characterized monoclonal antibodies to human proteins associated with cancer.

  8. The Clinical Proteomic Technologies for Cancer | Antibody Scientific Committee

    Science.gov (United States)

    An objective of the Reagents and Resources component of NCI's Clinical Proteomic Technologies for Cancer Initiative is to generate highly characterized monoclonal antibodies to human proteins associated with cancer.

  9. The Clinical Proteomic Technologies for Cancer | Characterization Process

    Science.gov (United States)

    An objective of the Reagents and Resources component of NCI's Clinical Proteomic Technologies for Cancer Initiative is to generate highly characterized monoclonal antibodies to human proteins associated with cancer.

  10. The Clinical Proteomic Technologies for Cancer | Reagent Opportunities

    Science.gov (United States)

    An objective of the Reagents and Resources component of NCI's Clinical Proteomic Technologies for Cancer Initiative is to generate highly characterized monoclonal antibodies to human proteins associated with cancer.

  11. Comparative testis proteome dataset between cattleyak and yak.

    Science.gov (United States)

    Yang, Fang; Mipam, TserangDonko; Sun, Lei; Yu, Shumin; Cai, Xin

    2016-09-01

    Cattleyak are hybrid between cattle and yak, which exhibit equivalent adaptability on the Qinghai-Tibetan Plateau as yak and much higher capability in economic traits. However, the F1 males of cattleyak are infertile due to spermatogenic arrest and this greatly restricts the effective utilization of this hybrid. In this data article, differentially expressed proteins (DEPs) were identified from testis proteome of cattleyak and yak using high-performance liquid chromatography-electrospray tandem mass spectrometry (LC-ESI-MS/MS). All the DEPs were subjected to functional classification by Gene Ontology (GO) analysis and gene-pathway annotation by Kyoto Encyclopedia of Genes and Genomes (KEGG). The comparative testis proteome dataset here can shed new light on the molecular characteristics of male infertility of cattleyak on proteome level, "Comparative iTRAQ proteomics revealed proteins associated with spermatogenic arrest of cattleyak" [1]. PMID:27366779

  12. Integrated proteomic and genomic analysis of colorectal cancer

    Science.gov (United States)

    Investigators who analyzed 95 human colorectal tumor samples have determined how gene alterations identified in previous analyses of the same samples are expressed at the protein level. The integration of proteomic and genomic data, or proteogenomics, pro

  13. Urine proteome of autosomal dominant polycystic kidney disease patients

    OpenAIRE

    Bakun, Magda; Niemczyk, Mariusz; Domanski, Dominik; Jazwiec, Radek; Perzanowska, Anna; Niemczyk, Stanislaw; Kistowski, Michal; Fabijanska, Agnieszka; Borowiec, Agnieszka; Paczek, Leszek; Dadlez, Michal

    2012-01-01

    Background Autosomal dominant polycystic kidney disease (ADPKD) is responsible for 10% of cases of the end stage renal disease. Early diagnosis, especially of potential fast progressors would be of benefit for efficient planning of therapy. Urine excreted proteome has become a promising field of the search for marker patterns of renal diseases including ADPKD. Up to now however, only the low molecular weight fraction of ADPKD proteomic fingerprint was studied. The aim of our study was to char...

  14. Quantitative Proteome Profiling of C. burnetii under Tetracycline Stress Conditions

    OpenAIRE

    Iosif Vranakis; Pieter-Jan De Bock; Anastasia Papadioti; Yannis Tselentis; Kris Gevaert; Georgios Tsiotis; Anna Psaroulaki

    2012-01-01

    The recommended antibiotic regimen against Coxiella burnetii, the etiological agent of Q fever, is based on a semi-synthetic, second-generation tetracycline, doxycycline. Here, we report on the comparison of the proteomes of a C. burnetii reference strain either cultured under control conditions or under tetracycline stress conditions. Using the MS-driven combined fractional diagonal chromatography proteomics technique, out of the 531 proteins identified, 5 and 19 proteins were found signific...

  15. Understanding the responses of rice to environmental stress using proteomics.

    Science.gov (United States)

    Singh, Raksha; Jwa, Nam-Soo

    2013-11-01

    Diverse abiotic and biotic stresses have marked effects on plant growth and productivity. To combat such stresses, plants have evolved complex but not well understood responses. Common effects upon perception of environmental stress are differential expression of the plant proteome and the synthesis of novel regulatory proteins for protection from and acclimation to stress conditions. Plants respond differently in terms of activation of stress-responsive signaling pathways depending upon the type and nature of the stresses to which they are exposed. Progress in proteomics and systems biology approaches has made it possible to identify the novel proteins and their interactions that function in abiotic stress responses. This will enable elucidation of the functions of individual proteins and their roles in signaling networks. Proteomic analysis of the responses to various stress conditions is performed most commonly using 2D gel electrophoresis and high-throughput identification by LC-MS/MS. Because of recent developments in proteomics techniques, numerous proteomics studies of rice under abiotic stress conditions have been performed. In this review, proteomics studies addressing rice responses to the major environmental stresses--including cold, heat, drought, salt, heavy metals, minerals, UV radiation, and ozone--are discussed. Unique or common protein responses to these stress conditions are summarized and interpreted according to their possible physiological responses in each stress. Additionally, proteomics studies on various plant systems under various abiotic stress conditions are compared to provide deeper understanding of specific and common proteome responses in rice and other plant systems, which will further contribute to the identification of abiotic stress tolerance factor at protein level. Functional analysis of stress-responsive proteins will provide new research objectives with the aim of achieving stable crop productivity in the face of the

  16. Proteomic tools in clinical tissues: unlocking the pathology archives

    OpenAIRE

    Faoro, Valentina

    1982-01-01

    Background: Clinical proteomics aims to characterize the protein networks altered by pathologic processes or therapeutic treatment, and to develop biomarker profiling technologies to promptly detect diseases and treat them more effectively. The challenge of translating proteomic profiling to the bedside lies in applying technologies for the analysis of human tissues, which are routinely obtained by biopsy or surgery, without substantially modifying the clinical workflow. Formalin-fixed and...

  17. TrSDB: a proteome database of transcription factors

    OpenAIRE

    Hermoso, Antoni; Aguilar, Daniel; Aviles, Francesc X.; Querol, Enrique

    2004-01-01

    TrSDB—TranScout Database—(http://ibb.uab.es/trsdb) is a proteome database of eukaryotic transcription factors based upon predicted motifs by TranScout and data sources such as InterPro and Gene Ontology Annotation. Nine eukaryotic proteomes are included in the current version. Extensive and diverse information for each database entry, different analyses considering TranScout classification and similarity relationships are offered for research on transcription factors or gene expression.

  18. Proteomic study on gender differences in aging kidney of mice

    OpenAIRE

    Cristobal Susana; Amelina Hanna

    2009-01-01

    Abstract Background This study aims to analyze sex differences in mice aging kidney. We applied a proteomic technique based on subfractionation, and liquid chromatography coupled with 2-DE. Samples from male and female CD1-Swiss outbred mice from 28 weeks, 52 weeks, and 76 weeks were analysed by 2-DE, and selected proteins were identified by matrix assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS). Results This proteomic analysis detected age-related changes...

  19. Proteomics Applied to Porcine and Human Neural Stem Cell Differentiation

    Czech Academy of Sciences Publication Activity Database

    Mairychová, Kateřina; Skalníková, Helena; Tylečková, Jiřina; Halada, Petr; Marsala, M.; Kovářová, Hana

    Liběchov : Institute of Animal Physiology and Genetics AS CR, v.v.i, 2010. s. 61-61. [Informal Proteomic Meeting 2010. 09.11.2010-10.11.2010, Liblice] R&D Projects: GA MŠk 1M0538; GA MŠk(CZ) ME10044 Institutional research plan: CEZ:AV0Z50450515; CEZ:AV0Z50200510 Keywords : proteomics * cell differentiation * neural stem cell s Subject RIV: FH - Neurology

  20. Insight of Saffron Proteome by Gel-Electrophoresis

    OpenAIRE

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

    2016-01-01

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

  1. Proteomics approaches for the studies of bone metabolism

    OpenAIRE

    Lee, Ji-Hyun; Cho, Je-Yoel

    2014-01-01

    Bone is an active tissue, in which bone formation by osteoblast is followed by bone resorption by osteoclasts, in a repeating cycle. Proteomics approaches may allow the detection of changes in cell signal transduction, and the regulatory mechanism of cell differentiation. LC-MS/MS-based quantitative methods can be used with labeling strategies, such as SILAC, iTRAQ, TMT and enzymatic labeling. When used in combination with specific protein enrichment strategies, quantitative proteomics method...

  2. Cell wall proteins: a new insight through proteomics

    OpenAIRE

    Jamet, Elisabeth; Canut, Hervé; Boudart, Georges; Pont-Lezica, Rafael F

    2006-01-01

    Cell wall proteins are essential constituents of plant cell walls; they are involved in modifications of cell wall components, wall structure, signaling and interactions with plasma membrane proteins at the cell surface. The application of proteomic approaches to the cell wall compartment raises important questions: are there technical problems specific to cell wall proteomics? What kinds of proteins can be found in Arabidopsis walls? Are some of them unexpected? What sort of post-translation...

  3. Web Resources for Mass Spectrometry-based Proteomics

    OpenAIRE

    Tao CHEN; Zhao, Jie; Ma, Jie; Zhu, Yunping

    2015-01-01

    With the development of high-resolution and high-throughput mass spectrometry (MS) technology, a large quantum of proteomic data is continually being generated. Collecting and sharing these data are a challenge that requires immense and sustained human effort. In this report, we provide a classification of important web resources for MS-based proteomics and present rating of these web resources, based on whether raw data are stored, whether data submission is supported, and whether data analy...

  4. Innovative mass spectrometry-based analytical strategies in proteomics

    OpenAIRE

    Milioli, Marco

    2015-01-01

    This PhD thesis was divided in four main sections. In particular, the first section is composed by fourth chapters showing the main components of a mass spectrometer such as sources, analyzers and detectors followed by a brief introduction of mass spectrometry-based proteomics. In the second chapter, the proteomics analysis of platelet-derived microparticles under different agonist stimulations has been described. In the third chapter, the PTMs analysis of platelet-derived microparticles has ...

  5. Preliminary separation and qualitative analysis of carotenoids in Arthrobacter sp.%一株节杆菌发酵产物中类胡萝卜素的分离及组分分析的初探

    Institute of Scientific and Technical Information of China (English)

    翟玉贵; 张伟国; 钱和

    2014-01-01

    [目的]对实验室保存的一株红色球菌进行菌株鉴定,并对色素提取液的组分进行定性分析.[方法]采取形态学观察、16S rDNA序列同源性分析和生理生化分析相结合的方法确定菌株的分类地位.使用乙醇-丙酮混合液提取胞内色素,采用硅胶G薄板层析法对色素提取液进行初步分离纯化,并结合其光谱吸收特性、质谱结果进行定性分析.[结果]实验结果表明此菌株属于节杆菌属(Arthrobacter sp.).薄板层析结果显示该菌株内主要有4种色素组分,且靠近溶剂前沿组分为黄色,其它组分皆为橘红色.吸收光谱特性、质谱结果显示黄色组分可能为β-胡萝卜素,橘红色组分可能为螺菌黄质系类胡萝卜素.[结论]此株节杆菌以较为廉价的糖蜜和玉米浆作为营养物质用于满足自身生长需要,并且积累胞内类胡萝卜素,因此该菌的进一步研究有一定的价值.

  6. Quantitative interaction proteomics of neurodegenerative disease proteins.

    Science.gov (United States)

    Hosp, Fabian; Vossfeldt, Hannes; Heinig, Matthias; Vasiljevic, Djordje; Arumughan, Anup; Wyler, Emanuel; Landthaler, Markus; Hubner, Norbert; Wanker, Erich E; Lannfelt, Lars; Ingelsson, Martin; Lalowski, Maciej; Voigt, Aaron; Selbach, Matthias

    2015-05-19

    Several proteins have been linked to neurodegenerative disorders (NDDs), but their molecular function is not completely understood. Here, we used quantitative interaction proteomics to identify binding partners of Amyloid beta precursor protein (APP) and Presenilin-1 (PSEN1) for Alzheimer's disease (AD), Huntingtin (HTT) for Huntington's disease, Parkin (PARK2) for Parkinson's disease, and Ataxin-1 (ATXN1) for spinocerebellar ataxia type 1. Our network reveals common signatures of protein degradation and misfolding and recapitulates known biology. Toxicity modifier screens and comparison to genome-wide association studies show that interaction partners are significantly linked to disease phenotypes in vivo. Direct comparison of wild-type proteins and disease-associated variants identified binders involved in pathogenesis, highlighting the value of differential interactome mapping. Finally, we show that the mitochondrial protein LRPPRC interacts preferentially with an early-onset AD variant of APP. This interaction appears to induce mitochondrial dysfunction, which is an early phenotype of AD. PMID:25959826

  7. Data extraction from proteomics raw data

    DEFF Research Database (Denmark)

    Mancuso, Francesco; Bunkenborg, Jakob; Wierer, Michael;

    2012-01-01

    In shot-gun proteomics raw tandem MS data are processed with extraction tools to produce condensed peak lists that can be uploaded to database search engines. Many extraction tools are available but to our knowledge, a systematic comparison of such tools has not yet been carried out. Using raw data...... and agreement in-between tools. Processing a primary data set with 9 different tandem MS extraction tools resulted in a low overlap of identified peptides. The tools differ by assigned charge states of precursors, precursor and fragment ion masses, and we show that peptides identified very confidently using one...... extraction tool might not be matched when using another tool. We also found a bias towards peptides of lower charge state when extracting fragment ion data from higher resolution raw data without deconvolution. Collecting and comparing the extracted data from the same raw data allow adjusting parameters...

  8. Application of proteomics to translational research

    International Nuclear Information System (INIS)

    Deriving public benefit from basic biomedical research requires a dedicated and highly coordinated effort between basic scientists, physicians, bioinformaticians, clinical trial coordinators, MD and PhD trainees and fellows, and a host of other skilled participants. The Istituto Superiore di Sanita/George Mason University US-Italy Oncoproteomics program, established in 2005, is a successful example of a synergistic creative collaboration between basic scientists and clinical investigators conducting translational research. This program focuses on the application of the new field of proteomics to three urgent and fundamental clinical needs in cancer medicine: 1.) Biomarkers for early diagnosis of cancer, when it is still treatable, 2.) Individualizing patient therapy for molecular targeted inhibitors that block signal pathways driving cancer pathogenesis and 3.) Cancer Progenitor Cells (CSCs): When do the lethal progenitors of cancer first emerge, and how can we treat these CSCs with molecular targeted inhibitors

  9. Proteome analysis of the hypercholestrolemic rat, RICO

    International Nuclear Information System (INIS)

    In an attempt to develop novel markers for hypercholesterolemia, hepatic tissues and serum prepared from hypeicholesterolemic rat (i e RICO) were analyzed by two-dimensional electrophoresis (2DE) and matrix-assisted laser desorption ionization mass spectrometry (MALDI-ToF). Results were compared to those of paired inbreed rat (WKY). Comparative analysis of the respective spot patterns in 2DE revealed that the numbers of differential expression proteins were identified in serum and liver tissues of RICO. Some of the representative proteins annotated in 2DE were apolipoprotein family and numerous lipid metabolism related proteins. Especially, we found that protein disulfide isomerase subunits (ER-60) in 2DE have differential post-translational modification pattern by MALDI-ToF analysis. Our results suggest that the proteomic analysis of these proteins might be a novel approach to identify the molecular events in detail during lipid disorder such atherosclerosis

  10. Proteomic profiling of exosomes: Current perspectives

    DEFF Research Database (Denmark)

    Simpson, Richard J; Jensen, Søren S; Lim, Justin W E

    2008-01-01

    Exosomes are 40-100 nm membrane vesicles of endocytic origin secreted by most cell types in vitro. Recent studies have shown that exosomes are also found in vivo in body fluids such as blood, urine, amniotic fluid, malignant ascites, bronchoalveolar lavage fluid, synovial fluid, and breast milk....... While the biological function of exosomes is still unclear, they can mediate communication between cells, facilitating processes such as antigen presentation and in trans signaling to neighboring cells. Exosome-like vesicles identified in Drosophila (referred to as argosomes) may be potential vehicles...... for the spread of morphogens in epithelia. The advent of current MS-based proteomic technologies has contributed significantly to our understanding of the molecular composition of exosomes. In addition to a common set of membrane and cytosolic proteins, it is becoming increasingly apparent that exosomes harbor...

  11. Tissue proteomics of the human mammary gland

    DEFF Research Database (Denmark)

    Moreira, José Manuel Alfonso; Cabezón, Teresa; Gromova, Irina;

    2010-01-01

    phenotypes of the different cell subpopulations present in normal human mammary tissue, partly due to the formidable heterogeneity of mammary tissue, but also due to limitations of the current proteomic technologies. Work in our laboratories has attempted to address in a systematic fashion some of these...... biomarker discovery program. We review and present new data on the putative cell-progenitor marker cytokeratin 15 (CK15), and describe a novel marker, dihydropyriminidase-related protein 3 (DRP3) that in combination with CK15 and other well known proteins were used to define molecular phenotypes of normal...... human breast epithelial cells and their progenitors in resting acini, lactating alveoli, and large collecting ducts of the nipple. Preliminary results are also presented concerning DRP3 positive usual ductal hyperplasias (UDHs) and on single cell layer columnar cells (CCCs). At least two bona fide...

  12. Infectious Disease Proteome Biomarkers: Final Technical Report

    Energy Technology Data Exchange (ETDEWEB)

    Bailey, Charles L.

    2011-12-31

    Research for the DOE Infectious Disease Proteome Biomarkers focused on Rift Valley fever virus (RVFV) and Venezuelan Equine Encephalitis Virus (VEEV). RVFV and VEEV are Category A and B pathogens respectively. Among the priority threats, RVFV and VEEV rank high in their potential for being weaponized and introduced to the United States, spreading quickly, and having a large health and economic impact. In addition, they both have live attenuated vaccine, which allows work to be performed at BSL-2. While the molecular biology of RVFV and VEEV are increasingly well-characterized, little is known about its host-pathogen interactions. Our research is aimed at determining critical alterations in host signaling pathways to identify therapeutics targeted against the host.

  13. Proteomics perspectives in rotator cuff research

    DEFF Research Database (Denmark)

    Sejersen, Maria Hee Jung; Frost, Poul; Hansen, Torben Bæk;

    2015-01-01

    Background Rotator cuff tendinopathy including tears is a cause of significant morbidity. The molecular pathogenesis of the disorder is largely unknown. This review aimed to present an overview of the literature on gene expression and protein composition in human rotator cuff tendinopathy and other...... studies on objectively quantified differential gene expression and/or protein composition in human rotator cuff tendinopathy and other tendinopathies as compared to control tissue. Results We identified 2199 studies, of which 54 were included; 25 studies focussed on rotator cuff or biceps tendinopathy......, which only allowed simultaneous quantification of a limited number of prespecified mRNA molecules or proteins, several proteins appeared to be differentially expressed/represented in rotator cuff tendinopathy and other tendinopathies. No proteomics studies fulfilled our inclusion criteria, although...

  14. Barley seed proteomics from spots to structures

    DEFF Research Database (Denmark)

    Finnie, Christine; Svensson, Birte

    2009-01-01

    information from rice and other cereals facilitate identification of barley proteins. Several hundred barley seed proteins are identified and lower abundance proteins including membrane proteins are now being analysed. In the present review we focus on variation in protein profiles of seed tissues during......Barley is a major cereal crop grown mainly for feed and malting. Two-dimensional gel electrophoresis has been used to analyse barley proteins for over 20 years and more recently, mass spectrometry was applied. In the absence of a genome sequence, barley gene and EST sequences combined with...... grain filling, maturation, germination and radicle elongation. Cultivar comparisons and genetic mapping of polymorphic protein spots in doubled haploid populations provide a means to link the genome to the proteome and identify proteins that can influence grain quality. Many proteins appear in multiple...

  15. Milk bottom-up proteomics: method optimisation.

    Directory of Open Access Journals (Sweden)

    Delphine eVincent

    2016-01-01

    Full Text Available Milk is a complex fluid whose proteome displays a diverse set of proteins of high abundance such as caseins and medium to low abundance whey proteins such as ß-lactoglobulin, lactoferrin, immunoglobulins, glycoproteins, peptide hormones and enzymes. A sample preparation method that enables high reproducibility and throughput is key in reliably identifying proteins present or proteins responding to conditions such as a diet, health or genetics. Using skim milk samples from Jersey and Holstein-Friesian cows, we compared three extraction procedures which have not previously been applied to samples of cows’ milk. Method A (urea involved a simple dilution of the milk in a urea-based buffer, method B (TCA/acetone involved a trichloroacetic acid (TCA/acetone precipitation and method C (methanol/chloroform involved a tri-phasic partition method in chloroform/methanol solution. Protein assays, SDS-PAGE profiling, and trypsin digestion followed by nanoHPLC-electrospray ionisation-tandem mass spectrometry (nLC-ESI-MS/MS analyses were performed to assess their efficiency. Replicates were used at each analytical step (extraction, digestion, injection to assess reproducibility. Mass spectrometry (MS data are available via ProteomeXchange with identifier PXD002529. Overall 186 unique accessions, major and minor proteins, were identified with a combination of methods. Method C (methanol/chloroform yielded the best resolved SDS-patterns and highest protein recovery rates, method A (urea yielded the greatest number of accessions, and, of the three procedures, method B (TCA/acetone was the least compatible of all with a wide range of downstream analytical procedures. Our results also highlighted breed differences between the proteins in milk of Jersey and Holstein-Friesian cows.

  16. Origin and evolution of the peroxisomal proteome

    Directory of Open Access Journals (Sweden)

    Tabak Henk

    2006-03-01

    Full Text Available Abstract Background Peroxisomes are ubiquitous eukaryotic organelles involved in various oxidative reactions. Their enzymatic content varies between species, but the presence of common protein import and organelle biogenesis systems support a single evolutionary origin. The precise scenario for this origin remains however to be established. The ability of peroxisomes to divide and import proteins post-translationally, just like mitochondria and chloroplasts, supports an endosymbiotic origin. However, this view has been challenged by recent discoveries that mutant, peroxisome-less cells restore peroxisomes upon introduction of the wild-type gene, and that peroxisomes are formed from the Endoplasmic Reticulum. The lack of a peroxisomal genome precludes the use of classical analyses, as those performed with mitochondria or chloroplasts, to settle the debate. We therefore conducted large-scale phylogenetic analyses of the yeast and rat peroxisomal proteomes. Results Our results show that most peroxisomal proteins (39–58% are of eukaryotic origin, comprising all proteins involved in organelle biogenesis or maintenance. A significant fraction (13–18%, consisting mainly of enzymes, has an alpha-proteobacterial origin and appears to be the result of the recruitment of proteins originally targeted to mitochondria. Consistent with the findings that peroxisomes are formed in the Endoplasmic Reticulum, we find that the most universally conserved Peroxisome biogenesis and maintenance proteins are homologous to proteins from the Endoplasmic Reticulum Assisted Decay pathway. Conclusion Altogether our results indicate that the peroxisome does not have an endosymbiotic origin and that its proteins were recruited from pools existing within the primitive eukaryote. Moreover the reconstruction of primitive peroxisomal proteomes suggests that ontogenetically as well as phylogenetically, peroxisomes stem from the Endoplasmic Reticulum. Reviewers This article was

  17. Proteomic Characterization of Yersinia pestis Virulence

    Energy Technology Data Exchange (ETDEWEB)

    Chromy, B; Murphy, G; Gonzales, A; Fitch, J P; McCutchen-Maloney, S L

    2005-01-05

    Yersinia pestis, the etiological agent of plague, functions via the Type III secretion mechanism whereby virulence factors are induced upon interactions with a mammalian host. Here, the Y. pestis proteome was studied by two-dimensional differential gel electrophoresis (2-D DIGE) under physiologically relevant growth conditions mimicking the calcium concentrations and temperatures that the pathogen would encounter in the flea vector and upon interaction with the mammalian host. Over 4100 individual protein spots were detected of which hundreds were differentially expressed in the entire comparative experiment. A total of 43 proteins that were differentially expressed between the vector and host growth conditions were identified by mass spectrometry. Expected differences in expression were observed for several known virulence factors including catalase-peroxidase (KatY), murine toxin (Ymt), plasminogen activator (Pla), and F1 capsule antigen (Caf1), as well as putative virulence factors. Chaperone proteins and signaling molecules hypothesized to be involved in virulence due to their role in Type III secretion were also identified. Other differentially expressed proteins not previously reported to contribute to virulence are candidates for more detailed mechanistic studies, representing potential new virulence determinants. For example, several sugar metabolism proteins were differentially regulated in response to lower calcium and higher temperature, suggesting these proteins, while not directly connected to virulence, either represent a metabolic switch for survival in the host environment or may facilitate production of virulence factors. Results presented here contribute to a more thorough understanding of the virulence mechanism of Y. pestis through proteomic characterization of the pathogen under induced virulence.

  18. Two-dimensional gel electrophoresis in platelet proteomics research.

    Science.gov (United States)

    García, Angel

    2007-01-01

    Proteomics technology allows a comprehensive and efficient analysis of the proteome and has become an indispensable tool in biomedical research. Since the late 80s, advances on mass spectrometry (MS) instrumentation and techniques have revolutionized the way proteins can be analyzed. Such analysis would only be possible with a proper sample preparation and separation ahead of the MS step. Different gel and nongel-based methods are available for protein separation. This chapter will focus on the use of two-dimensional gel electrophoresis (2-DE) in proteomics and its application to platelet research. 2-DE separates proteins according to their isoelectric point (pI) and size (molecular weight) and allows the detection of thousands of proteins at a time. Platelets are enucleated cells that play a critical function in the control of bleeding and wound healing. As platelets do not have a nucleus, proteomics offers a powerful alternative approach to provide data on protein expression in these cells, helping to address their biology. This chapter presents a protocol for an efficient sample preparation, protein separation by 2-DE, and protein digestion ahead of the MS analysis. The experimental approach, already successfully applied to the study of the platelet proteome, includes recommendations for an efficient platelet preparation for proteomics studies. PMID:18287684

  19. Severe childhood malaria syndromes defined by plasma proteome profiles.

    Directory of Open Access Journals (Sweden)

    Florence Burté

    Full Text Available BACKGROUND: Cerebral malaria (CM and severe malarial anemia (SMA are the most serious life-threatening clinical syndromes of Plasmodium falciparum infection in childhood. Therefore it is important to understand the pathology underlying the development of CM and SMA, as opposed to uncomplicated malaria (UM. Different host responses to infection are likely to be reflected in plasma proteome-patterns that associate with clinical status and therefore provide indicators of the pathogenesis of these syndromes. METHODS AND FINDINGS: Plasma and comprehensive clinical data for discovery and validation cohorts were obtained as part of a prospective case-control study of severe childhood malaria at the main tertiary hospital of the city of Ibadan, an urban and densely populated holoendemic malaria area in Nigeria. A total of 946 children participated in this study. Plasma was subjected to high-throughput proteomic profiling. Statistical pattern-recognition methods were used to find proteome-patterns that defined disease groups. Plasma proteome-patterns accurately distinguished children with CM and with SMA from those with UM, and from healthy or severely ill malaria-negative children. CONCLUSIONS: We report that an accurate definition of the major childhood malaria syndromes can be achieved using plasma proteome-patterns. Our proteomic data can be exploited to understand the pathogenesis of the different childhood severe malaria syndromes.

  20. Significance of Urinary Proteome Pattern in Renal Allograft Recipients

    Science.gov (United States)

    Suhail, Sufi M.

    2014-01-01

    Urinary proteomics is developing as a platform of urinary biomarkers of immense potential in recent years. The definition of urinary proteome in the context of renal allograft and characterization of different proteome patterns in various graft dysfunctions have led to the development of a distinct science of this noninvasive tool. Substantial numbers of studies have shown that different renal allograft disease states, both acute and chronic, could portray unique urinary proteome pattern enabling early diagnosis of graft dysfunction and proper manipulation of immunosuppressive strategy that could impact graft prognosis. The methodology of the urinary proteome is nonetheless not more complex than that of other sophisticated assays of conventional urinary protein analysis. Moreover, the need for a centralized database is also felt by the researchers as more and more studies have been presenting their results from different corners and as systems of organizing these newly emerging data being developed at international and national levels. In this context concept of urinary proteomics in renal allograft recipients would be of significant importance in clinical transplantation. PMID:24757556

  1. CAPER: a chromosome-assembled human proteome browsER.

    Science.gov (United States)

    Guo, Feifei; Wang, Dan; Liu, Zhongyang; Lu, Liang; Zhang, Wei; Sun, Haiyan; Zhang, Hongxing; Ma, Jie; Wu, Songfeng; Li, Ning; Jiang, Ying; Zhu, Weimin; Qin, Jun; Xu, Ping; Li, Dong; He, Fuchu

    2013-01-01

    High-throughput mass spectrometry and antibody-based experiments have begun to produce a large amount of proteomic data sets. Chromosome-based visualization of these data sets and their annotations can help effectively integrate, organize, and analyze them. Therefore, we developed a web-based, user-friendly Chromosome-Assembled human Proteome browsER (CAPER). To display proteomic data sets and related annotations comprehensively, CAPER employs two distinct visualization strategies: track-view for the sequence/site information and the correspondence between proteome, transcriptome, genome, and chromosome and heatmap-view for the qualitative and quantitative functional annotations. CAPER supports data browsing at multiple scales through Google Map-like smooth navigation, zooming, and positioning with chromosomes as the reference coordinate. Both track-view and heatmap-view can mutually switch, providing a high-quality user interface. Taken together, CAPER will greatly facilitate the complete annotation and functional interpretation of the human genome by proteomic approaches, thereby making a significant contribution to the Chromosome-Centric Human Proteome Project and even the human physiology/pathology research. CAPER can be accessed at http://www.bprc.ac.cn/CAPE . PMID:23256906

  2. Drafting the proteome landscape of myeloid-derived suppressor cells.

    Science.gov (United States)

    Gato, María; Blanco-Luquin, Idoia; Zudaire, Maribel; de Morentin, Xabier Martínez; Perez-Valderrama, Estela; Zabaleta, Aintzane; Kochan, Grazyna; Escors, David; Fernandez-Irigoyen, Joaquín; Santamaría, Enrique

    2016-01-01

    Myeloid-derived suppressor cells (MDSCs) are a heterogeneous population of cells that are defined by their myeloid origin, immature state, and ability to potently suppress T-cell responses. They regulate immune responses and the population significantly increases in the tumor microenvironment of patients with glioma and other malignant tumors. For their study, MDSCs are usually isolated from the spleen or directly of tumors from a large number of tumor-bearing mice although promising ex vivo differentiated MDSC production systems have been recently developed. During the last years, proteomics has emerged as a powerful approach to analyze MDSCs proteomes using shotgun-based mass spectrometry (MS), providing functional information about cellular homeostasis and metabolic state at a global level. Here, we will revise recent proteome profiling studies performed in MDSCs from different origins. Moreover, we will perform an integrative functional analysis of the protein compilation derived from these large-scale proteomic studies in order to obtain a comprehensive view of MDSCs biology. Finally, we will also discuss the potential application of high-throughput proteomic approaches to study global proteome dynamics and post-translational modifications (PTMs) during the differentiation process of MDSCs that will greatly boost the identification of novel MDSC-specific therapeutic targets to apply in cancer immunotherapy. PMID:26403437

  3. Significance of Urinary Proteome Pattern in Renal Allograft Recipients

    Directory of Open Access Journals (Sweden)

    Sufi M. Suhail

    2014-01-01

    Full Text Available Urinary proteomics is developing as a platform of urinary biomarkers of immense potential in recent years. The definition of urinary proteome in the context of renal allograft and characterization of different proteome patterns in various graft dysfunctions have led to the development of a distinct science of this noninvasive tool. Substantial numbers of studies have shown that different renal allograft disease states, both acute and chronic, could portray unique urinary proteome pattern enabling early diagnosis of graft dysfunction and proper manipulation of immunosuppressive strategy that could impact graft prognosis. The methodology of the urinary proteome is nonetheless not more complex than that of other sophisticated assays of conventional urinary protein analysis. Moreover, the need for a centralized database is also felt by the researchers as more and more studies have been presenting their results from different corners and as systems of organizing these newly emerging data being developed at international and national levels. In this context concept of urinary proteomics in renal allograft recipients would be of significant importance in clinical transplantation.

  4. Mass spectrometry-based proteomics: existing capabilities and future directions

    Energy Technology Data Exchange (ETDEWEB)

    Angel, Thomas E.; Aryal, Uma K.; Hengel, Shawna M.; Baker, Erin Shammel; Kelly, Ryan T.; Robinson, Errol W.; Smith, Richard D.

    2012-05-21

    Mass spectrometry-based proteomics provides a means for identification, characterization, and quantification of biomolecules that are integral components of the processes essential for life. Characterization of proteins present in a biological system at the proteome and sub-proteomes (e.g., the phosphoproteome, proteoglycome, or degradome/peptidome) levels provides a foundation for understanding fundamental aspects as well as potentially a range of translational applications. Emerging technologies such as ion mobility separations coupled with mass spectrometry and microchip-based - proteome measurements combined with continued enhancement of MS instrumentation and separation techniques, such as reversed phase liquid chromatography and potentially capillary electrophoresis, show great promise for both broad undirected as well as targeted measurements and will be critical for e.g., the proteome-wide characterization of post translational modifications and identification, or the verification, and validation of potential biomarkers of disease. MS-based proteomics is also increasingly demonstrating great potential for contributing to our understanding of the dynamics, reactions, and roles proteins and peptides play advancing our understanding of biology on a system wide level for a wide range of applications, from investigations of microbial communities, bioremediation, and human health and disease states alike.

  5. Biomarkers of HIV-1 associated dementia: proteomic investigation of sera

    Directory of Open Access Journals (Sweden)

    Duan Fenghai

    2009-03-01

    Full Text Available Abstract Background New, more sensitive and specific biomarkers are needed to support other means of clinical diagnosis of neurodegenerative disorders. Proteomics technology is widely used in discovering new biomarkers. There are several difficulties with in-depth analysis of human plasma/serum, including that there is no one proteomic platform that can offer complete identification of differences in proteomic profiles. Another set of problems is associated with heterogeneity of human samples in addition intrinsic variability associated with every step of proteomic investigation. Validation is the very last step of proteomic investigation and it is very often difficult to validate potential biomarker with desired sensitivity and specificity. Even though it may be possible to validate a differentially expressed protein, it may not necessarily prove to be a valid diagnostic biomarker. Results In the current study we report results of proteomic analysis of sera from HIV-infected individuals with or without cognitive impairment. Application of SELDI-TOF analysis followed by weak cation exchange chromatography and 1-dimensional electrophoresis led to discovery of gelsolin and prealbumin as differentially expressed proteins which were not detected in this cohort of samples when previously investigated by 2-dimensional electrophoresis with Difference Gel Electrophoresis technology. Conclusion Validation using western-blot analysis led us to conclude that relative change of the levels of these proteins in one patient during a timeframe might be more informative, sensitive and specific than application of average level estimated based on an even larger cohort of patients.

  6. Progress in Establishing Common Standards for Exchanging Proteomics Data: The Second Meeting of the HUPO Proteomics Standards Initiative

    Directory of Open Access Journals (Sweden)

    Rolf Apweiler

    2006-04-01

    Full Text Available The Proteomics Standards Initiative (PSI aims to define community standards for data representation in proteomics and to facilitate data comparison, exchange and verification. Rapid progress has been made in the development of common standards for data exchange in the fields of both mass spectrometry and protein–protein interactions since the first PSI meeting [1]. Both hardware and software manufacturers have agreed to work to ensure that a proteomics-specific extension is created for the emerging ASTM mass spectrometry standard and the data model for a proteomics experiment has advanced significantly. The Protein–Protein Interactions (PPI group expects to publish the Level 1 PSI data exchange format for protein–protein interactions by early summer this year, and discussion as to the additional content of Level 2 has been initiated.

  7. CPTAC Contributes to Healthdata.gov - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    Recently, proteomic data generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) funded by National Cancer Institute (NCI) was highlighted to the wider research community at Healthdata.gov. Healthdata.gov aims to make health data more acces

  8. Quantitative Phospho-proteomics to Investigate the Polo-like Kinase 1-Dependent Phospho-proteome*

    OpenAIRE

    Grosstessner-Hain, Karin; Hegemann, Björn; Novatchkova, Maria; Rameseder, Jonathan; Joughin, Brian A.; Hudecz, Otto; Roitinger, Elisabeth; Pichler, Peter; Kraut, Norbert; Yaffe, Michael B.; Peters, Jan-Michael; Mechtler, Karl

    2011-01-01

    Polo-like kinase 1 (PLK1) is a key regulator of mitotic progression and cell division, and small molecule inhibitors of PLK1 are undergoing clinical trials to evaluate their utility in cancer therapy. Despite this importance, current knowledge about the identity of PLK1 substrates is limited. Here we present the results of a proteome-wide analysis of PLK1-regulated phosphorylation sites in mitotic human cells. We compared phosphorylation sites in HeLa cells that were or were not treated with ...

  9. The APEX Quantitative Proteomics Tool: Generating protein quantitation estimates from LC-MS/MS proteomics results

    Directory of Open Access Journals (Sweden)

    Saeed Alexander I

    2008-12-01

    Full Text Available Abstract Background Mass spectrometry (MS based label-free protein quantitation has mainly focused on analysis of ion peak heights and peptide spectral counts. Most analyses of tandem mass spectrometry (MS/MS data begin with an enzymatic digestion of a complex protein mixture to generate smaller peptides that can be separated and identified by an MS/MS instrument. Peptide spectral counting techniques attempt to quantify protein abundance by counting the number of detected tryptic peptides and their corresponding MS spectra. However, spectral counting is confounded by the fact that peptide physicochemical properties severely affect MS detection resulting in each peptide having a different detection probability. Lu et al. (2007 described a modified spectral counting technique, Absolute Protein Expression (APEX, which improves on basic spectral counting methods by including a correction factor for each protein (called Oi value that accounts for variable peptide detection by MS techniques. The technique uses machine learning classification to derive peptide detection probabilities that are used to predict the number of tryptic peptides expected to be detected for one molecule of a particular protein (Oi. This predicted spectral count is compared to the protein's observed MS total spectral count during APEX computation of protein abundances. Results The APEX Quantitative Proteomics Tool, introduced here, is a free open source Java application that supports the APEX protein quantitation technique. The APEX tool uses data from standard tandem mass spectrometry proteomics experiments and provides computational support for APEX protein abundance quantitation through a set of graphical user interfaces that partition thparameter controls for the various processing tasks. The tool also provides a Z-score analysis for identification of significant differential protein expression, a utility to assess APEX classifier performance via cross validation, and a

  10. PatternLab for proteomics: a tool for differential shotgun proteomics

    Directory of Open Access Journals (Sweden)

    Yates John R

    2008-07-01

    Full Text Available Abstract Background A goal of proteomics is to distinguish between states of a biological system by identifying protein expression differences. Liu et al. demonstrated a method to perform semi-relative protein quantitation in shotgun proteomics data by correlating the number of tandem mass spectra obtained for each protein, or "spectral count", with its abundance in a mixture; however, two issues have remained open: how to normalize spectral counting data and how to efficiently pinpoint differences between profiles. Moreover, Chen et al. recently showed how to increase the number of identified proteins in shotgun proteomics by analyzing samples with different MS-compatible detergents while performing proteolytic digestion. The latter introduced new challenges as seen from the data analysis perspective, since replicate readings are not acquired. Results To address the open issues above, we present a program termed PatternLab for proteomics. This program implements existing strategies and adds two new methods to pinpoint differences in protein profiles. The first method, ACFold, addresses experiments with less than three replicates from each state or having assays acquired by different protocols as described by Chen et al. ACFold uses a combined criterion based on expression fold changes, the AC test, and the false-discovery rate, and can supply a "bird's-eye view" of differentially expressed proteins. The other method addresses experimental designs having multiple readings from each state and is referred to as nSVM (natural support vector machine because of its roots in evolutionary computing and in statistical learning theory. Our observations suggest that nSVM's niche comprises projects that select a minimum set of proteins for classification purposes; for example, the development of an early detection kit for a given pathology. We demonstrate the effectiveness of each method on experimental data and confront them with existing strategies

  11. Origin and evolution of the mitochondrial proteome.

    Science.gov (United States)

    Kurland, C G; Andersson, S G

    2000-12-01

    The endosymbiotic theory for the origin of mitochondria requires substantial modification. The three identifiable ancestral sources to the proteome of mitochondria are proteins descended from the ancestral alpha-proteobacteria symbiont, proteins with no homology to bacterial orthologs, and diverse proteins with bacterial affinities not derived from alpha-proteobacteria. Random mutations in the form of deletions large and small seem to have eliminated nonessential genes from the endosymbiont-mitochondrial genome lineages. This process, together with the transfer of genes from the endosymbiont-mitochondrial genome to nuclei, has led to a marked reduction in the size of mitochondrial genomes. All proteins of bacterial descent that are encoded by nuclear genes were probably transferred by the same mechanism, involving the disintegration of mitochondria or bacteria by the intracellular membranous vacuoles of cells to release nucleic acid fragments that transform the nuclear genome. This ongoing process has intermittently introduced bacterial genes to nuclear genomes. The genomes of the last common ancestor of all organisms, in particular of mitochondria, encoded cytochrome oxidase homologues. There are no phylogenetic indications either in the mitochondrial proteome or in the nuclear genomes that the initial or subsequent function of the ancestor to the mitochondria was anaerobic. In contrast, there are indications that relatively advanced eukaryotes adapted to anaerobiosis by dismantling their mitochondria and refitting them as hydrogenosomes. Accordingly, a continuous history of aerobic respiration seems to have been the fate of most mitochondrial lineages. The initial phases of this history may have involved aerobic respiration by the symbiont functioning as a scavenger of toxic oxygen. The transition to mitochondria capable of active ATP export to the host cell seems to have required recruitment of eukaryotic ATP transport proteins from the nucleus. The identity of

  12. Environmental Proteomics: a Paradigm Shift in Characterizing Microbial Activities at the Molecular Level

    OpenAIRE

    Keller, Martin; Hettich, Robert

    2009-01-01

    Summary: The increase in sequencing capacity led to a new wave of metagenomic projects, enabling and setting the prerequisite for the application of environmental proteomics technologies. This review describes the current status of environmental proteomics. It describes sample preparation as well as the two major technologies applied within this field: two-dimensional electrophoresis-based environmental proteomics and liquid chromatography-mass spectrometry-based environmental proteomics. It ...

  13. Significance analysis of microarray for relative quantitation of LC/MS data in proteomics

    OpenAIRE

    Li Qingbo; Roxas Bryan AP

    2008-01-01

    Abstract Background Although fold change is a commonly used criterion in quantitative proteomics for differentiating regulated proteins, it does not provide an estimation of false positive and false negative rates that is often desirable in a large-scale quantitative proteomic analysis. We explore the possibility of applying the Significance Analysis of Microarray (SAM) method (PNAS 98:5116-5121) to a differential proteomics problem of two samples with replicates. The quantitative proteomic a...

  14. The Gel Electrophoresis Markup Language (GelML) from the Proteomics Standards Initiative

    OpenAIRE

    Gibson, Frank; Hoogland, Christine; Martinez-Bartolomé, Salvador; Medina-Aunon, J. Alberto; Albar, Juan Pablo; Babnigg, Gyorgy; Wipat, Anil; Hermjakob, Henning; Almeida, Jonas S; Stanislaus, Romesh; Paton, Norman W.; Jones, Andrew R.

    2010-01-01

    The Human Proteome Organisation’s Proteomics Standards Initiative (HUPO-PSI) has developed the GelML data exchange format for representing gel electrophoresis experiments performed in proteomics investigations. The format closely follows the reporting guidelines for gel electrophoresis, which are part of the Minimum Information About a Proteomics Experiment (MIAPE) set of modules. GelML supports the capture of metadata (such as experimental protocols) and data (such as gel images) resulting f...

  15. Urinary proteomics as a novel tool for biomarker discovery in kidney diseases*

    OpenAIRE

    Wu, Jing; Chen, Yi-ding; Gu, Wei

    2010-01-01

    Urine has become one of the most attractive biofluids in clinical proteomics, for its procurement is easy and noninvasive and it contains sufficient proteins and peptides. Urinary proteomics has thus rapidly developed and has been extensively applied to biomarker discovery in clinical diseases, especially kidney diseases. In this review, we discuss two important aspects of urinary proteomics in detail, namely, sample preparation and proteomic technologies. In addition, data mining in urinary ...

  16. In-depth Proteomics Characterization of Embryogenesis of the Honey Bee Worker (Apis mellifera ligustica) *

    OpenAIRE

    Fang, Yu; Feng, Mao; Han, Bin; Lu, Xiaoshan; Ramadan, Haitham; Li, Jianke

    2014-01-01

    Identifying proteome changes of honey bee embryogenesis is of prime importance for unraveling the molecular mechanisms that they underlie. However, many proteomic changes during the embryonic period are not well characterized. We analyzed the proteomic alterations over the complete time course of honey bee worker embryogenesis at 24, 48, and 72 h of age, using mass spectrometry-based proteomics, label-free quantitation, and bioinformatics. Of the 1460 proteins identified the embryo of all thr...

  17. WallProtDB, a database resource for plant cell wall proteomics

    OpenAIRE

    San Clemente, Hélène; Jamet, Elisabeth

    2015-01-01

    Background During the last fifteen years, cell wall proteomics has become a major research field with the publication of more than 50 articles describing plant cell wall proteomes. The WallProtDB database has been designed as a tool to facilitate the inventory, the interpretation of cell wall proteomics data and the comparisons between cell wall proteomes. Results WallProtDB (http://www.polebio.lrsv.ups-tlse.fr/WallProtDB/) presently contains 2170 proteins and ESTs identified experimentally i...

  18. Regulation of developmental processes: insights from mass spectrometry-based proteomics

    OpenAIRE

    Veraksa, Alexey

    2012-01-01

    Mass spectrometry (MS)-based proteomics has become an indispensable tool for protein identification and quantification. In this review, common MS workflows are described, with an emphasis on applications of MS-based proteomics in developmental biology. Progress has been made in the analysis of proteome changes during tissue differentiation and in various genetic perturbations. MS-based proteomics has been particularly useful for identifying novel protein interactions by affinity purification-...

  19. Unraveling the pathogenesis of type 1 diabetes with proteomics: present and future directions

    DEFF Research Database (Denmark)

    Sparre, Thomas; Larsen, Martin Røssel; Heding, Peter E; Karlsen, Allan E; Jensen, Ole N; Pociot, Flemming Michael

    2005-01-01

    . Proteomics may be useful in describing the protein expression profile and thus the diabetic phenotype. Relatively few studies using proteomics technologies to investigate the T1D pathogenesis have been published to date despite the defined target organ, the beta-cell. Proteomics has been applied in studies...

  20. Identification of Hypoxia-Regulated Proteins Using MALDI-Mass Spectrometry Imaging Combined with Quantitative Proteomics

    DEFF Research Database (Denmark)

    Djidja, Marie-Claude; Chang, Joan; Hadjiprocopis, Andreas;

    2014-01-01

    quantitative proteomics combined with MALDI-mass spectrometry imaging (MALDI-MSI). Here we present a comprehensive hypoxic proteome study and are the first to investigate changes in situ using tumor samples. In vitro quantitative mass spectrometry analysis of the hypoxic proteome was performed on breast cancer...

  1. Current Status of Proteomic Studies on Defense Responses in Rice.

    Science.gov (United States)

    Chen, Xifeng; Bhadauria, Vijai; Ma, Bojun

    2016-01-01

    Biotic stresses are constraints to plant growth and development negatively impacting crop production. To counter such stresses, plants have developed stress-specific adaptations as well as simultaneous responses. The efficacy and magnitude of inducible adaptive responses are dependent on activation of signaling pathways and intracellular networks by modulating expression, or abundance, and/or post-translational modification of proteins associated with defense mechanisms. Proteomics plays an important role in elucidating plant defense mechanisms by mining the differential regulation of proteins to various biotic stresses. Rice, one of the most widely cultivated food crops in world, is constantly challenged by a variety of biotic stresses, and high-throughput proteomics approaches have been employed to unravel the molecular mechanism of the biotic stresses-response in rice. In this review, we summarize the latest advances of proteomic studies on defense responses and discuss the potential relevance of the proteins identified by proteomic means in rice defense mechanism. Furthermore, we provide perspective for proteomics in unraveling the molecular mechanism of rice immunity. PMID:26364119

  2. Artichoke and Cynar liqueur: two (not quite) entangled proteomes.

    Science.gov (United States)

    Saez, Vicente; Fasoli, Elisa; D'Amato, Alfonsina; Simó-Alfonso, Ernesto; Righetti, Pier Giorgio

    2013-01-01

    Combinatorial peptide ligand libraries (CPLLs) have been adopted to investigate the proteome of artichoke extracts, of a home-made alcoholic infusion and of the Italian Cynar liqueur. The aim of study was not only to perform the deepest investigation so far of the artichoke proteome but also to assess the genuineness of the commercial aperitif via a three-pronged attack. First, different extraction techniques have been used for the characterization of the artichoke's proteome, secondly a home-made infusion has been analyzed and finally the proteome of the commercial drink was checked. The artichoke proteome has been evaluated via prior capture with CPLLs at four different pH (2.2, 4.0, 7.2 and 9.3) values. Via mass spectrometry analysis of the recovered fractions, after elution of the captured populations in 4% boiling SDS, we could identify a total of 876 unique gene products in the artichoke extracts, 18 in the home-made infusion and no proteins at all in the Italian Cynar liqueur, casting severe doubts on the procedure stated by the manufacturer (that should be made by an infusion of artichoke leaves plus thirteen different herbs). This could be the starting point for investigating the genuineness and natural origin of commercial drinks in order to protect consumers from adulterated products. PMID:22968169

  3. Approaches for targeted proteomics and its potential applications in neuroscience

    Indian Academy of Sciences (India)

    Sumit Sethi; Dipti Chourasia; Ishwar S Parhar

    2015-09-01

    An extensive guide on practicable and significant quantitative proteomic approaches in neuroscience research is important not only because of the existing overwhelming limitations but also for gaining valuable understanding into brain function and deciphering proteomics from the workbench to the bedside. Early methodologies to understand the functioning of biological systems are now improving with high-throughput technologies, which allow analysis of various samples concurrently, or of thousand of analytes in a particular sample. Quantitative proteomic approaches include both gel-based and non-gel-based methods that can be further divided into different labelling approaches. This review will emphasize the role of existing technologies, their advantages and disadvantages, as well as their applications in neuroscience. This review will also discuss advanced approaches for targeted proteomics using isotope-coded affinity tag (ICAT) coupled with laser capture microdissection (LCM) followed by liquid chromatography tandem mass spectrometric (LC-MS/MS) analysis. This technology can further be extended to single cell proteomics in other areas of biological sciences and can be combined with other ‘omics’ approaches to reveal the mechanism of a cellular alterations. This approach may lead to further investigation in basic biology, disease analysis and surveillance, as well as drug discovery. Although numerous challenges still exist, we are confident that this approach will increase the understanding of pathological mechanisms involved in neuroendocrinology, neuropsychiatric and neurodegenerative disorders by delivering protein biomarker signatures for brain dysfunction.

  4. Standard guidelines for the chromosome-centric human proteome project.

    Science.gov (United States)

    Paik, Young-Ki; Omenn, Gilbert S; Uhlen, Mathias; Hanash, Samir; Marko-Varga, György; Aebersold, Ruedi; Bairoch, Amos; Yamamoto, Tadashi; Legrain, Pierre; Lee, Hyoung-Joo; Na, Keun; Jeong, Seul-Ki; He, Fuchu; Binz, Pierre-Alain; Nishimura, Toshihide; Keown, Paul; Baker, Mark S; Yoo, Jong Shin; Garin, Jerome; Archakov, Alexander; Bergeron, John; Salekdeh, Ghasem Hosseini; Hancock, William S

    2012-04-01

    The objective of the international Chromosome-Centric Human Proteome Project (C-HPP) is to map and annotate all proteins encoded by the genes on each human chromosome. The C-HPP consortium was established to organize a collaborative network among the research teams responsible for protein mapping of individual chromosomes and to identify compelling biological and genetic mechanisms influencing colocated genes and their protein products. The C-HPP aims to foster the development of proteome analysis and integration of the findings from related molecular -omics technology platforms through collaborations among universities, industries, and private research groups. The C-HPP consortium leadership has elicited broad input for standard guidelines to manage these international efforts more efficiently by mobilizing existing resources and collaborative networks. The C-HPP guidelines set out the collaborative consensus of the C-HPP teams, introduce topics associated with experimental approaches, data production, quality control, treatment, and transparency of data, governance of the consortium, and collaborative benefits. A companion approach for the Biology and Disease-Driven HPP (B/D-HPP) component of the Human Proteome Project is currently being organized, building upon the Human Proteome Organization's organ-based and biofluid-based initiatives (www.hupo.org/research). The common application of these guidelines in the participating laboratories is expected to facilitate the goal of a comprehensive analysis of the human proteome. PMID:22443261

  5. Ultra-Fast Sample Preparation for High-Throughput Proteomics

    Energy Technology Data Exchange (ETDEWEB)

    Lopez-Ferrer, Daniel; Hixson, Kim K.; Belov, Mikhail E.; Smith, Richard D.

    2011-06-21

    Sample preparation oftentimes can be the Achilles Heel of any analytical process and in the field of proteomics, preparing samples for mass spectrometric analysis is no exception. Current goals, concerning proteomic sample preparation on a large scale, include efforts toward improving reproducibility, reducing the time of processing and ultimately the automation of the entire workflow. This chapter reviews an array of recent approaches applied to bottom-up proteomics sample preparation to reduce the processing time down from hours to minutes. The current state-of-the-art in the field uses different energy inputs like microwave, ultrasound or pressure to perform the four basic steps in sample preparation: protein extraction, denaturation, reduction and alkylation, and digestion. No single energy input for enhancement of proteome sample preparation has become the universal gold standard. Instead, a combination of different energy inputs tend to produce the best results. This chapter further describes the future trends in the field such as the hyphenation of sample preparation with downstream detection and analysis systems. Finally, a detailed protocol describing the combined use of both pressure cycling technology and ultrasonic energy inputs to hasten proteomic sample preparation is presented.

  6. Sense and nonsense of pathway analysis software in proteomics.

    Science.gov (United States)

    Müller, Thorsten; Schrötter, Andreas; Loosse, Christina; Helling, Stefan; Stephan, Christian; Ahrens, Maike; Uszkoreit, Julian; Eisenacher, Martin; Meyer, Helmut E; Marcus, Katrin

    2011-12-01

    New developments in proteomics enable scientists to examine hundreds to thousands of proteins in parallel. Quantitative proteomics allows the comparison of different proteomes of cells, tissues, or body fluids with each other. Analyzing and especially organizing these data sets is often a Herculean task. Pathway Analysis software tools aim to take over this task based on present knowledge. Companies promise that their algorithms help to understand the significance of scientist's data, but the benefit remains questionable, and a fundamental systematic evaluation of the potential of such tools has not been performed until now. Here, we tested the commercial Ingenuity Pathway Analysis tool as well as the freely available software STRING using a well-defined study design in regard to the applicability and value of their results for proteome studies. It was our goal to cover a wide range of scientific issues by simulating different established pathways including mitochondrial apoptosis, tau phosphorylation, and Insulin-, App-, and Wnt-signaling. Next to a general assessment and comparison of the pathway analysis tools, we provide recommendations for users as well as for software developers to improve the added value of a pathway study implementation in proteomic pipelines. PMID:21978018

  7. Skeletal muscle proteomics: current approaches, technical challenges and emerging techniques

    LENUS (Irish Health Repository)

    Ohlendieck, Kay

    2011-02-01

    Abstract Background Skeletal muscle fibres represent one of the most abundant cell types in mammals. Their highly specialised contractile and metabolic functions depend on a large number of membrane-associated proteins with very high molecular masses, proteins with extensive posttranslational modifications and components that exist in highly complex supramolecular structures. This makes it extremely difficult to perform conventional biochemical studies of potential changes in protein clusters during physiological adaptations or pathological processes. Results Skeletal muscle proteomics attempts to establish the global identification and biochemical characterisation of all members of the muscle-associated protein complement. A considerable number of proteomic studies have employed large-scale separation techniques, such as high-resolution two-dimensional gel electrophoresis or liquid chromatography, and combined them with mass spectrometry as the method of choice for high-throughput protein identification. Muscle proteomics has been applied to the comprehensive biochemical profiling of developing, maturing and aging muscle, as well as the analysis of contractile tissues undergoing physiological adaptations seen in disuse atrophy, physical exercise and chronic muscle transformation. Biomedical investigations into proteome-wide alterations in skeletal muscle tissues were also used to establish novel biomarker signatures of neuromuscular disorders. Importantly, mass spectrometric studies have confirmed the enormous complexity of posttranslational modifications in skeletal muscle proteins. Conclusions This review critically examines the scientific impact of modern muscle proteomics and discusses its successful application for a better understanding of muscle biology, but also outlines its technical limitations and emerging techniques to establish new biomarker candidates.

  8. Quantitative Interaction Proteomics of Neurodegenerative Disease Proteins

    Directory of Open Access Journals (Sweden)

    Fabian Hosp

    2015-05-01

    Full Text Available Several proteins have been linked to neurodegenerative disorders (NDDs, but their molecular function is not completely understood. Here, we used quantitative interaction proteomics to identify binding partners of Amyloid beta precursor protein (APP and Presenilin-1 (PSEN1 for Alzheimer’s disease (AD, Huntingtin (HTT for Huntington’s disease, Parkin (PARK2 for Parkinson’s disease, and Ataxin-1 (ATXN1 for spinocerebellar ataxia type 1. Our network reveals common signatures of protein degradation and misfolding and recapitulates known biology. Toxicity modifier screens and comparison to genome-wide association studies show that interaction partners are significantly linked to disease phenotypes in vivo. Direct comparison of wild-type proteins and disease-associated variants identified binders involved in pathogenesis, highlighting the value of differential interactome mapping. Finally, we show that the mitochondrial protein LRPPRC interacts preferentially with an early-onset AD variant of APP. This interaction appears to induce mitochondrial dysfunction, which is an early phenotype of AD.

  9. Honeybee (Apis mellifera ligustica) drone embryo proteomes.

    Science.gov (United States)

    Li, Jianke; Fang, Yu; Zhang, Lan; Begna, Desalegn

    2011-03-01

    Little attention has been paid to the drone honeybee (Apis mellifera ligustica) which is a haploid individual carrying only the set of alleles that it inherits from its mother. Molecular mechanisms underlying drone embryogenesis are poorly understood. This study evaluated protein expression profiles of drone embryogenesis at embryonic ages of 24, 48 and 72h. More than 100 reproducible proteins were analyzed by mass spectrometry on 2D electrophoresis gels. Sixty-two proteins were significantly changed at the selected three experimental age points. Expression of the metabolic energy requirement-related protein peaked at the embryonic age of 48h, whereas development and metabolizing amino acid-related proteins expressed optimally at 72h. Cytoskeleton, protein folding and antioxidant-related proteins were highly expressed at 48 and 72h. Protein networks of the identified proteins were constructed and protein expressions were validated at the transcription level. This first proteomic study of drone embryogenesis in the honeybee may provide geneticists an exact timetable and candidate protein outline for further manipulations of drone stem cells. PMID:21172355

  10. Bacillus subtilis Spore Inner Membrane Proteome.

    Science.gov (United States)

    Zheng, Linli; Abhyankar, Wishwas; Ouwerling, Natasja; Dekker, Henk L; van Veen, Henk; van der Wel, Nicole N; Roseboom, Winfried; de Koning, Leo J; Brul, Stanley; de Koster, Chris G

    2016-02-01

    The endospore is the dormant form of Bacillus subtilis and many other Firmicutes. By sporulation, these spore formers can survive very harsh physical and chemical conditions. Yet, they need to go through germination to return to their growing form. The spore inner membrane (IM) has been shown to play an essential role in triggering the initiation of germination. In this study, we isolated the IM of bacterial spores, in parallel with the isolation of the membrane of vegetative cells. With the use of GeLC-MS/MS, over 900 proteins were identified from the B. subtilis spore IM preparations. By bioinformatics-based membrane protein predictions, ca. one-third could be predicted to be membrane-localized. A large number of unique proteins as well as proteins common to the two membrane proteomes were identified. In addition to previously known IM proteins, a number of IM proteins were newly identified, at least some of which are likely to provide new insights into IM physiology, unveiling proteins putatively involved in spore germination machinery and hence putative germination inhibition targets. PMID:26731423

  11. Phosphoprotein analysis: from proteins to proteomes

    Directory of Open Access Journals (Sweden)

    Delom Frédéric

    2006-07-01

    Full Text Available Abstract Characterization of protein modification by phosphorylation is one of the major tasks that have to be accomplished in the post-genomic era. Phosphorylation is a key reversible modification occurring mainly on serine, threonine and tyrosine residues that can regulate enzymatic activity, subcellular localization, complex formation and degradation of proteins. The understanding of the regulatory role played by phosphorylation begins with the discovery and identification of phosphoproteins and then by determining how, where and when these phosphorylation events take place. Because phosphorylation is a dynamic process difficult to quantify, we must at first acquire an inventory of phosphoproteins and characterize their phosphorylation sites. Several experimental strategies can be used to explore the phosphorylation status of proteins from individual moieties to phosphoproteomes. In this review, we will examine and catalogue how proteomics techniques can be used to answer specific questions related to protein phosphorylation. Hence, we will discuss the different methods for enrichment of phospho-proteins and -peptides, and then the various technologies for their identification, quantitation and validation.

  12. Proteomic Analysis of the Schistosoma mansoni Miracidium.

    Science.gov (United States)

    Wang, Tianfang; Zhao, Min; Rotgans, Bronwyn A; Strong, April; Liang, Di; Ni, Guoying; Limpanont, Yanin; Ramasoota, Pongrama; McManus, Donald P; Cummins, Scott F

    2016-01-01

    Despite extensive control efforts, schistosomiasis continues to be a major public health problem in developing nations in the tropics and sub-tropics. The miracidium, along with the cercaria, both of which are water-borne and free-living, are the only two stages in the life-cycle of Schistosoma mansoni which are involved in host invasion. Miracidia penetrate intermediate host snails and develop into sporocysts, which lead to cercariae that can infect humans. Infection of the snail host by the miracidium represents an ideal point at which to interrupt the parasite's life-cycle. This research focuses on an analysis of the miracidium proteome, including those proteins that are secreted. We have identified a repertoire of proteins in the S. mansoni miracidium at 2 hours post-hatch, including proteases, venom allergen-like proteins, receptors and HSP70, which might play roles in snail-parasite interplay. Proteins involved in energy production and conservation were prevalent, as were proteins predicted to be associated with defence. This study also provides a strong foundation for further understanding the roles that neurohormones play in host-seeking by schistosomes, with the potential for development of novel anthelmintics that interfere with its various life-cycle stages. PMID:26799066

  13. Proteomic characterization of the human sperm nucleus.

    Science.gov (United States)

    de Mateo, Sara; Castillo, Judit; Estanyol, Josep Maria; Ballescà, José Luis; Oliva, Rafael

    2011-07-01

    Generating a catalogue of sperm nuclear proteins is an important first step towards the clarification of the function of the paternal chromatin transmitted to the oocyte upon fertilization. With this goal, sperm nuclei were obtained through CTAB treatment and isolated to over 99.9% purity without any tail fragments, acrosome or mitochondria as assessed by optical microscopy and transmission electron microscopy. The nuclear proteins were extracted and separated in 2-D and 1-D gels and the 2-D spots and 1-D bands were excised and analysed to identify the proteins through LC-MS/MS. With this approach, 403 different proteins have been identified from the isolated sperm nuclei. The most abundant family of proteins identified are the histones, for which several novel members had not been reported previously as present in the spermatogenic cell line or in the human mature spermatozoa. More than half (52.6%) of the proteins had not been detected in the previous human whole sperm cell proteome reports. Of relevance, several chromatin-related proteins, such as zinc fingers and transcription factors, so far not known to be associated with the sperm chromatin, have also been detected. This provides additional information about the nuclear proteins that are potentially relevant for epigenetic marking, proper fertilization and embryo development. PMID:21630459

  14. High-throughput proteomics : optical approaches.

    Energy Technology Data Exchange (ETDEWEB)

    Davidson, George S.

    2008-09-01

    Realistic cell models could greatly accelerate our ability to engineer biochemical pathways and the production of valuable organic products, which would be of great use in the development of biofuels, pharmaceuticals, and the crops for the next green revolution. However, this level of engineering will require a great deal more knowledge about the mechanisms of life than is currently available. In particular, we need to understand the interactome (which proteins interact) as it is situated in the three dimensional geometry of the cell (i.e., a situated interactome), and the regulation/dynamics of these interactions. Methods for optical proteomics have become available that allow the monitoring and even disruption/control of interacting proteins in living cells. Here, a range of these methods is reviewed with respect to their role in elucidating the interactome and the relevant spatial localizations. Development of these technologies and their integration into the core competencies of research organizations can position whole institutions and teams of researchers to lead in both the fundamental science and the engineering applications of cellular biology. That leadership could be particularly important with respect to problems of national urgency centered around security, biofuels, and healthcare.

  15. Genomics, metagenomics and proteomics in biomining microorganisms.

    Science.gov (United States)

    Valenzuela, Lissette; Chi, An; Beard, Simon; Orell, Alvaro; Guiliani, Nicolas; Shabanowitz, Jeff; Hunt, Donald F; Jerez, Carlos A

    2006-01-01

    The use of acidophilic, chemolithotrophic microorganisms capable of oxidizing iron and sulfur in industrial processes to recover metals from minerals containing copper, gold and uranium is a well established biotechnology with distinctive advantages over traditional mining. A consortium of different microorganisms participates in the oxidative reactions resulting in the extraction of dissolved metal values from ores. Considerable effort has been spent in the last years to understand the biochemistry of iron and sulfur compounds oxidation, bacteria-mineral interactions (chemotaxis, quorum sensing, adhesion, biofilm formation) and several adaptive responses allowing the microorganisms to survive in a bioleaching environment. All of these are considered key phenomena for understanding the process of biomining. The use of genomics, metagenomics and high throughput proteomics to study the global regulatory responses that the biomining community uses to adapt to their changing environment is just beginning to emerge in the last years. These powerful approaches are reviewed here since they offer the possibility of exciting new findings that will allow analyzing the community as a microbial system, determining the extent to which each of the individual participants contributes to the process, how they evolve in time to keep the conglomerate healthy and therefore efficient during the entire process of bioleaching. PMID:16288845

  16. Neural Tube Defects: From a Proteomic Standpoint

    Directory of Open Access Journals (Sweden)

    Tania M. Puvirajesinghe

    2015-03-01

    Full Text Available Neural tube defects (NTDs are congenital birth defects classified according to their resulting morphological characteristics in newborn patients. Current diagnosis of NTDs relies largely on the structural evaluation of fetuses using ultrasound imaging, with biochemical characterization used as secondary screening tools. The multigene etiology of NTDs has been aided by genetic studies, which have discovered panels of genes mutated in these diseases that encode receptors and cytoplasmic signaling molecules with poorly defined functions. Animal models ranging from flies to mice have been used to determine the function of these genes and identify their associated molecular cascades. More emphasis is now being placed on the identification of biochemical markers from clinical samples and model systems based on mass spectrometry, which open novel avenues in the understanding of NTDs at protein, metabolic and molecular levels. This article reviews how the use of proteomics can push forward the identification of novel biomarkers and molecular networks implicated in NTDs, an indispensable step in the improvement of patient management.

  17. Quantitative Proteomic Approaches for Studying Phosphotyrosine Signaling

    Energy Technology Data Exchange (ETDEWEB)

    Ding, Shi-Jian; Qian, Weijun; Smith, Richard D.

    2007-02-01

    Protein tyrosine phosphorylation is a fundamental mechanism for controlling many aspects of cellular processes, as well as aspects of human health and diseases. Compared to phosphoserine (pSer) and phosphothreonine (pThr), phosphotyrosine (pTyr) signaling is more tightly regulated, but often more challenging to characterize due to significantly lower level of tyrosine phosphorylation (a relative abundance of 1800:200:1 was estimated for pSer/pThr/pTyr in vertebrate cells[1]). In this review, we outline the recent advances in analytical methodologies for enrichment, identification, and accurate quantitation of tyrosine phosphorylated proteins and peptides using antibody-based technologies, capillary liquid chromatography (LC) coupled with mass spectrometry (MS), and various stable isotope labeling strategies, as well as non-MS-based methods such as protein or peptide array methods. These proteomic technological advances provide powerful tools for potentially understanding signal transduction at the system level and provide a basis for discovering novel drug targets for human diseases. [1] Hunter, T. (1998) The Croonian Lecture 1997. The phosphorylation of proteins on tyrosine: its role in cell growth and disease. Philos. Trans. R. Soc. Lond. B Biol. Sci. 353, 583–605

  18. Proteomic signature of the murine intervertebral disc.

    Directory of Open Access Journals (Sweden)

    Matthew R McCann

    Full Text Available Low back pain is the most common musculoskeletal problem and the single most common cause of disability, often attributed to degeneration of the intervertebral disc. Lack of effective treatment is directly related to our limited understanding of the pathways responsible for maintaining disc health. While transcriptional analysis has permitted initial insights into the biology of the intervertebral disc, complete proteomic characterization is required. We therefore employed liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS protein/peptide separation and mass spectrometric analyses to characterize the protein content of intervertebral discs from skeletally mature wild-type mice. A total of 1360 proteins were identified and categorized using PANTHER. Identified proteins were primarily intracellular/plasma membrane (35%, organelle (30%, macromolecular complex (10%, extracellular region (9%. Molecular function categorization resulted in three distinct categories: catalytic activity (33%, binding (molecule interactions (29%, and structural activity (13%. To validate our list, we confirmed the presence of 14 of 20 previously identified IVD-associated markers, including matrix proteins, transcriptional regulators, and secreted proteins. Immunohistochemical analysis confirmed distinct localization patterns of select protein with the intervertebral disc. Characterization of the protein composition of healthy intervertebral disc tissue is an important first step in identifying cellular processes and pathways disrupted during aging or disease progression.

  19. Targeted Proteomics Approach for Precision Plant Breeding.

    Science.gov (United States)

    Chawade, Aakash; Alexandersson, Erik; Bengtsson, Therese; Andreasson, Erik; Levander, Fredrik

    2016-02-01

    Selected reaction monitoring (SRM) is a targeted mass spectrometry technique that enables precise quantitation of hundreds of peptides in a single run. This technique provides new opportunities for multiplexed protein biomarker measurements. For precision plant breeding, DNA-based markers have been used extensively, but the potential of protein biomarkers has not been exploited. In this work, we developed an SRM marker panel with assays for 104 potato (Solanum tuberosum) peptides selected using univariate and multivariate statistics. Thereafter, using random forest classification, the prediction markers were identified for Phytopthora infestans resistance in leaves, P. infestans resistance in tubers, and plant yield in potato leaf secretome samples. The results suggest that the marker panel has the predictive potential for three traits, two of which have no commercial DNA markers so far. Furthermore, the marker panel was also tested and found to be applicable to potato clones not used during the marker development. The proposed workflow is thus a proof-of-concept for targeted proteomics as an efficient readout in accelerated breeding for complex and agronomically important traits. PMID:26704985

  20. A molecular scanner to automate proteomic research and to display proteome images.

    Science.gov (United States)

    Binz, P A; Müller, M; Walther, D; Bienvenut, W V; Gras, R; Hoogland, C; Bouchet, G; Gasteiger, E; Fabbretti, R; Gay, S; Palagi, P; Wilkins, M R; Rouge, V; Tonella, L; Paesano, S; Rossellat, G; Karmime, A; Bairoch, A; Sanchez, J C; Appel, R D; Hochstrasser, D F

    1999-11-01

    Identification and characterization of all proteins expressed by a genome in biological samples represent major challenges in proteomics. Today's commonly used high-throughput approaches combine two-dimensional electrophoresis (2-DE) with peptide mass fingerprinting (PMF) analysis. Although automation is often possible, a number of limitations still adversely affect the rate of protein identification and annotation in 2-DE databases: the sequential excision process of pieces of gel containing protein; the enzymatic digestion step; the interpretation of mass spectra (reliability of identifications); and the manual updating of 2-DE databases. We present a highly automated method that generates a fully annoated 2-DE map. Using a parallel process, all proteins of a 2-DE are first simultaneously digested proteolytically and electro-transferred onto a poly(vinylidene difluoride) membrane. The membrane is then directly scanned by MALDI-TOF MS. After automated protein identification from the obtained peptide mass fingerprints using PeptIdent software (http://www.expasy.ch/tools/peptident.html + ++), a fully annotated 2-D map is created on-line. It is a multidimensional representation of a proteome that contains interpreted PMF data in addition to protein identification results. This "MS-imaging" method represents a major step toward the development of a clinical molecular scanner. PMID:10565287